diff --git a/.github/workflows/validate.yml b/.github/workflows/validate.yml index a872f64..963d405 100644 --- a/.github/workflows/validate.yml +++ b/.github/workflows/validate.yml @@ -26,5 +26,17 @@ jobs: - name: Regenerate manifest run: node scripts/generate-manifest.js --root . --output manifest.generated.json + - name: Regenerate slim manifest + run: node scripts/generate-manifest.js --root . --slim --output manifest-slim.generated.json + + - name: Regenerate gallery + run: node scripts/generate-gallery.js --root . --output gallery.generated.json + - name: Check manifest is up to date - run: diff -u manifest.json manifest.generated.json \ No newline at end of file + run: diff -u manifest.json manifest.generated.json + + - name: Check slim manifest is up to date + run: diff -u manifest-slim.json manifest-slim.generated.json + + - name: Check gallery is up to date + run: diff -u gallery.json gallery.generated.json \ No newline at end of file diff --git a/Contributed/README.md b/Contributed/README.md deleted file mode 100644 index e69de29..0000000 diff --git a/Contributed/BNGPlayground_Examples/biology/aktsignaling/README.md b/Examples/biology/aktsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/aktsignaling/README.md rename to Examples/biology/aktsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/aktsignaling/akt-signaling.bngl b/Examples/biology/aktsignaling/akt-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/aktsignaling/akt-signaling.bngl rename to Examples/biology/aktsignaling/akt-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/aktsignaling/metadata.yaml b/Examples/biology/aktsignaling/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/aktsignaling/metadata.yaml rename to Examples/biology/aktsignaling/metadata.yaml index c98f92a..aef1085 100644 --- a/Contributed/BNGPlayground_Examples/biology/aktsignaling/metadata.yaml +++ b/Examples/biology/aktsignaling/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/akt-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/allostericactivation/README.md b/Examples/biology/allostericactivation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/allostericactivation/README.md rename to Examples/biology/allostericactivation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/allostericactivation/allosteric-activation.bngl b/Examples/biology/allostericactivation/allosteric-activation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/allostericactivation/allosteric-activation.bngl rename to Examples/biology/allostericactivation/allosteric-activation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/allostericactivation/metadata.yaml b/Examples/biology/allostericactivation/metadata.yaml similarity index 88% rename from Contributed/BNGPlayground_Examples/biology/allostericactivation/metadata.yaml rename to Examples/biology/allostericactivation/metadata.yaml index 6e78ed5..2b92498 100644 --- a/Contributed/BNGPlayground_Examples/biology/allostericactivation/metadata.yaml +++ b/Examples/biology/allostericactivation/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/allosteric-activation.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["metabolism","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/ampksignaling/README.md b/Examples/biology/ampksignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/ampksignaling/README.md rename to Examples/biology/ampksignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/ampksignaling/ampk-signaling.bngl b/Examples/biology/ampksignaling/ampk-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/ampksignaling/ampk-signaling.bngl rename to Examples/biology/ampksignaling/ampk-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/ampksignaling/metadata.yaml b/Examples/biology/ampksignaling/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/ampksignaling/metadata.yaml rename to Examples/biology/ampksignaling/metadata.yaml index 1e89dd9..6e5845d 100644 --- a/Contributed/BNGPlayground_Examples/biology/ampksignaling/metadata.yaml +++ b/Examples/biology/ampksignaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/ampk-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["neuroscience","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/apoptosiscascade/README.md b/Examples/biology/apoptosiscascade/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/apoptosiscascade/README.md rename to Examples/biology/apoptosiscascade/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/apoptosiscascade/apoptosis-cascade.bngl b/Examples/biology/apoptosiscascade/apoptosis-cascade.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/apoptosiscascade/apoptosis-cascade.bngl rename to Examples/biology/apoptosiscascade/apoptosis-cascade.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/apoptosiscascade/metadata.yaml b/Examples/biology/apoptosiscascade/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/apoptosiscascade/metadata.yaml rename to Examples/biology/apoptosiscascade/metadata.yaml index ebc2b7e..213491d 100644 --- a/Contributed/BNGPlayground_Examples/biology/apoptosiscascade/metadata.yaml +++ b/Examples/biology/apoptosiscascade/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/apoptosis-cascade.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cell-cycle","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/autoactivationloop/README.md b/Examples/biology/autoactivationloop/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/autoactivationloop/README.md rename to Examples/biology/autoactivationloop/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/autoactivationloop/auto-activation-loop.bngl b/Examples/biology/autoactivationloop/auto-activation-loop.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/autoactivationloop/auto-activation-loop.bngl rename to Examples/biology/autoactivationloop/auto-activation-loop.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/autoactivationloop/metadata.yaml b/Examples/biology/autoactivationloop/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/autoactivationloop/metadata.yaml rename to Examples/biology/autoactivationloop/metadata.yaml index c447946..56df9c5 100644 --- a/Contributed/BNGPlayground_Examples/biology/autoactivationloop/metadata.yaml +++ b/Examples/biology/autoactivationloop/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/auto-activation-loop.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["metabolism","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/autophagyregulation/README.md b/Examples/biology/autophagyregulation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/autophagyregulation/README.md rename to Examples/biology/autophagyregulation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/autophagyregulation/autophagy-regulation.bngl b/Examples/biology/autophagyregulation/autophagy-regulation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/autophagyregulation/autophagy-regulation.bngl rename to Examples/biology/autophagyregulation/autophagy-regulation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/autophagyregulation/metadata.yaml b/Examples/biology/autophagyregulation/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/autophagyregulation/metadata.yaml rename to Examples/biology/autophagyregulation/metadata.yaml index e552850..0c56ed9 100644 --- a/Contributed/BNGPlayground_Examples/biology/autophagyregulation/metadata.yaml +++ b/Examples/biology/autophagyregulation/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/autophagy-regulation.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["metabolism","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/bcrsignaling/README.md b/Examples/biology/bcrsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/bcrsignaling/README.md rename to Examples/biology/bcrsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/bcrsignaling/bcr-signaling.bngl b/Examples/biology/bcrsignaling/bcr-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/bcrsignaling/bcr-signaling.bngl rename to Examples/biology/bcrsignaling/bcr-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/bcrsignaling/metadata.yaml b/Examples/biology/bcrsignaling/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/bcrsignaling/metadata.yaml rename to Examples/biology/bcrsignaling/metadata.yaml index ff9f285..3ff750b 100644 --- a/Contributed/BNGPlayground_Examples/biology/bcrsignaling/metadata.yaml +++ b/Examples/biology/bcrsignaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/bcr-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/betaadrenergicresponse/README.md b/Examples/biology/betaadrenergicresponse/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/betaadrenergicresponse/README.md rename to Examples/biology/betaadrenergicresponse/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/betaadrenergicresponse/beta-adrenergic-response.bngl b/Examples/biology/betaadrenergicresponse/beta-adrenergic-response.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/betaadrenergicresponse/beta-adrenergic-response.bngl rename to Examples/biology/betaadrenergicresponse/beta-adrenergic-response.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/betaadrenergicresponse/metadata.yaml b/Examples/biology/betaadrenergicresponse/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/betaadrenergicresponse/metadata.yaml rename to Examples/biology/betaadrenergicresponse/metadata.yaml index 7461918..87ff0a6 100644 --- a/Contributed/BNGPlayground_Examples/biology/betaadrenergicresponse/metadata.yaml +++ b/Examples/biology/betaadrenergicresponse/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/beta-adrenergic-response.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["neuroscience","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/bistabletoggleswitch/README.md b/Examples/biology/bistabletoggleswitch/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/bistabletoggleswitch/README.md rename to Examples/biology/bistabletoggleswitch/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/bistabletoggleswitch/bistable-toggle-switch.bngl b/Examples/biology/bistabletoggleswitch/bistable-toggle-switch.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/bistabletoggleswitch/bistable-toggle-switch.bngl rename to Examples/biology/bistabletoggleswitch/bistable-toggle-switch.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/bistabletoggleswitch/metadata.yaml b/Examples/biology/bistabletoggleswitch/metadata.yaml similarity index 91% rename from Contributed/BNGPlayground_Examples/biology/bistabletoggleswitch/metadata.yaml rename to Examples/biology/bistabletoggleswitch/metadata.yaml index b02f01a..d875c60 100644 --- a/Contributed/BNGPlayground_Examples/biology/bistabletoggleswitch/metadata.yaml +++ b/Examples/biology/bistabletoggleswitch/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/bistable-toggle-switch.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/bloodcoagulationthrombin/README.md b/Examples/biology/bloodcoagulationthrombin/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/bloodcoagulationthrombin/README.md rename to Examples/biology/bloodcoagulationthrombin/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin.bngl b/Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin.bngl rename to Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/bloodcoagulationthrombin/metadata.yaml b/Examples/biology/bloodcoagulationthrombin/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/bloodcoagulationthrombin/metadata.yaml rename to Examples/biology/bloodcoagulationthrombin/metadata.yaml index 8f27065..3df63ca 100644 --- a/Contributed/BNGPlayground_Examples/biology/bloodcoagulationthrombin/metadata.yaml +++ b/Examples/biology/bloodcoagulationthrombin/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/blood-coagulation-thrombin.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/bmpsignaling/README.md b/Examples/biology/bmpsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/bmpsignaling/README.md rename to Examples/biology/bmpsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/bmpsignaling/bmp-signaling.bngl b/Examples/biology/bmpsignaling/bmp-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/bmpsignaling/bmp-signaling.bngl rename to Examples/biology/bmpsignaling/bmp-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/bmpsignaling/metadata.yaml b/Examples/biology/bmpsignaling/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/bmpsignaling/metadata.yaml rename to Examples/biology/bmpsignaling/metadata.yaml index b643dc8..fc12417 100644 --- a/Contributed/BNGPlayground_Examples/biology/bmpsignaling/metadata.yaml +++ b/Examples/biology/bmpsignaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/bmp-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["developmental","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/brusselatoroscillator/README.md b/Examples/biology/brusselatoroscillator/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/brusselatoroscillator/README.md rename to Examples/biology/brusselatoroscillator/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/brusselatoroscillator/brusselator-oscillator.bngl b/Examples/biology/brusselatoroscillator/brusselator-oscillator.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/brusselatoroscillator/brusselator-oscillator.bngl rename to Examples/biology/brusselatoroscillator/brusselator-oscillator.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/brusselatoroscillator/metadata.yaml b/Examples/biology/brusselatoroscillator/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/brusselatoroscillator/metadata.yaml rename to Examples/biology/brusselatoroscillator/metadata.yaml index 4a7e0bf..359484b 100644 --- a/Contributed/BNGPlayground_Examples/biology/brusselatoroscillator/metadata.yaml +++ b/Examples/biology/brusselatoroscillator/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/brusselator-oscillator.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["physics","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/calcineurinnfatpathway/README.md b/Examples/biology/calcineurinnfatpathway/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/calcineurinnfatpathway/README.md rename to Examples/biology/calcineurinnfatpathway/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway.bngl b/Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway.bngl rename to Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/calcineurinnfatpathway/metadata.yaml b/Examples/biology/calcineurinnfatpathway/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/calcineurinnfatpathway/metadata.yaml rename to Examples/biology/calcineurinnfatpathway/metadata.yaml index 4043cf1..3a2f4b3 100644 --- a/Contributed/BNGPlayground_Examples/biology/calcineurinnfatpathway/metadata.yaml +++ b/Examples/biology/calcineurinnfatpathway/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/calcineurin-nfat-pathway.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["neuroscience","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/calciumspikesignaling/README.md b/Examples/biology/calciumspikesignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/calciumspikesignaling/README.md rename to Examples/biology/calciumspikesignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/calciumspikesignaling/calcium-spike-signaling.bngl b/Examples/biology/calciumspikesignaling/calcium-spike-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/calciumspikesignaling/calcium-spike-signaling.bngl rename to Examples/biology/calciumspikesignaling/calcium-spike-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/calciumspikesignaling/metadata.yaml b/Examples/biology/calciumspikesignaling/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/calciumspikesignaling/metadata.yaml rename to Examples/biology/calciumspikesignaling/metadata.yaml index 7224be7..b0d87e8 100644 --- a/Contributed/BNGPlayground_Examples/biology/calciumspikesignaling/metadata.yaml +++ b/Examples/biology/calciumspikesignaling/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: true uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/calcium-spike-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["neuroscience","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/caspaseactivationloop/README.md b/Examples/biology/caspaseactivationloop/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/caspaseactivationloop/README.md rename to Examples/biology/caspaseactivationloop/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/caspaseactivationloop/caspase-activation-loop.bngl b/Examples/biology/caspaseactivationloop/caspase-activation-loop.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/caspaseactivationloop/caspase-activation-loop.bngl rename to Examples/biology/caspaseactivationloop/caspase-activation-loop.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/caspaseactivationloop/metadata.yaml b/Examples/biology/caspaseactivationloop/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/biology/caspaseactivationloop/metadata.yaml rename to Examples/biology/caspaseactivationloop/metadata.yaml index fa89854..2c76c8a 100644 --- a/Contributed/BNGPlayground_Examples/biology/caspaseactivationloop/metadata.yaml +++ b/Examples/biology/caspaseactivationloop/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/caspase-activation-loop.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cell-cycle","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/cd40signaling/README.md b/Examples/biology/cd40signaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/cd40signaling/README.md rename to Examples/biology/cd40signaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/cd40signaling/cd40-signaling.bngl b/Examples/biology/cd40signaling/cd40-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/cd40signaling/cd40-signaling.bngl rename to Examples/biology/cd40signaling/cd40-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/cd40signaling/metadata.yaml b/Examples/biology/cd40signaling/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/cd40signaling/metadata.yaml rename to Examples/biology/cd40signaling/metadata.yaml index 7b2144a..562b1a8 100644 --- a/Contributed/BNGPlayground_Examples/biology/cd40signaling/metadata.yaml +++ b/Examples/biology/cd40signaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/cd40-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/cellcyclecheckpoint/README.md b/Examples/biology/cellcyclecheckpoint/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/cellcyclecheckpoint/README.md rename to Examples/biology/cellcyclecheckpoint/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint.bngl b/Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint.bngl rename to Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/cellcyclecheckpoint/metadata.yaml b/Examples/biology/cellcyclecheckpoint/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/cellcyclecheckpoint/metadata.yaml rename to Examples/biology/cellcyclecheckpoint/metadata.yaml index 93b0b1c..b4dac77 100644 --- a/Contributed/BNGPlayground_Examples/biology/cellcyclecheckpoint/metadata.yaml +++ b/Examples/biology/cellcyclecheckpoint/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/cell-cycle-checkpoint.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cell-cycle","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/checkpointkinasesignaling/README.md b/Examples/biology/checkpointkinasesignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/checkpointkinasesignaling/README.md rename to Examples/biology/checkpointkinasesignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling.bngl b/Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling.bngl rename to Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/checkpointkinasesignaling/metadata.yaml b/Examples/biology/checkpointkinasesignaling/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/biology/checkpointkinasesignaling/metadata.yaml rename to Examples/biology/checkpointkinasesignaling/metadata.yaml index d596c06..26666b8 100644 --- a/Contributed/BNGPlayground_Examples/biology/checkpointkinasesignaling/metadata.yaml +++ b/Examples/biology/checkpointkinasesignaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/checkpoint-kinase-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/chemotaxissignaltransduction/README.md b/Examples/biology/chemotaxissignaltransduction/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/chemotaxissignaltransduction/README.md rename to Examples/biology/chemotaxissignaltransduction/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction.bngl b/Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction.bngl rename to Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/chemotaxissignaltransduction/metadata.yaml b/Examples/biology/chemotaxissignaltransduction/metadata.yaml similarity index 91% rename from Contributed/BNGPlayground_Examples/biology/chemotaxissignaltransduction/metadata.yaml rename to Examples/biology/chemotaxissignaltransduction/metadata.yaml index 3d8d8dd..d940bb4 100644 --- a/Contributed/BNGPlayground_Examples/biology/chemotaxissignaltransduction/metadata.yaml +++ b/Examples/biology/chemotaxissignaltransduction/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/chemotaxis-signal-transduction.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/circadianoscillator/README.md b/Examples/biology/circadianoscillator/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/circadianoscillator/README.md rename to Examples/biology/circadianoscillator/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/circadianoscillator/circadian-oscillator.bngl b/Examples/biology/circadianoscillator/circadian-oscillator.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/circadianoscillator/circadian-oscillator.bngl rename to Examples/biology/circadianoscillator/circadian-oscillator.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/circadianoscillator/metadata.yaml b/Examples/biology/circadianoscillator/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/circadianoscillator/metadata.yaml rename to Examples/biology/circadianoscillator/metadata.yaml index f5f60fb..402fd37 100644 --- a/Contributed/BNGPlayground_Examples/biology/circadianoscillator/metadata.yaml +++ b/Examples/biology/circadianoscillator/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/circadian-oscillator.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/clockbmal1genecircuit/README.md b/Examples/biology/clockbmal1genecircuit/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/clockbmal1genecircuit/README.md rename to Examples/biology/clockbmal1genecircuit/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit.bngl b/Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit.bngl rename to Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/clockbmal1genecircuit/metadata.yaml b/Examples/biology/clockbmal1genecircuit/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/clockbmal1genecircuit/metadata.yaml rename to Examples/biology/clockbmal1genecircuit/metadata.yaml index 4100696..10fe366 100644 --- a/Contributed/BNGPlayground_Examples/biology/clockbmal1genecircuit/metadata.yaml +++ b/Examples/biology/clockbmal1genecircuit/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/clock-bmal1-gene-circuit.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cell-cycle","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/competitiveenzymeinhibition/README.md b/Examples/biology/competitiveenzymeinhibition/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/competitiveenzymeinhibition/README.md rename to Examples/biology/competitiveenzymeinhibition/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition.bngl b/Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition.bngl rename to Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/competitiveenzymeinhibition/metadata.yaml b/Examples/biology/competitiveenzymeinhibition/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/competitiveenzymeinhibition/metadata.yaml rename to Examples/biology/competitiveenzymeinhibition/metadata.yaml index 0b825fc..5979973 100644 --- a/Contributed/BNGPlayground_Examples/biology/competitiveenzymeinhibition/metadata.yaml +++ b/Examples/biology/competitiveenzymeinhibition/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/competitive-enzyme-inhibition.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["metabolism","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/complementactivationcascade/README.md b/Examples/biology/complementactivationcascade/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/complementactivationcascade/README.md rename to Examples/biology/complementactivationcascade/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/complementactivationcascade/complement-activation-cascade.bngl b/Examples/biology/complementactivationcascade/complement-activation-cascade.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/complementactivationcascade/complement-activation-cascade.bngl rename to Examples/biology/complementactivationcascade/complement-activation-cascade.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/complementactivationcascade/metadata.yaml b/Examples/biology/complementactivationcascade/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/complementactivationcascade/metadata.yaml rename to Examples/biology/complementactivationcascade/metadata.yaml index b196d9b..6535786 100644 --- a/Contributed/BNGPlayground_Examples/biology/complementactivationcascade/metadata.yaml +++ b/Examples/biology/complementactivationcascade/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/complement-activation-cascade.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/contactinhibitionhippoyap/README.md b/Examples/biology/contactinhibitionhippoyap/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/contactinhibitionhippoyap/README.md rename to Examples/biology/contactinhibitionhippoyap/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl b/Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl rename to Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/contactinhibitionhippoyap/metadata.yaml b/Examples/biology/contactinhibitionhippoyap/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/contactinhibitionhippoyap/metadata.yaml rename to Examples/biology/contactinhibitionhippoyap/metadata.yaml index 7311878..1905656 100644 --- a/Contributed/BNGPlayground_Examples/biology/contactinhibitionhippoyap/metadata.yaml +++ b/Examples/biology/contactinhibitionhippoyap/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/contact-inhibition-hippo-yap.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/cooperativebinding/README.md b/Examples/biology/cooperativebinding/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/cooperativebinding/README.md rename to Examples/biology/cooperativebinding/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/cooperativebinding/cooperative-binding.bngl b/Examples/biology/cooperativebinding/cooperative-binding.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/cooperativebinding/cooperative-binding.bngl rename to Examples/biology/cooperativebinding/cooperative-binding.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/cooperativebinding/metadata.yaml b/Examples/biology/cooperativebinding/metadata.yaml similarity index 91% rename from Contributed/BNGPlayground_Examples/biology/cooperativebinding/metadata.yaml rename to Examples/biology/cooperativebinding/metadata.yaml index 8224a84..270f027 100644 --- a/Contributed/BNGPlayground_Examples/biology/cooperativebinding/metadata.yaml +++ b/Examples/biology/cooperativebinding/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/cooperative-binding.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/dnadamagerepair/README.md b/Examples/biology/dnadamagerepair/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/dnadamagerepair/README.md rename to Examples/biology/dnadamagerepair/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/dnadamagerepair/dna-damage-repair.bngl b/Examples/biology/dnadamagerepair/dna-damage-repair.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/dnadamagerepair/dna-damage-repair.bngl rename to Examples/biology/dnadamagerepair/dna-damage-repair.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/dnadamagerepair/metadata.yaml b/Examples/biology/dnadamagerepair/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/dnadamagerepair/metadata.yaml rename to Examples/biology/dnadamagerepair/metadata.yaml index c8850ee..f916c5b 100644 --- a/Contributed/BNGPlayground_Examples/biology/dnadamagerepair/metadata.yaml +++ b/Examples/biology/dnadamagerepair/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/dna-damage-repair.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/dnamethylationdynamics/README.md b/Examples/biology/dnamethylationdynamics/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/dnamethylationdynamics/README.md rename to Examples/biology/dnamethylationdynamics/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/dnamethylationdynamics/dna-methylation-dynamics.bngl b/Examples/biology/dnamethylationdynamics/dna-methylation-dynamics.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/dnamethylationdynamics/dna-methylation-dynamics.bngl rename to Examples/biology/dnamethylationdynamics/dna-methylation-dynamics.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/dnamethylationdynamics/metadata.yaml b/Examples/biology/dnamethylationdynamics/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/dnamethylationdynamics/metadata.yaml rename to Examples/biology/dnamethylationdynamics/metadata.yaml index cc3160b..197172e 100644 --- a/Contributed/BNGPlayground_Examples/biology/dnamethylationdynamics/metadata.yaml +++ b/Examples/biology/dnamethylationdynamics/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/dna-methylation-dynamics.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/dr5apoptosissignaling/README.md b/Examples/biology/dr5apoptosissignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/dr5apoptosissignaling/README.md rename to Examples/biology/dr5apoptosissignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling.bngl b/Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling.bngl rename to Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/dr5apoptosissignaling/metadata.yaml b/Examples/biology/dr5apoptosissignaling/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/biology/dr5apoptosissignaling/metadata.yaml rename to Examples/biology/dr5apoptosissignaling/metadata.yaml index 77dd980..47404f0 100644 --- a/Contributed/BNGPlayground_Examples/biology/dr5apoptosissignaling/metadata.yaml +++ b/Examples/biology/dr5apoptosissignaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/dr5-apoptosis-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cell-cycle","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/dualsitephosphorylation/README.md b/Examples/biology/dualsitephosphorylation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/dualsitephosphorylation/README.md rename to Examples/biology/dualsitephosphorylation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/dualsitephosphorylation/dual-site-phosphorylation.bngl b/Examples/biology/dualsitephosphorylation/dual-site-phosphorylation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/dualsitephosphorylation/dual-site-phosphorylation.bngl rename to Examples/biology/dualsitephosphorylation/dual-site-phosphorylation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/dualsitephosphorylation/metadata.yaml b/Examples/biology/dualsitephosphorylation/metadata.yaml similarity index 91% rename from Contributed/BNGPlayground_Examples/biology/dualsitephosphorylation/metadata.yaml rename to Examples/biology/dualsitephosphorylation/metadata.yaml index 0c8f6c2..b876524 100644 --- a/Contributed/BNGPlayground_Examples/biology/dualsitephosphorylation/metadata.yaml +++ b/Examples/biology/dualsitephosphorylation/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/dual-site-phosphorylation.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/e2frbcellcycleswitch/README.md b/Examples/biology/e2frbcellcycleswitch/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/e2frbcellcycleswitch/README.md rename to Examples/biology/e2frbcellcycleswitch/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch.bngl b/Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch.bngl rename to Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/e2frbcellcycleswitch/metadata.yaml b/Examples/biology/e2frbcellcycleswitch/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/e2frbcellcycleswitch/metadata.yaml rename to Examples/biology/e2frbcellcycleswitch/metadata.yaml index 718ef88..d7d77db 100644 --- a/Contributed/BNGPlayground_Examples/biology/e2frbcellcycleswitch/metadata.yaml +++ b/Examples/biology/e2frbcellcycleswitch/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/e2f-rb-cell-cycle-switch.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cell-cycle","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/egfrsignalingpathway/README.md b/Examples/biology/egfrsignalingpathway/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/egfrsignalingpathway/README.md rename to Examples/biology/egfrsignalingpathway/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/egfrsignalingpathway/egfr-signaling-pathway.bngl b/Examples/biology/egfrsignalingpathway/egfr-signaling-pathway.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/egfrsignalingpathway/egfr-signaling-pathway.bngl rename to Examples/biology/egfrsignalingpathway/egfr-signaling-pathway.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/egfrsignalingpathway/metadata.yaml b/Examples/biology/egfrsignalingpathway/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/egfrsignalingpathway/metadata.yaml rename to Examples/biology/egfrsignalingpathway/metadata.yaml index 676b1ee..5e481af 100644 --- a/Contributed/BNGPlayground_Examples/biology/egfrsignalingpathway/metadata.yaml +++ b/Examples/biology/egfrsignalingpathway/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/egfr-signaling-pathway.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/eif2astressresponse/README.md b/Examples/biology/eif2astressresponse/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/eif2astressresponse/README.md rename to Examples/biology/eif2astressresponse/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/eif2astressresponse/eif2a-stress-response.bngl b/Examples/biology/eif2astressresponse/eif2a-stress-response.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/eif2astressresponse/eif2a-stress-response.bngl rename to Examples/biology/eif2astressresponse/eif2a-stress-response.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/eif2astressresponse/metadata.yaml b/Examples/biology/eif2astressresponse/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/eif2astressresponse/metadata.yaml rename to Examples/biology/eif2astressresponse/metadata.yaml index 23c419a..53b0f09 100644 --- a/Contributed/BNGPlayground_Examples/biology/eif2astressresponse/metadata.yaml +++ b/Examples/biology/eif2astressresponse/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/eif2a-stress-response.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/endosomalsortingrab/README.md b/Examples/biology/endosomalsortingrab/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/endosomalsortingrab/README.md rename to Examples/biology/endosomalsortingrab/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/endosomalsortingrab/endosomal-sorting-rab.bngl b/Examples/biology/endosomalsortingrab/endosomal-sorting-rab.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/endosomalsortingrab/endosomal-sorting-rab.bngl rename to Examples/biology/endosomalsortingrab/endosomal-sorting-rab.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/endosomalsortingrab/metadata.yaml b/Examples/biology/endosomalsortingrab/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/endosomalsortingrab/metadata.yaml rename to Examples/biology/endosomalsortingrab/metadata.yaml index 4a7fa40..aea7c21 100644 --- a/Contributed/BNGPlayground_Examples/biology/endosomalsortingrab/metadata.yaml +++ b/Examples/biology/endosomalsortingrab/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/endosomal-sorting-rab.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/erknucleartranslocation/README.md b/Examples/biology/erknucleartranslocation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/erknucleartranslocation/README.md rename to Examples/biology/erknucleartranslocation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/erknucleartranslocation/erk-nuclear-translocation.bngl b/Examples/biology/erknucleartranslocation/erk-nuclear-translocation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/erknucleartranslocation/erk-nuclear-translocation.bngl rename to Examples/biology/erknucleartranslocation/erk-nuclear-translocation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/erknucleartranslocation/metadata.yaml b/Examples/biology/erknucleartranslocation/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/erknucleartranslocation/metadata.yaml rename to Examples/biology/erknucleartranslocation/metadata.yaml index 5e0d3bd..f8f6bc7 100644 --- a/Contributed/BNGPlayground_Examples/biology/erknucleartranslocation/metadata.yaml +++ b/Examples/biology/erknucleartranslocation/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/erk-nuclear-translocation.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/erstressresponse/README.md b/Examples/biology/erstressresponse/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/erstressresponse/README.md rename to Examples/biology/erstressresponse/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/erstressresponse/er-stress-response.bngl b/Examples/biology/erstressresponse/er-stress-response.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/erstressresponse/er-stress-response.bngl rename to Examples/biology/erstressresponse/er-stress-response.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/erstressresponse/metadata.yaml b/Examples/biology/erstressresponse/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/erstressresponse/metadata.yaml rename to Examples/biology/erstressresponse/metadata.yaml index 79f4653..8311e07 100644 --- a/Contributed/BNGPlayground_Examples/biology/erstressresponse/metadata.yaml +++ b/Examples/biology/erstressresponse/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/er-stress-response.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/fgfsignalingpathway/README.md b/Examples/biology/fgfsignalingpathway/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/fgfsignalingpathway/README.md rename to Examples/biology/fgfsignalingpathway/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/fgfsignalingpathway/fgf-signaling-pathway.bngl b/Examples/biology/fgfsignalingpathway/fgf-signaling-pathway.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/fgfsignalingpathway/fgf-signaling-pathway.bngl rename to Examples/biology/fgfsignalingpathway/fgf-signaling-pathway.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/fgfsignalingpathway/metadata.yaml b/Examples/biology/fgfsignalingpathway/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/fgfsignalingpathway/metadata.yaml rename to Examples/biology/fgfsignalingpathway/metadata.yaml index fb650ee..887672b 100644 --- a/Contributed/BNGPlayground_Examples/biology/fgfsignalingpathway/metadata.yaml +++ b/Examples/biology/fgfsignalingpathway/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/fgf-signaling-pathway.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["developmental","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/gas6axlsignaling/README.md b/Examples/biology/gas6axlsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/gas6axlsignaling/README.md rename to Examples/biology/gas6axlsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/gas6axlsignaling/gas6-axl-signaling.bngl b/Examples/biology/gas6axlsignaling/gas6-axl-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/gas6axlsignaling/gas6-axl-signaling.bngl rename to Examples/biology/gas6axlsignaling/gas6-axl-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/gas6axlsignaling/metadata.yaml b/Examples/biology/gas6axlsignaling/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/gas6axlsignaling/metadata.yaml rename to Examples/biology/gas6axlsignaling/metadata.yaml index 36f6ebf..8dd37a5 100644 --- a/Contributed/BNGPlayground_Examples/biology/gas6axlsignaling/metadata.yaml +++ b/Examples/biology/gas6axlsignaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/gas6-axl-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/geneexpressiontoggle/README.md b/Examples/biology/geneexpressiontoggle/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/geneexpressiontoggle/README.md rename to Examples/biology/geneexpressiontoggle/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/geneexpressiontoggle/gene-expression-toggle.bngl b/Examples/biology/geneexpressiontoggle/gene-expression-toggle.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/geneexpressiontoggle/gene-expression-toggle.bngl rename to Examples/biology/geneexpressiontoggle/gene-expression-toggle.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/geneexpressiontoggle/metadata.yaml b/Examples/biology/geneexpressiontoggle/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/geneexpressiontoggle/metadata.yaml rename to Examples/biology/geneexpressiontoggle/metadata.yaml index bd8e46c..15656a3 100644 --- a/Contributed/BNGPlayground_Examples/biology/geneexpressiontoggle/metadata.yaml +++ b/Examples/biology/geneexpressiontoggle/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/gene-expression-toggle.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/glioblastomaegfrviiisignaling/README.md b/Examples/biology/glioblastomaegfrviiisignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/glioblastomaegfrviiisignaling/README.md rename to Examples/biology/glioblastomaegfrviiisignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling.bngl b/Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling.bngl rename to Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/glioblastomaegfrviiisignaling/metadata.yaml b/Examples/biology/glioblastomaegfrviiisignaling/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/biology/glioblastomaegfrviiisignaling/metadata.yaml rename to Examples/biology/glioblastomaegfrviiisignaling/metadata.yaml index ab13780..d5ec0c4 100644 --- a/Contributed/BNGPlayground_Examples/biology/glioblastomaegfrviiisignaling/metadata.yaml +++ b/Examples/biology/glioblastomaegfrviiisignaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/glioblastoma-egfrviii-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/glycolysisbranchpoint/README.md b/Examples/biology/glycolysisbranchpoint/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/glycolysisbranchpoint/README.md rename to Examples/biology/glycolysisbranchpoint/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/glycolysisbranchpoint/glycolysis-branch-point.bngl b/Examples/biology/glycolysisbranchpoint/glycolysis-branch-point.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/glycolysisbranchpoint/glycolysis-branch-point.bngl rename to Examples/biology/glycolysisbranchpoint/glycolysis-branch-point.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/glycolysisbranchpoint/metadata.yaml b/Examples/biology/glycolysisbranchpoint/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/glycolysisbranchpoint/metadata.yaml rename to Examples/biology/glycolysisbranchpoint/metadata.yaml index bb998fd..e838ca8 100644 --- a/Contributed/BNGPlayground_Examples/biology/glycolysisbranchpoint/metadata.yaml +++ b/Examples/biology/glycolysisbranchpoint/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/glycolysis-branch-point.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["metabolism","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/gpcrdesensitizationarrestin/README.md b/Examples/biology/gpcrdesensitizationarrestin/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/gpcrdesensitizationarrestin/README.md rename to Examples/biology/gpcrdesensitizationarrestin/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin.bngl b/Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin.bngl rename to Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/gpcrdesensitizationarrestin/metadata.yaml b/Examples/biology/gpcrdesensitizationarrestin/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/gpcrdesensitizationarrestin/metadata.yaml rename to Examples/biology/gpcrdesensitizationarrestin/metadata.yaml index 3e7a696..39524be 100644 --- a/Contributed/BNGPlayground_Examples/biology/gpcrdesensitizationarrestin/metadata.yaml +++ b/Examples/biology/gpcrdesensitizationarrestin/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/gpcr-desensitization-arrestin.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/hedgehogsignalingpathway/README.md b/Examples/biology/hedgehogsignalingpathway/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/hedgehogsignalingpathway/README.md rename to Examples/biology/hedgehogsignalingpathway/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/hedgehogsignalingpathway/hedgehog-signaling-pathway.bngl b/Examples/biology/hedgehogsignalingpathway/hedgehog-signaling-pathway.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/hedgehogsignalingpathway/hedgehog-signaling-pathway.bngl rename to Examples/biology/hedgehogsignalingpathway/hedgehog-signaling-pathway.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/hedgehogsignalingpathway/metadata.yaml b/Examples/biology/hedgehogsignalingpathway/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/hedgehogsignalingpathway/metadata.yaml rename to Examples/biology/hedgehogsignalingpathway/metadata.yaml index 7c73a4e..f54accb 100644 --- a/Contributed/BNGPlayground_Examples/biology/hedgehogsignalingpathway/metadata.yaml +++ b/Examples/biology/hedgehogsignalingpathway/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/hedgehog-signaling-pathway.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["developmental","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/hematopoieticgrowthfactor/README.md b/Examples/biology/hematopoieticgrowthfactor/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/hematopoieticgrowthfactor/README.md rename to Examples/biology/hematopoieticgrowthfactor/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/hematopoieticgrowthfactor/hematopoietic-growth-factor.bngl b/Examples/biology/hematopoieticgrowthfactor/hematopoietic-growth-factor.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/hematopoieticgrowthfactor/hematopoietic-growth-factor.bngl rename to Examples/biology/hematopoieticgrowthfactor/hematopoietic-growth-factor.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/hematopoieticgrowthfactor/metadata.yaml b/Examples/biology/hematopoieticgrowthfactor/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/hematopoieticgrowthfactor/metadata.yaml rename to Examples/biology/hematopoieticgrowthfactor/metadata.yaml index e86e23e..8583545 100644 --- a/Contributed/BNGPlayground_Examples/biology/hematopoieticgrowthfactor/metadata.yaml +++ b/Examples/biology/hematopoieticgrowthfactor/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/hematopoietic-growth-factor.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/hif1adegradationloop/README.md b/Examples/biology/hif1adegradationloop/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/hif1adegradationloop/README.md rename to Examples/biology/hif1adegradationloop/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/hif1adegradationloop/hif1a_degradation_loop.bngl b/Examples/biology/hif1adegradationloop/hif1a_degradation_loop.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/hif1adegradationloop/hif1a_degradation_loop.bngl rename to Examples/biology/hif1adegradationloop/hif1a_degradation_loop.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/hif1adegradationloop/metadata.yaml b/Examples/biology/hif1adegradationloop/metadata.yaml similarity index 91% rename from Contributed/BNGPlayground_Examples/biology/hif1adegradationloop/metadata.yaml rename to Examples/biology/hif1adegradationloop/metadata.yaml index 49075fb..4df43b3 100644 --- a/Contributed/BNGPlayground_Examples/biology/hif1adegradationloop/metadata.yaml +++ b/Examples/biology/hif1adegradationloop/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/hif1a_degradation_loop.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/hypoxiaresponsesignaling/README.md b/Examples/biology/hypoxiaresponsesignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/hypoxiaresponsesignaling/README.md rename to Examples/biology/hypoxiaresponsesignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/hypoxiaresponsesignaling/hypoxia-response-signaling.bngl b/Examples/biology/hypoxiaresponsesignaling/hypoxia-response-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/hypoxiaresponsesignaling/hypoxia-response-signaling.bngl rename to Examples/biology/hypoxiaresponsesignaling/hypoxia-response-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/hypoxiaresponsesignaling/metadata.yaml b/Examples/biology/hypoxiaresponsesignaling/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/hypoxiaresponsesignaling/metadata.yaml rename to Examples/biology/hypoxiaresponsesignaling/metadata.yaml index f442f3d..21767de 100644 --- a/Contributed/BNGPlayground_Examples/biology/hypoxiaresponsesignaling/metadata.yaml +++ b/Examples/biology/hypoxiaresponsesignaling/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/hypoxia-response-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/il1bsignaling/README.md b/Examples/biology/il1bsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/il1bsignaling/README.md rename to Examples/biology/il1bsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/il1bsignaling/il1b-signaling.bngl b/Examples/biology/il1bsignaling/il1b-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/il1bsignaling/il1b-signaling.bngl rename to Examples/biology/il1bsignaling/il1b-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/il1bsignaling/metadata.yaml b/Examples/biology/il1bsignaling/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/il1bsignaling/metadata.yaml rename to Examples/biology/il1bsignaling/metadata.yaml index c177eb0..ee1147e 100644 --- a/Contributed/BNGPlayground_Examples/biology/il1bsignaling/metadata.yaml +++ b/Examples/biology/il1bsignaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/il1b-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/il6jakstatpathway/README.md b/Examples/biology/il6jakstatpathway/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/il6jakstatpathway/README.md rename to Examples/biology/il6jakstatpathway/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/il6jakstatpathway/il6-jak-stat-pathway.bngl b/Examples/biology/il6jakstatpathway/il6-jak-stat-pathway.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/il6jakstatpathway/il6-jak-stat-pathway.bngl rename to Examples/biology/il6jakstatpathway/il6-jak-stat-pathway.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/il6jakstatpathway/metadata.yaml b/Examples/biology/il6jakstatpathway/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/il6jakstatpathway/metadata.yaml rename to Examples/biology/il6jakstatpathway/metadata.yaml index c55a3b2..300dada 100644 --- a/Contributed/BNGPlayground_Examples/biology/il6jakstatpathway/metadata.yaml +++ b/Examples/biology/il6jakstatpathway/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/il6-jak-stat-pathway.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/immunesynapseformation/README.md b/Examples/biology/immunesynapseformation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/immunesynapseformation/README.md rename to Examples/biology/immunesynapseformation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/immunesynapseformation/immune-synapse-formation.bngl b/Examples/biology/immunesynapseformation/immune-synapse-formation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/immunesynapseformation/immune-synapse-formation.bngl rename to Examples/biology/immunesynapseformation/immune-synapse-formation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/immunesynapseformation/metadata.yaml b/Examples/biology/immunesynapseformation/metadata.yaml similarity index 88% rename from Contributed/BNGPlayground_Examples/biology/immunesynapseformation/metadata.yaml rename to Examples/biology/immunesynapseformation/metadata.yaml index fa54441..2fcd966 100644 --- a/Contributed/BNGPlayground_Examples/biology/immunesynapseformation/metadata.yaml +++ b/Examples/biology/immunesynapseformation/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/immune-synapse-formation.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/inflammasomeactivation/README.md b/Examples/biology/inflammasomeactivation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/inflammasomeactivation/README.md rename to Examples/biology/inflammasomeactivation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/inflammasomeactivation/inflammasome-activation.bngl b/Examples/biology/inflammasomeactivation/inflammasome-activation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/inflammasomeactivation/inflammasome-activation.bngl rename to Examples/biology/inflammasomeactivation/inflammasome-activation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/inflammasomeactivation/metadata.yaml b/Examples/biology/inflammasomeactivation/metadata.yaml similarity index 88% rename from Contributed/BNGPlayground_Examples/biology/inflammasomeactivation/metadata.yaml rename to Examples/biology/inflammasomeactivation/metadata.yaml index 2105e08..f52dd1d 100644 --- a/Contributed/BNGPlayground_Examples/biology/inflammasomeactivation/metadata.yaml +++ b/Examples/biology/inflammasomeactivation/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/inflammasome-activation.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/inositolphosphatemetabolism/README.md b/Examples/biology/inositolphosphatemetabolism/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/inositolphosphatemetabolism/README.md rename to Examples/biology/inositolphosphatemetabolism/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/inositolphosphatemetabolism/inositol-phosphate-metabolism.bngl b/Examples/biology/inositolphosphatemetabolism/inositol-phosphate-metabolism.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/inositolphosphatemetabolism/inositol-phosphate-metabolism.bngl rename to Examples/biology/inositolphosphatemetabolism/inositol-phosphate-metabolism.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/inositolphosphatemetabolism/metadata.yaml b/Examples/biology/inositolphosphatemetabolism/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/biology/inositolphosphatemetabolism/metadata.yaml rename to Examples/biology/inositolphosphatemetabolism/metadata.yaml index 15f62b0..9d7e1c6 100644 --- a/Contributed/BNGPlayground_Examples/biology/inositolphosphatemetabolism/metadata.yaml +++ b/Examples/biology/inositolphosphatemetabolism/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/inositol-phosphate-metabolism.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["neuroscience","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/insulinglucosehomeostasis/README.md b/Examples/biology/insulinglucosehomeostasis/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/insulinglucosehomeostasis/README.md rename to Examples/biology/insulinglucosehomeostasis/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis.bngl b/Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis.bngl rename to Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/insulinglucosehomeostasis/metadata.yaml b/Examples/biology/insulinglucosehomeostasis/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/insulinglucosehomeostasis/metadata.yaml rename to Examples/biology/insulinglucosehomeostasis/metadata.yaml index bdfe742..01947eb 100644 --- a/Contributed/BNGPlayground_Examples/biology/insulinglucosehomeostasis/metadata.yaml +++ b/Examples/biology/insulinglucosehomeostasis/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: true uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/insulin-glucose-homeostasis.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["metabolism","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/interferonsignaling/README.md b/Examples/biology/interferonsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/interferonsignaling/README.md rename to Examples/biology/interferonsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/interferonsignaling/interferon-signaling.bngl b/Examples/biology/interferonsignaling/interferon-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/interferonsignaling/interferon-signaling.bngl rename to Examples/biology/interferonsignaling/interferon-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/interferonsignaling/metadata.yaml b/Examples/biology/interferonsignaling/metadata.yaml similarity index 88% rename from Contributed/BNGPlayground_Examples/biology/interferonsignaling/metadata.yaml rename to Examples/biology/interferonsignaling/metadata.yaml index 3df3c35..f910096 100644 --- a/Contributed/BNGPlayground_Examples/biology/interferonsignaling/metadata.yaml +++ b/Examples/biology/interferonsignaling/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/interferon-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/ire1axbp1erstress/README.md b/Examples/biology/ire1axbp1erstress/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/ire1axbp1erstress/README.md rename to Examples/biology/ire1axbp1erstress/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl b/Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl rename to Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/ire1axbp1erstress/metadata.yaml b/Examples/biology/ire1axbp1erstress/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/ire1axbp1erstress/metadata.yaml rename to Examples/biology/ire1axbp1erstress/metadata.yaml index 68df2fe..8419377 100644 --- a/Contributed/BNGPlayground_Examples/biology/ire1axbp1erstress/metadata.yaml +++ b/Examples/biology/ire1axbp1erstress/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/ire1a-xbp1-er-stress.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/jakstatcytokinesignaling/README.md b/Examples/biology/jakstatcytokinesignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/jakstatcytokinesignaling/README.md rename to Examples/biology/jakstatcytokinesignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling.bngl b/Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling.bngl rename to Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/jakstatcytokinesignaling/metadata.yaml b/Examples/biology/jakstatcytokinesignaling/metadata.yaml similarity index 88% rename from Contributed/BNGPlayground_Examples/biology/jakstatcytokinesignaling/metadata.yaml rename to Examples/biology/jakstatcytokinesignaling/metadata.yaml index dfea0df..23d4473 100644 --- a/Contributed/BNGPlayground_Examples/biology/jakstatcytokinesignaling/metadata.yaml +++ b/Examples/biology/jakstatcytokinesignaling/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/jak-stat-cytokine-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/jnkmapksignaling/README.md b/Examples/biology/jnkmapksignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/jnkmapksignaling/README.md rename to Examples/biology/jnkmapksignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/jnkmapksignaling/jnk-mapk-signaling.bngl b/Examples/biology/jnkmapksignaling/jnk-mapk-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/jnkmapksignaling/jnk-mapk-signaling.bngl rename to Examples/biology/jnkmapksignaling/jnk-mapk-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/jnkmapksignaling/metadata.yaml b/Examples/biology/jnkmapksignaling/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/jnkmapksignaling/metadata.yaml rename to Examples/biology/jnkmapksignaling/metadata.yaml index b90bd79..85869ab 100644 --- a/Contributed/BNGPlayground_Examples/biology/jnkmapksignaling/metadata.yaml +++ b/Examples/biology/jnkmapksignaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/jnk-mapk-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/kirchannelregulation/README.md b/Examples/biology/kirchannelregulation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/kirchannelregulation/README.md rename to Examples/biology/kirchannelregulation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/kirchannelregulation/kir-channel-regulation.bngl b/Examples/biology/kirchannelregulation/kir-channel-regulation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/kirchannelregulation/kir-channel-regulation.bngl rename to Examples/biology/kirchannelregulation/kir-channel-regulation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/kirchannelregulation/metadata.yaml b/Examples/biology/kirchannelregulation/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/kirchannelregulation/metadata.yaml rename to Examples/biology/kirchannelregulation/metadata.yaml index b905375..006f08f 100644 --- a/Contributed/BNGPlayground_Examples/biology/kirchannelregulation/metadata.yaml +++ b/Examples/biology/kirchannelregulation/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/kir-channel-regulation.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/lacoperonregulation/README.md b/Examples/biology/lacoperonregulation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/lacoperonregulation/README.md rename to Examples/biology/lacoperonregulation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/lacoperonregulation/lac-operon-regulation.bngl b/Examples/biology/lacoperonregulation/lac-operon-regulation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/lacoperonregulation/lac-operon-regulation.bngl rename to Examples/biology/lacoperonregulation/lac-operon-regulation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/lacoperonregulation/metadata.yaml b/Examples/biology/lacoperonregulation/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/lacoperonregulation/metadata.yaml rename to Examples/biology/lacoperonregulation/metadata.yaml index 078a9b9..4b33871 100644 --- a/Contributed/BNGPlayground_Examples/biology/lacoperonregulation/metadata.yaml +++ b/Examples/biology/lacoperonregulation/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/lac-operon-regulation.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["metabolism","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/README.md b/Examples/biology/lipidmediatedpip3signaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/README.md rename to Examples/biology/lipidmediatedpip3signaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl b/Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl rename to Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/metadata.yaml b/Examples/biology/lipidmediatedpip3signaling/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/metadata.yaml rename to Examples/biology/lipidmediatedpip3signaling/metadata.yaml index f0d01e4..49cf3a7 100644 --- a/Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/metadata.yaml +++ b/Examples/biology/lipidmediatedpip3signaling/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/lipid-mediated-pip3-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/ltypecalciumchanneldynamics/README.md b/Examples/biology/ltypecalciumchanneldynamics/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/ltypecalciumchanneldynamics/README.md rename to Examples/biology/ltypecalciumchanneldynamics/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics.bngl b/Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics.bngl rename to Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/ltypecalciumchanneldynamics/metadata.yaml b/Examples/biology/ltypecalciumchanneldynamics/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/biology/ltypecalciumchanneldynamics/metadata.yaml rename to Examples/biology/ltypecalciumchanneldynamics/metadata.yaml index d2fdd32..4b61850 100644 --- a/Contributed/BNGPlayground_Examples/biology/ltypecalciumchanneldynamics/metadata.yaml +++ b/Examples/biology/ltypecalciumchanneldynamics/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/l-type-calcium-channel-dynamics.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["neuroscience","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/mapksignalingcascade/README.md b/Examples/biology/mapksignalingcascade/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/mapksignalingcascade/README.md rename to Examples/biology/mapksignalingcascade/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/mapksignalingcascade/mapk-signaling-cascade.bngl b/Examples/biology/mapksignalingcascade/mapk-signaling-cascade.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/mapksignalingcascade/mapk-signaling-cascade.bngl rename to Examples/biology/mapksignalingcascade/mapk-signaling-cascade.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/mapksignalingcascade/metadata.yaml b/Examples/biology/mapksignalingcascade/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/mapksignalingcascade/metadata.yaml rename to Examples/biology/mapksignalingcascade/metadata.yaml index c62a123..798f143 100644 --- a/Contributed/BNGPlayground_Examples/biology/mapksignalingcascade/metadata.yaml +++ b/Examples/biology/mapksignalingcascade/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/mapk-signaling-cascade.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/michaelismentenkinetics/README.md b/Examples/biology/michaelismentenkinetics/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/michaelismentenkinetics/README.md rename to Examples/biology/michaelismentenkinetics/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/michaelismentenkinetics/metadata.yaml b/Examples/biology/michaelismentenkinetics/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/michaelismentenkinetics/metadata.yaml rename to Examples/biology/michaelismentenkinetics/metadata.yaml index 98633e6..e494ff5 100644 --- a/Contributed/BNGPlayground_Examples/biology/michaelismentenkinetics/metadata.yaml +++ b/Examples/biology/michaelismentenkinetics/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/michaelis-menten-kinetics.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["metabolism","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/michaelismentenkinetics/michaelis-menten-kinetics.bngl b/Examples/biology/michaelismentenkinetics/michaelis-menten-kinetics.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/michaelismentenkinetics/michaelis-menten-kinetics.bngl rename to Examples/biology/michaelismentenkinetics/michaelis-menten-kinetics.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/mtorc2signaling/README.md b/Examples/biology/mtorc2signaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/mtorc2signaling/README.md rename to Examples/biology/mtorc2signaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/mtorc2signaling/metadata.yaml b/Examples/biology/mtorc2signaling/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/mtorc2signaling/metadata.yaml rename to Examples/biology/mtorc2signaling/metadata.yaml index 403957d..9285815 100644 --- a/Contributed/BNGPlayground_Examples/biology/mtorc2signaling/metadata.yaml +++ b/Examples/biology/mtorc2signaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/mtorc2-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/mtorc2signaling/mtorc2-signaling.bngl b/Examples/biology/mtorc2signaling/mtorc2-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/mtorc2signaling/mtorc2-signaling.bngl rename to Examples/biology/mtorc2signaling/mtorc2-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/mtorsignaling/README.md b/Examples/biology/mtorsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/mtorsignaling/README.md rename to Examples/biology/mtorsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/mtorsignaling/metadata.yaml b/Examples/biology/mtorsignaling/metadata.yaml similarity index 88% rename from Contributed/BNGPlayground_Examples/biology/mtorsignaling/metadata.yaml rename to Examples/biology/mtorsignaling/metadata.yaml index d18277a..c5e508f 100644 --- a/Contributed/BNGPlayground_Examples/biology/mtorsignaling/metadata.yaml +++ b/Examples/biology/mtorsignaling/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/mtor-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["neuroscience","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/mtorsignaling/mtor-signaling.bngl b/Examples/biology/mtorsignaling/mtor-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/mtorsignaling/mtor-signaling.bngl rename to Examples/biology/mtorsignaling/mtor-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/myogenicdifferentiation/README.md b/Examples/biology/myogenicdifferentiation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/myogenicdifferentiation/README.md rename to Examples/biology/myogenicdifferentiation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/myogenicdifferentiation/metadata.yaml b/Examples/biology/myogenicdifferentiation/metadata.yaml similarity index 88% rename from Contributed/BNGPlayground_Examples/biology/myogenicdifferentiation/metadata.yaml rename to Examples/biology/myogenicdifferentiation/metadata.yaml index efbc5a6..cd2cf72 100644 --- a/Contributed/BNGPlayground_Examples/biology/myogenicdifferentiation/metadata.yaml +++ b/Examples/biology/myogenicdifferentiation/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/myogenic-differentiation.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["developmental","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/myogenicdifferentiation/myogenic-differentiation.bngl b/Examples/biology/myogenicdifferentiation/myogenic-differentiation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/myogenicdifferentiation/myogenic-differentiation.bngl rename to Examples/biology/myogenicdifferentiation/myogenic-differentiation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/negativefeedbackloop/README.md b/Examples/biology/negativefeedbackloop/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/negativefeedbackloop/README.md rename to Examples/biology/negativefeedbackloop/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/negativefeedbackloop/metadata.yaml b/Examples/biology/negativefeedbackloop/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/negativefeedbackloop/metadata.yaml rename to Examples/biology/negativefeedbackloop/metadata.yaml index 552e494..cfd8f9c 100644 --- a/Contributed/BNGPlayground_Examples/biology/negativefeedbackloop/metadata.yaml +++ b/Examples/biology/negativefeedbackloop/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/negative-feedback-loop.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/negativefeedbackloop/negative-feedback-loop.bngl b/Examples/biology/negativefeedbackloop/negative-feedback-loop.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/negativefeedbackloop/negative-feedback-loop.bngl rename to Examples/biology/negativefeedbackloop/negative-feedback-loop.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/neurotransmitterrelease/README.md b/Examples/biology/neurotransmitterrelease/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/neurotransmitterrelease/README.md rename to Examples/biology/neurotransmitterrelease/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/neurotransmitterrelease/metadata.yaml b/Examples/biology/neurotransmitterrelease/metadata.yaml similarity index 88% rename from Contributed/BNGPlayground_Examples/biology/neurotransmitterrelease/metadata.yaml rename to Examples/biology/neurotransmitterrelease/metadata.yaml index 848485c..379b27f 100644 --- a/Contributed/BNGPlayground_Examples/biology/neurotransmitterrelease/metadata.yaml +++ b/Examples/biology/neurotransmitterrelease/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/neurotransmitter-release.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["neuroscience","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/neurotransmitterrelease/neurotransmitter-release.bngl b/Examples/biology/neurotransmitterrelease/neurotransmitter-release.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/neurotransmitterrelease/neurotransmitter-release.bngl rename to Examples/biology/neurotransmitterrelease/neurotransmitter-release.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/nfkbfeedback/README.md b/Examples/biology/nfkbfeedback/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/nfkbfeedback/README.md rename to Examples/biology/nfkbfeedback/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/nfkbfeedback/metadata.yaml b/Examples/biology/nfkbfeedback/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/nfkbfeedback/metadata.yaml rename to Examples/biology/nfkbfeedback/metadata.yaml index 97c4313..c16ec08 100644 --- a/Contributed/BNGPlayground_Examples/biology/nfkbfeedback/metadata.yaml +++ b/Examples/biology/nfkbfeedback/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/nfkb-feedback.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/nfkbfeedback/nfkb-feedback.bngl b/Examples/biology/nfkbfeedback/nfkb-feedback.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/nfkbfeedback/nfkb-feedback.bngl rename to Examples/biology/nfkbfeedback/nfkb-feedback.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/nocgmpsignaling/README.md b/Examples/biology/nocgmpsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/nocgmpsignaling/README.md rename to Examples/biology/nocgmpsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/nocgmpsignaling/metadata.yaml b/Examples/biology/nocgmpsignaling/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/nocgmpsignaling/metadata.yaml rename to Examples/biology/nocgmpsignaling/metadata.yaml index e075fc1..57a0eed 100644 --- a/Contributed/BNGPlayground_Examples/biology/nocgmpsignaling/metadata.yaml +++ b/Examples/biology/nocgmpsignaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/no-cgmp-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["metabolism","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/nocgmpsignaling/no-cgmp-signaling.bngl b/Examples/biology/nocgmpsignaling/no-cgmp-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/nocgmpsignaling/no-cgmp-signaling.bngl rename to Examples/biology/nocgmpsignaling/no-cgmp-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/notchdeltalateralinhibition/README.md b/Examples/biology/notchdeltalateralinhibition/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/notchdeltalateralinhibition/README.md rename to Examples/biology/notchdeltalateralinhibition/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/notchdeltalateralinhibition/metadata.yaml b/Examples/biology/notchdeltalateralinhibition/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/notchdeltalateralinhibition/metadata.yaml rename to Examples/biology/notchdeltalateralinhibition/metadata.yaml index f4c7d82..a13eb8d 100644 --- a/Contributed/BNGPlayground_Examples/biology/notchdeltalateralinhibition/metadata.yaml +++ b/Examples/biology/notchdeltalateralinhibition/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/notch-delta-lateral-inhibition.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["developmental","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition.bngl b/Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition.bngl rename to Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/oxidativestressresponse/README.md b/Examples/biology/oxidativestressresponse/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/oxidativestressresponse/README.md rename to Examples/biology/oxidativestressresponse/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/oxidativestressresponse/metadata.yaml b/Examples/biology/oxidativestressresponse/metadata.yaml similarity index 91% rename from Contributed/BNGPlayground_Examples/biology/oxidativestressresponse/metadata.yaml rename to Examples/biology/oxidativestressresponse/metadata.yaml index 65373f7..1a6debb 100644 --- a/Contributed/BNGPlayground_Examples/biology/oxidativestressresponse/metadata.yaml +++ b/Examples/biology/oxidativestressresponse/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/oxidative-stress-response.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl b/Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl rename to Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/p38mapksignaling/README.md b/Examples/biology/p38mapksignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/p38mapksignaling/README.md rename to Examples/biology/p38mapksignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/p38mapksignaling/metadata.yaml b/Examples/biology/p38mapksignaling/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/biology/p38mapksignaling/metadata.yaml rename to Examples/biology/p38mapksignaling/metadata.yaml index 217bf59..fe05f69 100644 --- a/Contributed/BNGPlayground_Examples/biology/p38mapksignaling/metadata.yaml +++ b/Examples/biology/p38mapksignaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/p38-mapk-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl b/Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl rename to Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/README.md b/Examples/biology/p53mdm2oscillator/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/README.md rename to Examples/biology/p53mdm2oscillator/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/metadata.yaml b/Examples/biology/p53mdm2oscillator/metadata.yaml similarity index 88% rename from Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/metadata.yaml rename to Examples/biology/p53mdm2oscillator/metadata.yaml index d296777..80360b6 100644 --- a/Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/metadata.yaml +++ b/Examples/biology/p53mdm2oscillator/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/p53-mdm2-oscillator.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cell-cycle","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl b/Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl rename to Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/README.md b/Examples/biology/parp1mediateddnarepair/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/README.md rename to Examples/biology/parp1mediateddnarepair/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/metadata.yaml b/Examples/biology/parp1mediateddnarepair/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/metadata.yaml rename to Examples/biology/parp1mediateddnarepair/metadata.yaml index 3f97ba1..8759952 100644 --- a/Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/metadata.yaml +++ b/Examples/biology/parp1mediateddnarepair/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/parp1-mediated-dna-repair.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cell-cycle","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl b/Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl rename to Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/phosphorelaychain/README.md b/Examples/biology/phosphorelaychain/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/phosphorelaychain/README.md rename to Examples/biology/phosphorelaychain/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/phosphorelaychain/metadata.yaml b/Examples/biology/phosphorelaychain/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/phosphorelaychain/metadata.yaml rename to Examples/biology/phosphorelaychain/metadata.yaml index 54a87d3..ac2f1b9 100644 --- a/Contributed/BNGPlayground_Examples/biology/phosphorelaychain/metadata.yaml +++ b/Examples/biology/phosphorelaychain/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/phosphorelay-chain.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/phosphorelaychain/phosphorelay-chain.bngl b/Examples/biology/phosphorelaychain/phosphorelay-chain.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/phosphorelaychain/phosphorelay-chain.bngl rename to Examples/biology/phosphorelaychain/phosphorelay-chain.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/plateletactivation/README.md b/Examples/biology/plateletactivation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/plateletactivation/README.md rename to Examples/biology/plateletactivation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/plateletactivation/metadata.yaml b/Examples/biology/plateletactivation/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/plateletactivation/metadata.yaml rename to Examples/biology/plateletactivation/metadata.yaml index 8c69367..e834d55 100644 --- a/Contributed/BNGPlayground_Examples/biology/plateletactivation/metadata.yaml +++ b/Examples/biology/plateletactivation/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/platelet-activation.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/plateletactivation/platelet-activation.bngl b/Examples/biology/plateletactivation/platelet-activation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/plateletactivation/platelet-activation.bngl rename to Examples/biology/plateletactivation/platelet-activation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/README.md b/Examples/biology/predatorpreydynamics/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/README.md rename to Examples/biology/predatorpreydynamics/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/metadata.yaml b/Examples/biology/predatorpreydynamics/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/metadata.yaml rename to Examples/biology/predatorpreydynamics/metadata.yaml index 7082692..bb813d6 100644 --- a/Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/metadata.yaml +++ b/Examples/biology/predatorpreydynamics/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/predator-prey-dynamics.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl b/Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl rename to Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/README.md b/Examples/biology/quorumsensingcircuit/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/README.md rename to Examples/biology/quorumsensingcircuit/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/metadata.yaml b/Examples/biology/quorumsensingcircuit/metadata.yaml similarity index 91% rename from Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/metadata.yaml rename to Examples/biology/quorumsensingcircuit/metadata.yaml index e8c6633..3166938 100644 --- a/Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/metadata.yaml +++ b/Examples/biology/quorumsensingcircuit/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/quorum-sensing-circuit.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl b/Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl similarity index 95% rename from Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl rename to Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl index a2edc7e..143fd45 100644 --- a/Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl +++ b/Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl @@ -33,7 +33,6 @@ begin reaction rules Autoinducer() + Gene(state~off) -> Gene(state~on) + Autoinducer() k_activate Gene(state~on) -> Gene(state~on) + Protein() k_export Protein() -> 0 k_import - # FIX: Add Autoinducer dynamics (was conserved) Protein() -> Protein() + Autoinducer() 0.1 # Protein produces AI Autoinducer() -> 0 0.05 # AI degradation Autoinducer_env() -> 0 0.02 # Environmental AI clearance diff --git a/Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/README.md b/Examples/biology/rabgtpasecycle/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/README.md rename to Examples/biology/rabgtpasecycle/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/metadata.yaml b/Examples/biology/rabgtpasecycle/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/metadata.yaml rename to Examples/biology/rabgtpasecycle/metadata.yaml index 43d32a6..3147c93 100644 --- a/Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/metadata.yaml +++ b/Examples/biology/rabgtpasecycle/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/rab-gtpase-cycle.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/rab-gtpase-cycle.bngl b/Examples/biology/rabgtpasecycle/rab-gtpase-cycle.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/rab-gtpase-cycle.bngl rename to Examples/biology/rabgtpasecycle/rab-gtpase-cycle.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/ranklranksignaling/README.md b/Examples/biology/ranklranksignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/ranklranksignaling/README.md rename to Examples/biology/ranklranksignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/ranklranksignaling/metadata.yaml b/Examples/biology/ranklranksignaling/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/ranklranksignaling/metadata.yaml rename to Examples/biology/ranklranksignaling/metadata.yaml index 8af4900..80d8eb1 100644 --- a/Contributed/BNGPlayground_Examples/biology/ranklranksignaling/metadata.yaml +++ b/Examples/biology/ranklranksignaling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/rankl-rank-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["developmental","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/ranklranksignaling/rankl-rank-signaling.bngl b/Examples/biology/ranklranksignaling/rankl-rank-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/ranklranksignaling/rankl-rank-signaling.bngl rename to Examples/biology/ranklranksignaling/rankl-rank-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/README.md b/Examples/biology/rasgefgapcycle/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/README.md rename to Examples/biology/rasgefgapcycle/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/metadata.yaml b/Examples/biology/rasgefgapcycle/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/metadata.yaml rename to Examples/biology/rasgefgapcycle/metadata.yaml index 58824e0..1eac248 100644 --- a/Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/metadata.yaml +++ b/Examples/biology/rasgefgapcycle/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/ras-gef-gap-cycle.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/ras-gef-gap-cycle.bngl b/Examples/biology/rasgefgapcycle/ras-gef-gap-cycle.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/ras-gef-gap-cycle.bngl rename to Examples/biology/rasgefgapcycle/ras-gef-gap-cycle.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/README.md b/Examples/biology/repressilatoroscillator/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/README.md rename to Examples/biology/repressilatoroscillator/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/metadata.yaml b/Examples/biology/repressilatoroscillator/metadata.yaml similarity index 91% rename from Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/metadata.yaml rename to Examples/biology/repressilatoroscillator/metadata.yaml index 20753fb..4bfd330 100644 --- a/Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/metadata.yaml +++ b/Examples/biology/repressilatoroscillator/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/repressilator-oscillator.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/repressilator-oscillator.bngl b/Examples/biology/repressilatoroscillator/repressilator-oscillator.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/repressilator-oscillator.bngl rename to Examples/biology/repressilatoroscillator/repressilator-oscillator.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/README.md b/Examples/biology/retinoicacidsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/README.md rename to Examples/biology/retinoicacidsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/metadata.yaml b/Examples/biology/retinoicacidsignaling/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/metadata.yaml rename to Examples/biology/retinoicacidsignaling/metadata.yaml index 2f6ebf5..e16c8a7 100644 --- a/Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/metadata.yaml +++ b/Examples/biology/retinoicacidsignaling/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/retinoic-acid-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["developmental","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/retinoic-acid-signaling.bngl b/Examples/biology/retinoicacidsignaling/retinoic-acid-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/retinoic-acid-signaling.bngl rename to Examples/biology/retinoicacidsignaling/retinoic-acid-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/README.md b/Examples/biology/rhogtpaseactincytoskeleton/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/README.md rename to Examples/biology/rhogtpaseactincytoskeleton/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml b/Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml rename to Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml index f8a9b51..562b546 100644 --- a/Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml +++ b/Examples/biology/rhogtpaseactincytoskeleton/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/rho-gtpase-actin-cytoskeleton.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton.bngl b/Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton.bngl rename to Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/README.md b/Examples/biology/shp2phosphataseregulation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/README.md rename to Examples/biology/shp2phosphataseregulation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/metadata.yaml b/Examples/biology/shp2phosphataseregulation/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/metadata.yaml rename to Examples/biology/shp2phosphataseregulation/metadata.yaml index d30cddb..e48befa 100644 --- a/Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/metadata.yaml +++ b/Examples/biology/shp2phosphataseregulation/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/shp2-phosphatase-regulation.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation.bngl b/Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation.bngl rename to Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/README.md b/Examples/biology/signalamplificationcascade/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/README.md rename to Examples/biology/signalamplificationcascade/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/metadata.yaml b/Examples/biology/signalamplificationcascade/metadata.yaml similarity index 91% rename from Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/metadata.yaml rename to Examples/biology/signalamplificationcascade/metadata.yaml index 156c02e..d701b85 100644 --- a/Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/metadata.yaml +++ b/Examples/biology/signalamplificationcascade/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/signal-amplification-cascade.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/signal-amplification-cascade.bngl b/Examples/biology/signalamplificationcascade/signal-amplification-cascade.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/signal-amplification-cascade.bngl rename to Examples/biology/signalamplificationcascade/signal-amplification-cascade.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/simpledimerization/README.md b/Examples/biology/simpledimerization/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/simpledimerization/README.md rename to Examples/biology/simpledimerization/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/simpledimerization/metadata.yaml b/Examples/biology/simpledimerization/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/simpledimerization/metadata.yaml rename to Examples/biology/simpledimerization/metadata.yaml index afec237..1748cdd 100644 --- a/Contributed/BNGPlayground_Examples/biology/simpledimerization/metadata.yaml +++ b/Examples/biology/simpledimerization/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/simple-dimerization.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/simpledimerization/simple-dimerization.bngl b/Examples/biology/simpledimerization/simple-dimerization.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/simpledimerization/simple-dimerization.bngl rename to Examples/biology/simpledimerization/simple-dimerization.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/README.md b/Examples/biology/sirepidemicmodel/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/README.md rename to Examples/biology/sirepidemicmodel/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/metadata.yaml b/Examples/biology/sirepidemicmodel/metadata.yaml similarity index 87% rename from Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/metadata.yaml rename to Examples/biology/sirepidemicmodel/metadata.yaml index c39dddc..08da27d 100644 --- a/Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/metadata.yaml +++ b/Examples/biology/sirepidemicmodel/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/sir-epidemic-model.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["ecology","tutorials","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/sir-epidemic-model.bngl b/Examples/biology/sirepidemicmodel/sir-epidemic-model.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/sir-epidemic-model.bngl rename to Examples/biology/sirepidemicmodel/sir-epidemic-model.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/README.md b/Examples/biology/smadtgfbetasignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/README.md rename to Examples/biology/smadtgfbetasignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/metadata.yaml b/Examples/biology/smadtgfbetasignaling/metadata.yaml similarity index 88% rename from Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/metadata.yaml rename to Examples/biology/smadtgfbetasignaling/metadata.yaml index bd30c97..5aab150 100644 --- a/Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/metadata.yaml +++ b/Examples/biology/smadtgfbetasignaling/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/smad-tgf-beta-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["developmental","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling.bngl b/Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling.bngl rename to Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/README.md b/Examples/biology/sonichedgehoggradient/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/README.md rename to Examples/biology/sonichedgehoggradient/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/metadata.yaml b/Examples/biology/sonichedgehoggradient/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/metadata.yaml rename to Examples/biology/sonichedgehoggradient/metadata.yaml index f41a5d1..fed2f2f 100644 --- a/Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/metadata.yaml +++ b/Examples/biology/sonichedgehoggradient/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/sonic-hedgehog-gradient.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["developmental","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient.bngl b/Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient.bngl rename to Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/README.md b/Examples/biology/stat3mediatedtranscription/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/README.md rename to Examples/biology/stat3mediatedtranscription/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/metadata.yaml b/Examples/biology/stat3mediatedtranscription/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/metadata.yaml rename to Examples/biology/stat3mediatedtranscription/metadata.yaml index 12fb78d..3e8884e 100644 --- a/Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/metadata.yaml +++ b/Examples/biology/stat3mediatedtranscription/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/stat3-mediated-transcription.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription.bngl b/Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription.bngl rename to Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/README.md b/Examples/biology/stressresponseadaptation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/README.md rename to Examples/biology/stressresponseadaptation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/metadata.yaml b/Examples/biology/stressresponseadaptation/metadata.yaml similarity index 91% rename from Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/metadata.yaml rename to Examples/biology/stressresponseadaptation/metadata.yaml index a89e7f7..4790cde 100644 --- a/Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/metadata.yaml +++ b/Examples/biology/stressresponseadaptation/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/stress-response-adaptation.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/stress-response-adaptation.bngl b/Examples/biology/stressresponseadaptation/stress-response-adaptation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/stress-response-adaptation.bngl rename to Examples/biology/stressresponseadaptation/stress-response-adaptation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/README.md b/Examples/biology/synapticplasticityltp/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/README.md rename to Examples/biology/synapticplasticityltp/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/metadata.yaml b/Examples/biology/synapticplasticityltp/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/metadata.yaml rename to Examples/biology/synapticplasticityltp/metadata.yaml index 3f1bb7a..3d91589 100644 --- a/Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/metadata.yaml +++ b/Examples/biology/synapticplasticityltp/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/synaptic-plasticity-ltp.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["neuroscience","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp.bngl b/Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp.bngl rename to Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/tcellactivation/README.md b/Examples/biology/tcellactivation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tcellactivation/README.md rename to Examples/biology/tcellactivation/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/tcellactivation/metadata.yaml b/Examples/biology/tcellactivation/metadata.yaml similarity index 88% rename from Contributed/BNGPlayground_Examples/biology/tcellactivation/metadata.yaml rename to Examples/biology/tcellactivation/metadata.yaml index 33f03ba..513ad5b 100644 --- a/Contributed/BNGPlayground_Examples/biology/tcellactivation/metadata.yaml +++ b/Examples/biology/tcellactivation/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/t-cell-activation.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/tcellactivation/t-cell-activation.bngl b/Examples/biology/tcellactivation/t-cell-activation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tcellactivation/t-cell-activation.bngl rename to Examples/biology/tcellactivation/t-cell-activation.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/README.md b/Examples/biology/tlr3dsrnasensing/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/README.md rename to Examples/biology/tlr3dsrnasensing/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/metadata.yaml b/Examples/biology/tlr3dsrnasensing/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/metadata.yaml rename to Examples/biology/tlr3dsrnasensing/metadata.yaml index e5731f7..4b66a09 100644 --- a/Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/metadata.yaml +++ b/Examples/biology/tlr3dsrnasensing/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/tlr3-dsrna-sensing.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing.bngl b/Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing.bngl rename to Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/README.md b/Examples/biology/tnfinducedapoptosis/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/README.md rename to Examples/biology/tnfinducedapoptosis/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/metadata.yaml b/Examples/biology/tnfinducedapoptosis/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/metadata.yaml rename to Examples/biology/tnfinducedapoptosis/metadata.yaml index 0964f3c..d8987ab 100644 --- a/Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/metadata.yaml +++ b/Examples/biology/tnfinducedapoptosis/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/tnf-induced-apoptosis.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cell-cycle","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis.bngl b/Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis.bngl rename to Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/twocomponentsystem/README.md b/Examples/biology/twocomponentsystem/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/twocomponentsystem/README.md rename to Examples/biology/twocomponentsystem/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/twocomponentsystem/metadata.yaml b/Examples/biology/twocomponentsystem/metadata.yaml similarity index 90% rename from Contributed/BNGPlayground_Examples/biology/twocomponentsystem/metadata.yaml rename to Examples/biology/twocomponentsystem/metadata.yaml index 2b7f2d5..a39f2d5 100644 --- a/Contributed/BNGPlayground_Examples/biology/twocomponentsystem/metadata.yaml +++ b/Examples/biology/twocomponentsystem/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/two-component-system.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/twocomponentsystem/two-component-system.bngl b/Examples/biology/twocomponentsystem/two-component-system.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/twocomponentsystem/two-component-system.bngl rename to Examples/biology/twocomponentsystem/two-component-system.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/README.md b/Examples/biology/vegfangiogenesis/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/README.md rename to Examples/biology/vegfangiogenesis/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/metadata.yaml b/Examples/biology/vegfangiogenesis/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/metadata.yaml rename to Examples/biology/vegfangiogenesis/metadata.yaml index 6045f70..e52b50e 100644 --- a/Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/metadata.yaml +++ b/Examples/biology/vegfangiogenesis/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/vegf-angiogenesis.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/vegf-angiogenesis.bngl b/Examples/biology/vegfangiogenesis/vegf-angiogenesis.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/vegf-angiogenesis.bngl rename to Examples/biology/vegfangiogenesis/vegf-angiogenesis.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/README.md b/Examples/biology/viralsensinginnateimmunity/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/README.md rename to Examples/biology/viralsensinginnateimmunity/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/metadata.yaml b/Examples/biology/viralsensinginnateimmunity/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/metadata.yaml rename to Examples/biology/viralsensinginnateimmunity/metadata.yaml index 42b86af..4ad35af 100644 --- a/Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/metadata.yaml +++ b/Examples/biology/viralsensinginnateimmunity/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/viral-sensing-innate-immunity.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity.bngl b/Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity.bngl rename to Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/README.md b/Examples/biology/wntbetacateninsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/README.md rename to Examples/biology/wntbetacateninsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/metadata.yaml b/Examples/biology/wntbetacateninsignaling/metadata.yaml similarity index 89% rename from Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/metadata.yaml rename to Examples/biology/wntbetacateninsignaling/metadata.yaml index a638b43..a0f48d2 100644 --- a/Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/metadata.yaml +++ b/Examples/biology/wntbetacateninsignaling/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/wnt-beta-catenin-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["developmental","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling.bngl b/Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling.bngl rename to Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/README.md b/Examples/biology/woundhealingpdgfsignaling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/README.md rename to Examples/biology/woundhealingpdgfsignaling/README.md diff --git a/Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/metadata.yaml b/Examples/biology/woundhealingpdgfsignaling/metadata.yaml similarity index 91% rename from Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/metadata.yaml rename to Examples/biology/woundhealingpdgfsignaling/metadata.yaml index 9e05913..2b160e6 100644 --- a/Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/metadata.yaml +++ b/Examples/biology/woundhealingpdgfsignaling/metadata.yaml @@ -11,7 +11,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "ai-generated" original_format: "bngl" @@ -19,6 +19,6 @@ source: source_path: "example-models/wound-healing-pdgf-signaling.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling.bngl b/Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling.bngl rename to Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling.bngl diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/README.md b/Examples/compartments/compartmentendocytosis/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/README.md rename to Examples/compartments/compartmentendocytosis/README.md diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl b/Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl rename to Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/metadata.yaml b/Examples/compartments/compartmentendocytosis/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/metadata.yaml rename to Examples/compartments/compartmentendocytosis/metadata.yaml index 576b36d..f2450bf 100644 --- a/Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/metadata.yaml +++ b/Examples/compartments/compartmentendocytosis/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/compartment_endocytosis.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/README.md b/Examples/compartments/compartmentmembranebound/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/README.md rename to Examples/compartments/compartmentmembranebound/README.md diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl b/Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl rename to Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/metadata.yaml b/Examples/compartments/compartmentmembranebound/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/metadata.yaml rename to Examples/compartments/compartmentmembranebound/metadata.yaml index ed23ba0..17e9bba 100644 --- a/Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/metadata.yaml +++ b/Examples/compartments/compartmentmembranebound/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/compartment_membrane_bound.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/README.md b/Examples/compartments/compartmentnestedtransport/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/README.md rename to Examples/compartments/compartmentnestedtransport/README.md diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl b/Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl rename to Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/metadata.yaml b/Examples/compartments/compartmentnestedtransport/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/metadata.yaml rename to Examples/compartments/compartmentnestedtransport/metadata.yaml index f3cfa3c..a7614f8 100644 --- a/Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/metadata.yaml +++ b/Examples/compartments/compartmentnestedtransport/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/compartment_nested_transport.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/README.md b/Examples/compartments/compartmentnucleartransport/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/README.md rename to Examples/compartments/compartmentnucleartransport/README.md diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl b/Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl rename to Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/metadata.yaml b/Examples/compartments/compartmentnucleartransport/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/metadata.yaml rename to Examples/compartments/compartmentnucleartransport/metadata.yaml index e838152..5312e5c 100644 --- a/Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/metadata.yaml +++ b/Examples/compartments/compartmentnucleartransport/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/compartment_nuclear_transport.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/README.md b/Examples/compartments/compartmentorganelleexchange/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/README.md rename to Examples/compartments/compartmentorganelleexchange/README.md diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl b/Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl rename to Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl diff --git a/Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/metadata.yaml b/Examples/compartments/compartmentorganelleexchange/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/metadata.yaml rename to Examples/compartments/compartmentorganelleexchange/metadata.yaml index 5d64bc0..117bb56 100644 --- a/Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/metadata.yaml +++ b/Examples/compartments/compartmentorganelleexchange/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/compartment_organelle_exchange.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/cs/csdiffiehellman/README.md b/Examples/cs/csdiffiehellman/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csdiffiehellman/README.md rename to Examples/cs/csdiffiehellman/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl b/Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl rename to Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl diff --git a/Contributed/BNGPlayground_Examples/cs/csdiffiehellman/metadata.yaml b/Examples/cs/csdiffiehellman/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/cs/csdiffiehellman/metadata.yaml rename to Examples/cs/csdiffiehellman/metadata.yaml index 8060f75..f2cea06 100644 --- a/Contributed/BNGPlayground_Examples/cs/csdiffiehellman/metadata.yaml +++ b/Examples/cs/csdiffiehellman/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/cs_diffie_hellman.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["cs","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/cs/cshashfunction/README.md b/Examples/cs/cshashfunction/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cshashfunction/README.md rename to Examples/cs/cshashfunction/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/cshashfunction/cs_hash_function.bngl b/Examples/cs/cshashfunction/cs_hash_function.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cshashfunction/cs_hash_function.bngl rename to Examples/cs/cshashfunction/cs_hash_function.bngl diff --git a/Contributed/BNGPlayground_Examples/cs/cshashfunction/metadata.yaml b/Examples/cs/cshashfunction/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/cs/cshashfunction/metadata.yaml rename to Examples/cs/cshashfunction/metadata.yaml index b7b0c72..ab0695d 100644 --- a/Contributed/BNGPlayground_Examples/cs/cshashfunction/metadata.yaml +++ b/Examples/cs/cshashfunction/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/cs_hash_function.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["cs","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/cs/cshuffman/README.md b/Examples/cs/cshuffman/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cshuffman/README.md rename to Examples/cs/cshuffman/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/cshuffman/cs_huffman.bngl b/Examples/cs/cshuffman/cs_huffman.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cshuffman/cs_huffman.bngl rename to Examples/cs/cshuffman/cs_huffman.bngl diff --git a/Contributed/BNGPlayground_Examples/cs/cshuffman/metadata.yaml b/Examples/cs/cshuffman/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/cs/cshuffman/metadata.yaml rename to Examples/cs/cshuffman/metadata.yaml index 0cc6809..3106e7c 100644 --- a/Contributed/BNGPlayground_Examples/cs/cshuffman/metadata.yaml +++ b/Examples/cs/cshuffman/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/cs_huffman.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["cs","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/cs/csmontecarlopi/README.md b/Examples/cs/csmontecarlopi/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csmontecarlopi/README.md rename to Examples/cs/csmontecarlopi/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl b/Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl rename to Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl diff --git a/Contributed/BNGPlayground_Examples/cs/csmontecarlopi/metadata.yaml b/Examples/cs/csmontecarlopi/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/cs/csmontecarlopi/metadata.yaml rename to Examples/cs/csmontecarlopi/metadata.yaml index 440f429..058023f 100644 --- a/Contributed/BNGPlayground_Examples/cs/csmontecarlopi/metadata.yaml +++ b/Examples/cs/csmontecarlopi/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/cs_monte_carlo_pi.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["cs","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/cs/cspagerank/README.md b/Examples/cs/cspagerank/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cspagerank/README.md rename to Examples/cs/cspagerank/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/cspagerank/cs_pagerank.bngl b/Examples/cs/cspagerank/cs_pagerank.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cspagerank/cs_pagerank.bngl rename to Examples/cs/cspagerank/cs_pagerank.bngl diff --git a/Contributed/BNGPlayground_Examples/cs/cspagerank/metadata.yaml b/Examples/cs/cspagerank/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/cs/cspagerank/metadata.yaml rename to Examples/cs/cspagerank/metadata.yaml index 0b61b62..74cb2bd 100644 --- a/Contributed/BNGPlayground_Examples/cs/cspagerank/metadata.yaml +++ b/Examples/cs/cspagerank/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/cs_pagerank.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["cs","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/cs/cspidcontroller/README.md b/Examples/cs/cspidcontroller/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/cspidcontroller/README.md rename to Examples/cs/cspidcontroller/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/cspidcontroller/cs_pid_controller.bngl b/Examples/cs/cspidcontroller/cs_pid_controller.bngl similarity index 96% rename from Contributed/BNGPlayground_Examples/cs/cspidcontroller/cs_pid_controller.bngl rename to Examples/cs/cspidcontroller/cs_pid_controller.bngl index 23847ab..3890693 100644 --- a/Contributed/BNGPlayground_Examples/cs/cspidcontroller/cs_pid_controller.bngl +++ b/Examples/cs/cspidcontroller/cs_pid_controller.bngl @@ -78,8 +78,7 @@ begin functions P_term() + I_term() + D_term(),0) # Disturbance function (step at t=disturb_time) - # Hack: use a very steep sigmoid to approximate step function - Disturb_rate() = disturb_mag / (1 + exp(-10*(t - disturb_time))) + Disturb_rate() = if(t > disturb_time, disturb_mag, 0) end functions begin reaction rules diff --git a/Contributed/BNGPlayground_Examples/cs/cspidcontroller/metadata.yaml b/Examples/cs/cspidcontroller/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/cs/cspidcontroller/metadata.yaml rename to Examples/cs/cspidcontroller/metadata.yaml index 6fd3d3e..047171b 100644 --- a/Contributed/BNGPlayground_Examples/cs/cspidcontroller/metadata.yaml +++ b/Examples/cs/cspidcontroller/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/cs_pid_controller.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["cs","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/cs/csregexnfa/README.md b/Examples/cs/csregexnfa/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csregexnfa/README.md rename to Examples/cs/csregexnfa/README.md diff --git a/Contributed/BNGPlayground_Examples/cs/csregexnfa/cs_regex_nfa.bngl b/Examples/cs/csregexnfa/cs_regex_nfa.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/cs/csregexnfa/cs_regex_nfa.bngl rename to Examples/cs/csregexnfa/cs_regex_nfa.bngl diff --git a/Contributed/BNGPlayground_Examples/cs/csregexnfa/metadata.yaml b/Examples/cs/csregexnfa/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/cs/csregexnfa/metadata.yaml rename to Examples/cs/csregexnfa/metadata.yaml index 03a6ce6..6e59131 100644 --- a/Contributed/BNGPlayground_Examples/cs/csregexnfa/metadata.yaml +++ b/Examples/cs/csregexnfa/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/cs_regex_nfa.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["cs","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/README.md b/Examples/ecology/ecocoevolutionhostparasite/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/README.md rename to Examples/ecology/ecocoevolutionhostparasite/README.md diff --git a/Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl b/Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl rename to Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl diff --git a/Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/metadata.yaml b/Examples/ecology/ecocoevolutionhostparasite/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/metadata.yaml rename to Examples/ecology/ecocoevolutionhostparasite/metadata.yaml index eed8aab..57a5f19 100644 --- a/Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/metadata.yaml +++ b/Examples/ecology/ecocoevolutionhostparasite/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/eco_coevolution_host_parasite.bngl" playground: visible: false - gallery_category: "ecology" + gallery_categories: ["ecology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/README.md b/Examples/ecology/ecofoodwebchaos3sp/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/README.md rename to Examples/ecology/ecofoodwebchaos3sp/README.md diff --git a/Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl b/Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl similarity index 96% rename from Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl rename to Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl index 3f63d01..acd4c93 100644 --- a/Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl +++ b/Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl @@ -65,7 +65,7 @@ begin reaction rules # 4. Death C() -> 0 d1 P() -> 0 d2 - # FIX: Add resource dynamics (total R was conserved) + 0 -> R() 1.0 # Resource regeneration R() -> 0 0.01 # Resource natural decay end reaction rules diff --git a/Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/metadata.yaml b/Examples/ecology/ecofoodwebchaos3sp/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/metadata.yaml rename to Examples/ecology/ecofoodwebchaos3sp/metadata.yaml index 8d60941..07b284a 100644 --- a/Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/metadata.yaml +++ b/Examples/ecology/ecofoodwebchaos3sp/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/eco_food_web_chaos_3sp.bngl" playground: visible: false - gallery_category: "ecology" + gallery_categories: ["ecology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/README.md b/Examples/ecology/ecolotkavolterragrid/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/README.md rename to Examples/ecology/ecolotkavolterragrid/README.md diff --git a/Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl b/Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl rename to Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl diff --git a/Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/metadata.yaml b/Examples/ecology/ecolotkavolterragrid/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/metadata.yaml rename to Examples/ecology/ecolotkavolterragrid/metadata.yaml index 8a19c1b..ef56b02 100644 --- a/Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/metadata.yaml +++ b/Examples/ecology/ecolotkavolterragrid/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/eco_lotka_volterra_grid.bngl" playground: visible: false - gallery_category: "ecology" + gallery_categories: ["ecology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/README.md b/Examples/ecology/ecomutualismobligate/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/README.md rename to Examples/ecology/ecomutualismobligate/README.md diff --git a/Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl b/Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl rename to Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl diff --git a/Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/metadata.yaml b/Examples/ecology/ecomutualismobligate/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/metadata.yaml rename to Examples/ecology/ecomutualismobligate/metadata.yaml index 8f83f55..3292a50 100644 --- a/Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/metadata.yaml +++ b/Examples/ecology/ecomutualismobligate/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/eco_mutualism_obligate.bngl" playground: visible: false - gallery_category: "ecology" + gallery_categories: ["ecology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/README.md b/Examples/ecology/ecorockpaperscissorsspatial/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/README.md rename to Examples/ecology/ecorockpaperscissorsspatial/README.md diff --git a/Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl b/Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl rename to Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl diff --git a/Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml b/Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml rename to Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml index 81509c0..7b776ba 100644 --- a/Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml +++ b/Examples/ecology/ecorockpaperscissorsspatial/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/eco_rock_paper_scissors_spatial.bngl" playground: visible: false - gallery_category: "ecology" + gallery_categories: ["ecology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/energy/energyallosterymwc/README.md b/Examples/energy/energyallosterymwc/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energyallosterymwc/README.md rename to Examples/energy/energyallosterymwc/README.md diff --git a/Contributed/BNGPlayground_Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl b/Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl rename to Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl diff --git a/Contributed/BNGPlayground_Examples/energy/energyallosterymwc/metadata.yaml b/Examples/energy/energyallosterymwc/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/energy/energyallosterymwc/metadata.yaml rename to Examples/energy/energyallosterymwc/metadata.yaml index e170882..212fd97 100644 --- a/Contributed/BNGPlayground_Examples/energy/energyallosterymwc/metadata.yaml +++ b/Examples/energy/energyallosterymwc/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/energy_allostery_mwc.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/energy/energycatalysismm/README.md b/Examples/energy/energycatalysismm/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energycatalysismm/README.md rename to Examples/energy/energycatalysismm/README.md diff --git a/Contributed/BNGPlayground_Examples/energy/energycatalysismm/energy_catalysis_mm.bngl b/Examples/energy/energycatalysismm/energy_catalysis_mm.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energycatalysismm/energy_catalysis_mm.bngl rename to Examples/energy/energycatalysismm/energy_catalysis_mm.bngl diff --git a/Contributed/BNGPlayground_Examples/energy/energycatalysismm/metadata.yaml b/Examples/energy/energycatalysismm/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/energy/energycatalysismm/metadata.yaml rename to Examples/energy/energycatalysismm/metadata.yaml index 53030a5..d0943cb 100644 --- a/Contributed/BNGPlayground_Examples/energy/energycatalysismm/metadata.yaml +++ b/Examples/energy/energycatalysismm/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/energy_catalysis_mm.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/energy/energycooperativityadh/README.md b/Examples/energy/energycooperativityadh/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energycooperativityadh/README.md rename to Examples/energy/energycooperativityadh/README.md diff --git a/Contributed/BNGPlayground_Examples/energy/energycooperativityadh/energy_cooperativity_adh.bngl b/Examples/energy/energycooperativityadh/energy_cooperativity_adh.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energycooperativityadh/energy_cooperativity_adh.bngl rename to Examples/energy/energycooperativityadh/energy_cooperativity_adh.bngl diff --git a/Contributed/BNGPlayground_Examples/energy/energycooperativityadh/metadata.yaml b/Examples/energy/energycooperativityadh/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/energy/energycooperativityadh/metadata.yaml rename to Examples/energy/energycooperativityadh/metadata.yaml index c048440..2bfa8da 100644 --- a/Contributed/BNGPlayground_Examples/energy/energycooperativityadh/metadata.yaml +++ b/Examples/energy/energycooperativityadh/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/energy_cooperativity_adh.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/energy/energylinearchain/README.md b/Examples/energy/energylinearchain/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energylinearchain/README.md rename to Examples/energy/energylinearchain/README.md diff --git a/Contributed/BNGPlayground_Examples/energy/energylinearchain/energy_linear_chain.bngl b/Examples/energy/energylinearchain/energy_linear_chain.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energylinearchain/energy_linear_chain.bngl rename to Examples/energy/energylinearchain/energy_linear_chain.bngl diff --git a/Contributed/BNGPlayground_Examples/energy/energylinearchain/metadata.yaml b/Examples/energy/energylinearchain/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/energy/energylinearchain/metadata.yaml rename to Examples/energy/energylinearchain/metadata.yaml index e5a4004..5b11762 100644 --- a/Contributed/BNGPlayground_Examples/energy/energylinearchain/metadata.yaml +++ b/Examples/energy/energylinearchain/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/energy_linear_chain.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/energy/energytransportpump/README.md b/Examples/energy/energytransportpump/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energytransportpump/README.md rename to Examples/energy/energytransportpump/README.md diff --git a/Contributed/BNGPlayground_Examples/energy/energytransportpump/energy_transport_pump.bngl b/Examples/energy/energytransportpump/energy_transport_pump.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/energy/energytransportpump/energy_transport_pump.bngl rename to Examples/energy/energytransportpump/energy_transport_pump.bngl diff --git a/Contributed/BNGPlayground_Examples/energy/energytransportpump/metadata.yaml b/Examples/energy/energytransportpump/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/energy/energytransportpump/metadata.yaml rename to Examples/energy/energytransportpump/metadata.yaml index 8b05e06..3c53ea6 100644 --- a/Contributed/BNGPlayground_Examples/energy/energytransportpump/metadata.yaml +++ b/Examples/energy/energytransportpump/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/energy_transport_pump.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featurefunctionalratesvolume/README.md b/Examples/feature-demos/featurefunctionalratesvolume/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/feature-demos/featurefunctionalratesvolume/README.md rename to Examples/feature-demos/featurefunctionalratesvolume/README.md diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume.bngl b/Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume.bngl rename to Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume.bngl diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featurefunctionalratesvolume/metadata.yaml b/Examples/feature-demos/featurefunctionalratesvolume/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/feature-demos/featurefunctionalratesvolume/metadata.yaml rename to Examples/feature-demos/featurefunctionalratesvolume/metadata.yaml index d630f1e..ebaa1c3 100644 --- a/Contributed/BNGPlayground_Examples/feature-demos/featurefunctionalratesvolume/metadata.yaml +++ b/Examples/feature-demos/featurefunctionalratesvolume/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/feature_functional_rates_volume.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/README.md b/Examples/feature-demos/featureglobalfunctionsscan/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/README.md rename to Examples/feature-demos/featureglobalfunctionsscan/README.md diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl b/Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl rename to Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/metadata.yaml b/Examples/feature-demos/featureglobalfunctionsscan/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/metadata.yaml rename to Examples/feature-demos/featureglobalfunctionsscan/metadata.yaml index 9a201e3..df436d6 100644 --- a/Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/metadata.yaml +++ b/Examples/feature-demos/featureglobalfunctionsscan/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/feature_global_functions_scan.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featurelocalfunctionsexplicit/README.md b/Examples/feature-demos/featurelocalfunctionsexplicit/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/feature-demos/featurelocalfunctionsexplicit/README.md rename to Examples/feature-demos/featurelocalfunctionsexplicit/README.md diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit.bngl b/Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit.bngl rename to Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit.bngl diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featurelocalfunctionsexplicit/metadata.yaml b/Examples/feature-demos/featurelocalfunctionsexplicit/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/feature-demos/featurelocalfunctionsexplicit/metadata.yaml rename to Examples/feature-demos/featurelocalfunctionsexplicit/metadata.yaml index 5b42497..2934ef9 100644 --- a/Contributed/BNGPlayground_Examples/feature-demos/featurelocalfunctionsexplicit/metadata.yaml +++ b/Examples/feature-demos/featurelocalfunctionsexplicit/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/feature_local_functions_explicit.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featuresymmetryfactorscyclic/README.md b/Examples/feature-demos/featuresymmetryfactorscyclic/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/feature-demos/featuresymmetryfactorscyclic/README.md rename to Examples/feature-demos/featuresymmetryfactorscyclic/README.md diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic.bngl b/Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic.bngl rename to Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic.bngl diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featuresymmetryfactorscyclic/metadata.yaml b/Examples/feature-demos/featuresymmetryfactorscyclic/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/feature-demos/featuresymmetryfactorscyclic/metadata.yaml rename to Examples/feature-demos/featuresymmetryfactorscyclic/metadata.yaml index 8529da6..faa877f 100644 --- a/Contributed/BNGPlayground_Examples/feature-demos/featuresymmetryfactorscyclic/metadata.yaml +++ b/Examples/feature-demos/featuresymmetryfactorscyclic/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/feature_symmetry_factors_cyclic.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featuresynthesisdegradationss/README.md b/Examples/feature-demos/featuresynthesisdegradationss/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/feature-demos/featuresynthesisdegradationss/README.md rename to Examples/feature-demos/featuresynthesisdegradationss/README.md diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss.bngl b/Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss.bngl rename to Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss.bngl diff --git a/Contributed/BNGPlayground_Examples/feature-demos/featuresynthesisdegradationss/metadata.yaml b/Examples/feature-demos/featuresynthesisdegradationss/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/feature-demos/featuresynthesisdegradationss/metadata.yaml rename to Examples/feature-demos/featuresynthesisdegradationss/metadata.yaml index b0d4dbc..3486e42 100644 --- a/Contributed/BNGPlayground_Examples/feature-demos/featuresynthesisdegradationss/metadata.yaml +++ b/Examples/feature-demos/featuresynthesisdegradationss/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/feature_synthesis_degradation_ss.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/generative/gmgameoflife/README.md b/Examples/generative/gmgameoflife/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/generative/gmgameoflife/README.md rename to Examples/generative/gmgameoflife/README.md diff --git a/Contributed/BNGPlayground_Examples/generative/gmgameoflife/gm_game_of_life.bngl b/Examples/generative/gmgameoflife/gm_game_of_life.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/generative/gmgameoflife/gm_game_of_life.bngl rename to Examples/generative/gmgameoflife/gm_game_of_life.bngl diff --git a/Contributed/BNGPlayground_Examples/generative/gmgameoflife/metadata.yaml b/Examples/generative/gmgameoflife/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/generative/gmgameoflife/metadata.yaml rename to Examples/generative/gmgameoflife/metadata.yaml index 94064f4..0da07cb 100644 --- a/Contributed/BNGPlayground_Examples/generative/gmgameoflife/metadata.yaml +++ b/Examples/generative/gmgameoflife/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/gm_game_of_life.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/generative/gmraymarcher/README.md b/Examples/generative/gmraymarcher/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/generative/gmraymarcher/README.md rename to Examples/generative/gmraymarcher/README.md diff --git a/Contributed/BNGPlayground_Examples/generative/gmraymarcher/gm_ray_marcher.bngl b/Examples/generative/gmraymarcher/gm_ray_marcher.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/generative/gmraymarcher/gm_ray_marcher.bngl rename to Examples/generative/gmraymarcher/gm_ray_marcher.bngl diff --git a/Contributed/BNGPlayground_Examples/generative/gmraymarcher/metadata.yaml b/Examples/generative/gmraymarcher/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/generative/gmraymarcher/metadata.yaml rename to Examples/generative/gmraymarcher/metadata.yaml index 58ecd62..587cf10 100644 --- a/Contributed/BNGPlayground_Examples/generative/gmraymarcher/metadata.yaml +++ b/Examples/generative/gmraymarcher/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/gm_ray_marcher.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/genetics/geneticbistabilityenergy/README.md b/Examples/genetics/geneticbistabilityenergy/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/genetics/geneticbistabilityenergy/README.md rename to Examples/genetics/geneticbistabilityenergy/README.md diff --git a/Contributed/BNGPlayground_Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy.bngl b/Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy.bngl rename to Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy.bngl diff --git a/Contributed/BNGPlayground_Examples/genetics/geneticbistabilityenergy/metadata.yaml b/Examples/genetics/geneticbistabilityenergy/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/genetics/geneticbistabilityenergy/metadata.yaml rename to Examples/genetics/geneticbistabilityenergy/metadata.yaml index 9e2f6ef..12a84d8 100644 --- a/Contributed/BNGPlayground_Examples/genetics/geneticbistabilityenergy/metadata.yaml +++ b/Examples/genetics/geneticbistabilityenergy/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/genetic_bistability_energy.bngl" playground: visible: false - gallery_category: "gene-expression" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/genetics/geneticdnareplicationstochastic/README.md b/Examples/genetics/geneticdnareplicationstochastic/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/genetics/geneticdnareplicationstochastic/README.md rename to Examples/genetics/geneticdnareplicationstochastic/README.md diff --git a/Contributed/BNGPlayground_Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic.bngl b/Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic.bngl rename to Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic.bngl diff --git a/Contributed/BNGPlayground_Examples/genetics/geneticdnareplicationstochastic/metadata.yaml b/Examples/genetics/geneticdnareplicationstochastic/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/genetics/geneticdnareplicationstochastic/metadata.yaml rename to Examples/genetics/geneticdnareplicationstochastic/metadata.yaml index 777f0b8..e6d059d 100644 --- a/Contributed/BNGPlayground_Examples/genetics/geneticdnareplicationstochastic/metadata.yaml +++ b/Examples/genetics/geneticdnareplicationstochastic/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/genetic_dna_replication_stochastic.bngl" playground: visible: false - gallery_category: "gene-expression" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/genetics/geneticgoodwinoscillator/README.md b/Examples/genetics/geneticgoodwinoscillator/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/genetics/geneticgoodwinoscillator/README.md rename to Examples/genetics/geneticgoodwinoscillator/README.md diff --git a/Contributed/BNGPlayground_Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator.bngl b/Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator.bngl rename to Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator.bngl diff --git a/Contributed/BNGPlayground_Examples/genetics/geneticgoodwinoscillator/metadata.yaml b/Examples/genetics/geneticgoodwinoscillator/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/genetics/geneticgoodwinoscillator/metadata.yaml rename to Examples/genetics/geneticgoodwinoscillator/metadata.yaml index 394492c..cf8138a 100644 --- a/Contributed/BNGPlayground_Examples/genetics/geneticgoodwinoscillator/metadata.yaml +++ b/Examples/genetics/geneticgoodwinoscillator/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/genetic_goodwin_oscillator.bngl" playground: visible: false - gallery_category: "gene-expression" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/genetics/genetictranslationkinetics/README.md b/Examples/genetics/genetictranslationkinetics/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/genetics/genetictranslationkinetics/README.md rename to Examples/genetics/genetictranslationkinetics/README.md diff --git a/Contributed/BNGPlayground_Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics.bngl b/Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics.bngl rename to Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics.bngl diff --git a/Contributed/BNGPlayground_Examples/genetics/genetictranslationkinetics/metadata.yaml b/Examples/genetics/genetictranslationkinetics/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/genetics/genetictranslationkinetics/metadata.yaml rename to Examples/genetics/genetictranslationkinetics/metadata.yaml index aaa7ad2..1500670 100644 --- a/Contributed/BNGPlayground_Examples/genetics/genetictranslationkinetics/metadata.yaml +++ b/Examples/genetics/genetictranslationkinetics/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/genetic_translation_kinetics.bngl" playground: visible: false - gallery_category: "gene-expression" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/genetics/geneticturingpattern1d/README.md b/Examples/genetics/geneticturingpattern1d/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/genetics/geneticturingpattern1d/README.md rename to Examples/genetics/geneticturingpattern1d/README.md diff --git a/Contributed/BNGPlayground_Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d.bngl b/Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d.bngl rename to Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d.bngl diff --git a/Contributed/BNGPlayground_Examples/genetics/geneticturingpattern1d/metadata.yaml b/Examples/genetics/geneticturingpattern1d/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/genetics/geneticturingpattern1d/metadata.yaml rename to Examples/genetics/geneticturingpattern1d/metadata.yaml index e9f771d..154c59e 100644 --- a/Contributed/BNGPlayground_Examples/genetics/geneticturingpattern1d/metadata.yaml +++ b/Examples/genetics/geneticturingpattern1d/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/genetic_turing_pattern_1d.bngl" playground: visible: false - gallery_category: "gene-expression" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/meta/metaformalgametheory/README.md b/Examples/meta/metaformalgametheory/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/metaformalgametheory/README.md rename to Examples/meta/metaformalgametheory/README.md diff --git a/Contributed/BNGPlayground_Examples/meta/metaformalgametheory/meta_formal_game_theory.bngl b/Examples/meta/metaformalgametheory/meta_formal_game_theory.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/metaformalgametheory/meta_formal_game_theory.bngl rename to Examples/meta/metaformalgametheory/meta_formal_game_theory.bngl diff --git a/Contributed/BNGPlayground_Examples/meta/metaformalgametheory/metadata.yaml b/Examples/meta/metaformalgametheory/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/meta/metaformalgametheory/metadata.yaml rename to Examples/meta/metaformalgametheory/metadata.yaml index 3b6cac7..f720a4f 100644 --- a/Contributed/BNGPlayground_Examples/meta/metaformalgametheory/metadata.yaml +++ b/Examples/meta/metaformalgametheory/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/meta_formal_game_theory.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/meta/metaformalmolecularclock/README.md b/Examples/meta/metaformalmolecularclock/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/metaformalmolecularclock/README.md rename to Examples/meta/metaformalmolecularclock/README.md diff --git a/Contributed/BNGPlayground_Examples/meta/metaformalmolecularclock/meta_formal_molecular_clock.bngl b/Examples/meta/metaformalmolecularclock/meta_formal_molecular_clock.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/metaformalmolecularclock/meta_formal_molecular_clock.bngl rename to Examples/meta/metaformalmolecularclock/meta_formal_molecular_clock.bngl diff --git a/Contributed/BNGPlayground_Examples/meta/metaformalmolecularclock/metadata.yaml b/Examples/meta/metaformalmolecularclock/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/meta/metaformalmolecularclock/metadata.yaml rename to Examples/meta/metaformalmolecularclock/metadata.yaml index f19aa00..9e4b92f 100644 --- a/Contributed/BNGPlayground_Examples/meta/metaformalmolecularclock/metadata.yaml +++ b/Examples/meta/metaformalmolecularclock/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/meta_formal_molecular_clock.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/meta/metaformalpetrinet/README.md b/Examples/meta/metaformalpetrinet/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/metaformalpetrinet/README.md rename to Examples/meta/metaformalpetrinet/README.md diff --git a/Contributed/BNGPlayground_Examples/meta/metaformalpetrinet/meta_formal_petri_net.bngl b/Examples/meta/metaformalpetrinet/meta_formal_petri_net.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/metaformalpetrinet/meta_formal_petri_net.bngl rename to Examples/meta/metaformalpetrinet/meta_formal_petri_net.bngl diff --git a/Contributed/BNGPlayground_Examples/meta/metaformalpetrinet/metadata.yaml b/Examples/meta/metaformalpetrinet/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/meta/metaformalpetrinet/metadata.yaml rename to Examples/meta/metaformalpetrinet/metadata.yaml index 32789b1..64be782 100644 --- a/Contributed/BNGPlayground_Examples/meta/metaformalpetrinet/metadata.yaml +++ b/Examples/meta/metaformalpetrinet/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/meta_formal_petri_net.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/meta/mtarithmeticcompiler/README.md b/Examples/meta/mtarithmeticcompiler/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/mtarithmeticcompiler/README.md rename to Examples/meta/mtarithmeticcompiler/README.md diff --git a/Contributed/BNGPlayground_Examples/meta/mtarithmeticcompiler/metadata.yaml b/Examples/meta/mtarithmeticcompiler/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/meta/mtarithmeticcompiler/metadata.yaml rename to Examples/meta/mtarithmeticcompiler/metadata.yaml index e766c43..fcaa99b 100644 --- a/Contributed/BNGPlayground_Examples/meta/mtarithmeticcompiler/metadata.yaml +++ b/Examples/meta/mtarithmeticcompiler/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/mt_arithmetic_compiler.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["cs","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/meta/mtarithmeticcompiler/mt_arithmetic_compiler.bngl b/Examples/meta/mtarithmeticcompiler/mt_arithmetic_compiler.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/mtarithmeticcompiler/mt_arithmetic_compiler.bngl rename to Examples/meta/mtarithmeticcompiler/mt_arithmetic_compiler.bngl diff --git a/Contributed/BNGPlayground_Examples/meta/mtbnglinterpreter/README.md b/Examples/meta/mtbnglinterpreter/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/mtbnglinterpreter/README.md rename to Examples/meta/mtbnglinterpreter/README.md diff --git a/Contributed/BNGPlayground_Examples/meta/mtbnglinterpreter/metadata.yaml b/Examples/meta/mtbnglinterpreter/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/meta/mtbnglinterpreter/metadata.yaml rename to Examples/meta/mtbnglinterpreter/metadata.yaml index 0e53107..a1805c1 100644 --- a/Contributed/BNGPlayground_Examples/meta/mtbnglinterpreter/metadata.yaml +++ b/Examples/meta/mtbnglinterpreter/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/mt_bngl_interpreter.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["cs","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/meta/mtbnglinterpreter/mt_bngl_interpreter.bngl b/Examples/meta/mtbnglinterpreter/mt_bngl_interpreter.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/mtbnglinterpreter/mt_bngl_interpreter.bngl rename to Examples/meta/mtbnglinterpreter/mt_bngl_interpreter.bngl diff --git a/Contributed/BNGPlayground_Examples/meta/mtmusicsequencer/README.md b/Examples/meta/mtmusicsequencer/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/mtmusicsequencer/README.md rename to Examples/meta/mtmusicsequencer/README.md diff --git a/Contributed/BNGPlayground_Examples/meta/mtmusicsequencer/metadata.yaml b/Examples/meta/mtmusicsequencer/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/meta/mtmusicsequencer/metadata.yaml rename to Examples/meta/mtmusicsequencer/metadata.yaml index ea4027e..54c8349 100644 --- a/Contributed/BNGPlayground_Examples/meta/mtmusicsequencer/metadata.yaml +++ b/Examples/meta/mtmusicsequencer/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/mt_music_sequencer.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["cs","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/meta/mtmusicsequencer/mt_music_sequencer.bngl b/Examples/meta/mtmusicsequencer/mt_music_sequencer.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/mtmusicsequencer/mt_music_sequencer.bngl rename to Examples/meta/mtmusicsequencer/mt_music_sequencer.bngl diff --git a/Contributed/BNGPlayground_Examples/meta/mtpascaltriangle/README.md b/Examples/meta/mtpascaltriangle/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/mtpascaltriangle/README.md rename to Examples/meta/mtpascaltriangle/README.md diff --git a/Contributed/BNGPlayground_Examples/meta/mtpascaltriangle/metadata.yaml b/Examples/meta/mtpascaltriangle/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/meta/mtpascaltriangle/metadata.yaml rename to Examples/meta/mtpascaltriangle/metadata.yaml index 9d3a552..b9ecb73 100644 --- a/Contributed/BNGPlayground_Examples/meta/mtpascaltriangle/metadata.yaml +++ b/Examples/meta/mtpascaltriangle/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/mt_pascal_triangle.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["cs","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/meta/mtpascaltriangle/mt_pascal_triangle.bngl b/Examples/meta/mtpascaltriangle/mt_pascal_triangle.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/mtpascaltriangle/mt_pascal_triangle.bngl rename to Examples/meta/mtpascaltriangle/mt_pascal_triangle.bngl diff --git a/Contributed/BNGPlayground_Examples/meta/mtquine/README.md b/Examples/meta/mtquine/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/mtquine/README.md rename to Examples/meta/mtquine/README.md diff --git a/Contributed/BNGPlayground_Examples/meta/mtquine/metadata.yaml b/Examples/meta/mtquine/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/meta/mtquine/metadata.yaml rename to Examples/meta/mtquine/metadata.yaml index cc884f2..a86b67e 100644 --- a/Contributed/BNGPlayground_Examples/meta/mtquine/metadata.yaml +++ b/Examples/meta/mtquine/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/mt_quine.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["cs","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/meta/mtquine/mt_quine.bngl b/Examples/meta/mtquine/mt_quine.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/meta/mtquine/mt_quine.bngl rename to Examples/meta/mtquine/mt_quine.bngl diff --git a/Contributed/BNGPlayground_Examples/ml/mlgradientdescent/README.md b/Examples/ml/mlgradientdescent/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ml/mlgradientdescent/README.md rename to Examples/ml/mlgradientdescent/README.md diff --git a/Contributed/BNGPlayground_Examples/ml/mlgradientdescent/metadata.yaml b/Examples/ml/mlgradientdescent/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/ml/mlgradientdescent/metadata.yaml rename to Examples/ml/mlgradientdescent/metadata.yaml index ce7fc81..a049865 100644 --- a/Contributed/BNGPlayground_Examples/ml/mlgradientdescent/metadata.yaml +++ b/Examples/ml/mlgradientdescent/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/ml_gradient_descent.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["ml-signal","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/ml/mlgradientdescent/ml_gradient_descent.bngl b/Examples/ml/mlgradientdescent/ml_gradient_descent.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ml/mlgradientdescent/ml_gradient_descent.bngl rename to Examples/ml/mlgradientdescent/ml_gradient_descent.bngl diff --git a/Contributed/BNGPlayground_Examples/ml/mlhopfield/README.md b/Examples/ml/mlhopfield/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ml/mlhopfield/README.md rename to Examples/ml/mlhopfield/README.md diff --git a/Contributed/BNGPlayground_Examples/ml/mlhopfield/metadata.yaml b/Examples/ml/mlhopfield/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/ml/mlhopfield/metadata.yaml rename to Examples/ml/mlhopfield/metadata.yaml index df198c1..d9f8756 100644 --- a/Contributed/BNGPlayground_Examples/ml/mlhopfield/metadata.yaml +++ b/Examples/ml/mlhopfield/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/ml_hopfield.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["ml-signal","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/ml/mlhopfield/ml_hopfield.bngl b/Examples/ml/mlhopfield/ml_hopfield.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ml/mlhopfield/ml_hopfield.bngl rename to Examples/ml/mlhopfield/ml_hopfield.bngl diff --git a/Contributed/BNGPlayground_Examples/ml/mlkmeans/README.md b/Examples/ml/mlkmeans/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ml/mlkmeans/README.md rename to Examples/ml/mlkmeans/README.md diff --git a/Contributed/BNGPlayground_Examples/ml/mlkmeans/metadata.yaml b/Examples/ml/mlkmeans/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/ml/mlkmeans/metadata.yaml rename to Examples/ml/mlkmeans/metadata.yaml index fe9f825..1bf04e3 100644 --- a/Contributed/BNGPlayground_Examples/ml/mlkmeans/metadata.yaml +++ b/Examples/ml/mlkmeans/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/ml_kmeans.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["ml-signal","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/ml/mlkmeans/ml_kmeans.bngl b/Examples/ml/mlkmeans/ml_kmeans.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ml/mlkmeans/ml_kmeans.bngl rename to Examples/ml/mlkmeans/ml_kmeans.bngl diff --git a/Contributed/BNGPlayground_Examples/ml/mlqlearning/README.md b/Examples/ml/mlqlearning/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ml/mlqlearning/README.md rename to Examples/ml/mlqlearning/README.md diff --git a/Contributed/BNGPlayground_Examples/ml/mlqlearning/metadata.yaml b/Examples/ml/mlqlearning/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/ml/mlqlearning/metadata.yaml rename to Examples/ml/mlqlearning/metadata.yaml index 2a5ee7a..41d1842 100644 --- a/Contributed/BNGPlayground_Examples/ml/mlqlearning/metadata.yaml +++ b/Examples/ml/mlqlearning/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/ml_q_learning.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["ml-signal","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/ml/mlqlearning/ml_q_learning.bngl b/Examples/ml/mlqlearning/ml_q_learning.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ml/mlqlearning/ml_q_learning.bngl rename to Examples/ml/mlqlearning/ml_q_learning.bngl diff --git a/Contributed/BNGPlayground_Examples/ml/mlsvm/README.md b/Examples/ml/mlsvm/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ml/mlsvm/README.md rename to Examples/ml/mlsvm/README.md diff --git a/Contributed/BNGPlayground_Examples/ml/mlsvm/metadata.yaml b/Examples/ml/mlsvm/metadata.yaml similarity index 91% rename from Contributed/BNGPlayground_Examples/ml/mlsvm/metadata.yaml rename to Examples/ml/mlsvm/metadata.yaml index bfa5572..fbef119 100644 --- a/Contributed/BNGPlayground_Examples/ml/mlsvm/metadata.yaml +++ b/Examples/ml/mlsvm/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/ml_svm.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["ml-signal","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/ml/mlsvm/ml_svm.bngl b/Examples/ml/mlsvm/ml_svm.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ml/mlsvm/ml_svm.bngl rename to Examples/ml/mlsvm/ml_svm.bngl diff --git a/Contributed/BNGPlayground_Examples/ml/nnxor/README.md b/Examples/ml/nnxor/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/ml/nnxor/README.md rename to Examples/ml/nnxor/README.md diff --git a/Contributed/BNGPlayground_Examples/ml/nnxor/metadata.yaml b/Examples/ml/nnxor/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/ml/nnxor/metadata.yaml rename to Examples/ml/nnxor/metadata.yaml index 6ca5605..d24d9c3 100644 --- a/Contributed/BNGPlayground_Examples/ml/nnxor/metadata.yaml +++ b/Examples/ml/nnxor/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/nn_xor.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["ml-signal","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/ml/nnxor/nn_xor.bngl b/Examples/ml/nnxor/nn_xor.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/ml/nnxor/nn_xor.bngl rename to Examples/ml/nnxor/nn_xor.bngl diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimaggregationgelation/README.md b/Examples/nfsim/nfsimaggregationgelation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimaggregationgelation/README.md rename to Examples/nfsim/nfsimaggregationgelation/README.md diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimaggregationgelation/metadata.yaml b/Examples/nfsim/nfsimaggregationgelation/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimaggregationgelation/metadata.yaml rename to Examples/nfsim/nfsimaggregationgelation/metadata.yaml index 2940c5c..869f8fd 100644 --- a/Contributed/BNGPlayground_Examples/nfsim/nfsimaggregationgelation/metadata.yaml +++ b/Examples/nfsim/nfsimaggregationgelation/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/nfsim_aggregation_gelation.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimaggregationgelation/nfsim_aggregation_gelation.bngl b/Examples/nfsim/nfsimaggregationgelation/nfsim_aggregation_gelation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimaggregationgelation/nfsim_aggregation_gelation.bngl rename to Examples/nfsim/nfsimaggregationgelation/nfsim_aggregation_gelation.bngl diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimcoarsegraining/README.md b/Examples/nfsim/nfsimcoarsegraining/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimcoarsegraining/README.md rename to Examples/nfsim/nfsimcoarsegraining/README.md diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimcoarsegraining/metadata.yaml b/Examples/nfsim/nfsimcoarsegraining/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimcoarsegraining/metadata.yaml rename to Examples/nfsim/nfsimcoarsegraining/metadata.yaml index 79ced8c..f3f98eb 100644 --- a/Contributed/BNGPlayground_Examples/nfsim/nfsimcoarsegraining/metadata.yaml +++ b/Examples/nfsim/nfsimcoarsegraining/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/nfsim_coarse_graining.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimcoarsegraining/nfsim_coarse_graining.bngl b/Examples/nfsim/nfsimcoarsegraining/nfsim_coarse_graining.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimcoarsegraining/nfsim_coarse_graining.bngl rename to Examples/nfsim/nfsimcoarsegraining/nfsim_coarse_graining.bngl diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimdynamiccompartments/README.md b/Examples/nfsim/nfsimdynamiccompartments/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimdynamiccompartments/README.md rename to Examples/nfsim/nfsimdynamiccompartments/README.md diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimdynamiccompartments/metadata.yaml b/Examples/nfsim/nfsimdynamiccompartments/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimdynamiccompartments/metadata.yaml rename to Examples/nfsim/nfsimdynamiccompartments/metadata.yaml index 617d5f9..5927280 100644 --- a/Contributed/BNGPlayground_Examples/nfsim/nfsimdynamiccompartments/metadata.yaml +++ b/Examples/nfsim/nfsimdynamiccompartments/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/nfsim_dynamic_compartments.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimdynamiccompartments/nfsim_dynamic_compartments.bngl b/Examples/nfsim/nfsimdynamiccompartments/nfsim_dynamic_compartments.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimdynamiccompartments/nfsim_dynamic_compartments.bngl rename to Examples/nfsim/nfsimdynamiccompartments/nfsim_dynamic_compartments.bngl diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimhybridparticlefield/README.md b/Examples/nfsim/nfsimhybridparticlefield/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimhybridparticlefield/README.md rename to Examples/nfsim/nfsimhybridparticlefield/README.md diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimhybridparticlefield/metadata.yaml b/Examples/nfsim/nfsimhybridparticlefield/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimhybridparticlefield/metadata.yaml rename to Examples/nfsim/nfsimhybridparticlefield/metadata.yaml index 93c8fa0..8ea02e9 100644 --- a/Contributed/BNGPlayground_Examples/nfsim/nfsimhybridparticlefield/metadata.yaml +++ b/Examples/nfsim/nfsimhybridparticlefield/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/nfsim_hybrid_particle_field.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimhybridparticlefield/nfsim_hybrid_particle_field.bngl b/Examples/nfsim/nfsimhybridparticlefield/nfsim_hybrid_particle_field.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimhybridparticlefield/nfsim_hybrid_particle_field.bngl rename to Examples/nfsim/nfsimhybridparticlefield/nfsim_hybrid_particle_field.bngl diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/README.md b/Examples/nfsim/nfsimringclosurepolymer/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/README.md rename to Examples/nfsim/nfsimringclosurepolymer/README.md diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/metadata.yaml b/Examples/nfsim/nfsimringclosurepolymer/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/metadata.yaml rename to Examples/nfsim/nfsimringclosurepolymer/metadata.yaml index 15e75b0..4efa9d3 100644 --- a/Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/metadata.yaml +++ b/Examples/nfsim/nfsimringclosurepolymer/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/nfsim_ring_closure_polymer.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer.bngl b/Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer.bngl rename to Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer.bngl diff --git a/Contributed/BNGPlayground_Examples/physics/phlorenzattractor/README.md b/Examples/physics/phlorenzattractor/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phlorenzattractor/README.md rename to Examples/physics/phlorenzattractor/README.md diff --git a/Contributed/BNGPlayground_Examples/physics/phlorenzattractor/metadata.yaml b/Examples/physics/phlorenzattractor/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/physics/phlorenzattractor/metadata.yaml rename to Examples/physics/phlorenzattractor/metadata.yaml index 1685d98..a7415cf 100644 --- a/Contributed/BNGPlayground_Examples/physics/phlorenzattractor/metadata.yaml +++ b/Examples/physics/phlorenzattractor/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/ph_lorenz_attractor.bngl" playground: visible: false - gallery_category: "physics" + gallery_categories: ["physics","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/physics/phlorenzattractor/ph_lorenz_attractor.bngl b/Examples/physics/phlorenzattractor/ph_lorenz_attractor.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phlorenzattractor/ph_lorenz_attractor.bngl rename to Examples/physics/phlorenzattractor/ph_lorenz_attractor.bngl diff --git a/Contributed/BNGPlayground_Examples/physics/phnbodygravity/README.md b/Examples/physics/phnbodygravity/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phnbodygravity/README.md rename to Examples/physics/phnbodygravity/README.md diff --git a/Contributed/BNGPlayground_Examples/physics/phnbodygravity/metadata.yaml b/Examples/physics/phnbodygravity/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/physics/phnbodygravity/metadata.yaml rename to Examples/physics/phnbodygravity/metadata.yaml index 5110f9e..d1f1cd5 100644 --- a/Contributed/BNGPlayground_Examples/physics/phnbodygravity/metadata.yaml +++ b/Examples/physics/phnbodygravity/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/ph_nbody_gravity.bngl" playground: visible: false - gallery_category: "physics" + gallery_categories: ["physics","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/physics/phnbodygravity/ph_nbody_gravity.bngl b/Examples/physics/phnbodygravity/ph_nbody_gravity.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phnbodygravity/ph_nbody_gravity.bngl rename to Examples/physics/phnbodygravity/ph_nbody_gravity.bngl diff --git a/Contributed/BNGPlayground_Examples/physics/phschrodinger/README.md b/Examples/physics/phschrodinger/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phschrodinger/README.md rename to Examples/physics/phschrodinger/README.md diff --git a/Contributed/BNGPlayground_Examples/physics/phschrodinger/metadata.yaml b/Examples/physics/phschrodinger/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/physics/phschrodinger/metadata.yaml rename to Examples/physics/phschrodinger/metadata.yaml index d3f7725..44774d6 100644 --- a/Contributed/BNGPlayground_Examples/physics/phschrodinger/metadata.yaml +++ b/Examples/physics/phschrodinger/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/ph_schrodinger.bngl" playground: visible: false - gallery_category: "physics" + gallery_categories: ["physics","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/physics/phschrodinger/ph_schrodinger.bngl b/Examples/physics/phschrodinger/ph_schrodinger.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phschrodinger/ph_schrodinger.bngl rename to Examples/physics/phschrodinger/ph_schrodinger.bngl diff --git a/Contributed/BNGPlayground_Examples/physics/phwaveequation/README.md b/Examples/physics/phwaveequation/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phwaveequation/README.md rename to Examples/physics/phwaveequation/README.md diff --git a/Contributed/BNGPlayground_Examples/physics/phwaveequation/metadata.yaml b/Examples/physics/phwaveequation/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/physics/phwaveequation/metadata.yaml rename to Examples/physics/phwaveequation/metadata.yaml index 5f811e1..801db30 100644 --- a/Contributed/BNGPlayground_Examples/physics/phwaveequation/metadata.yaml +++ b/Examples/physics/phwaveequation/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/ph_wave_equation.bngl" playground: visible: false - gallery_category: "physics" + gallery_categories: ["physics","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/physics/phwaveequation/ph_wave_equation.bngl b/Examples/physics/phwaveequation/ph_wave_equation.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/physics/phwaveequation/ph_wave_equation.bngl rename to Examples/physics/phwaveequation/ph_wave_equation.bngl diff --git a/Contributed/BNGPlayground_Examples/processes/processactintreadmilling/README.md b/Examples/processes/processactintreadmilling/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processactintreadmilling/README.md rename to Examples/processes/processactintreadmilling/README.md diff --git a/Contributed/BNGPlayground_Examples/processes/processactintreadmilling/metadata.yaml b/Examples/processes/processactintreadmilling/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/processes/processactintreadmilling/metadata.yaml rename to Examples/processes/processactintreadmilling/metadata.yaml index 68675ee..63e8a9b 100644 --- a/Contributed/BNGPlayground_Examples/processes/processactintreadmilling/metadata.yaml +++ b/Examples/processes/processactintreadmilling/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/process_actin_treadmilling.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl b/Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl rename to Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl diff --git a/Contributed/BNGPlayground_Examples/processes/processautophagyflux/README.md b/Examples/processes/processautophagyflux/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processautophagyflux/README.md rename to Examples/processes/processautophagyflux/README.md diff --git a/Contributed/BNGPlayground_Examples/processes/processautophagyflux/metadata.yaml b/Examples/processes/processautophagyflux/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/processes/processautophagyflux/metadata.yaml rename to Examples/processes/processautophagyflux/metadata.yaml index 8db1ecc..7321280 100644 --- a/Contributed/BNGPlayground_Examples/processes/processautophagyflux/metadata.yaml +++ b/Examples/processes/processautophagyflux/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/process_autophagy_flux.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/processes/processautophagyflux/process_autophagy_flux.bngl b/Examples/processes/processautophagyflux/process_autophagy_flux.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processautophagyflux/process_autophagy_flux.bngl rename to Examples/processes/processautophagyflux/process_autophagy_flux.bngl diff --git a/Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/README.md b/Examples/processes/processcelladhesionstrength/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/README.md rename to Examples/processes/processcelladhesionstrength/README.md diff --git a/Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/metadata.yaml b/Examples/processes/processcelladhesionstrength/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/metadata.yaml rename to Examples/processes/processcelladhesionstrength/metadata.yaml index 2af30b7..b99e743 100644 --- a/Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/metadata.yaml +++ b/Examples/processes/processcelladhesionstrength/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/process_cell_adhesion_strength.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl b/Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl rename to Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl diff --git a/Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/README.md b/Examples/processes/processkineticproofreadingtcr/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/README.md rename to Examples/processes/processkineticproofreadingtcr/README.md diff --git a/Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/metadata.yaml b/Examples/processes/processkineticproofreadingtcr/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/metadata.yaml rename to Examples/processes/processkineticproofreadingtcr/metadata.yaml index 31b7b9a..9dad7e9 100644 --- a/Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/metadata.yaml +++ b/Examples/processes/processkineticproofreadingtcr/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/process_kinetic_proofreading_tcr.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl b/Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl rename to Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl diff --git a/Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/README.md b/Examples/processes/processquorumsensingswitch/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/README.md rename to Examples/processes/processquorumsensingswitch/README.md diff --git a/Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/metadata.yaml b/Examples/processes/processquorumsensingswitch/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/metadata.yaml rename to Examples/processes/processquorumsensingswitch/metadata.yaml index 58f1a5d..4db1b85 100644 --- a/Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/metadata.yaml +++ b/Examples/processes/processquorumsensingswitch/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/process_quorum_sensing_switch.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl b/Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl rename to Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/README.md b/Examples/signal-processing/spfouriersynthesizer/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/README.md rename to Examples/signal-processing/spfouriersynthesizer/README.md diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/metadata.yaml b/Examples/signal-processing/spfouriersynthesizer/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/metadata.yaml rename to Examples/signal-processing/spfouriersynthesizer/metadata.yaml index 23e38b4..f8fa0ac 100644 --- a/Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/metadata.yaml +++ b/Examples/signal-processing/spfouriersynthesizer/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/sp_fourier_synthesizer.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["ml-signal","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl b/Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl similarity index 95% rename from Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl rename to Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl index d63aca1..b3289bf 100644 --- a/Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl +++ b/Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl @@ -87,7 +87,7 @@ begin functions ds1() = 1*omega * c1() dc1() = -1*omega * s1() - ds3() = 3*omega * (Cos1 - amp_offset) # Using Cos1 as approx + ds3() = 3*ds1() - 12*s1()*s1()*ds1() ds5() = 5*omega * (Cos1 - amp_offset) ds7() = 7*omega * (Cos1 - amp_offset) ds9() = 9*omega * (Cos1 - amp_offset) @@ -111,8 +111,7 @@ begin reaction rules C1() -> 0 if(dc1() < 0,-dc1()/max(Cos1,0.001),0) # 3rd harmonic: d(S3)/dt = 3*omega*cos(3*omega*t) - # Hack: use sin(3x) = 3*sin(x) - 4*sin^3(x) identity - # Actually,just couple each harmonic independently + # Uses sin(3x) = 3*sin(x) - 4*sin^3(x) identity 0 -> S3() if(ds3() > 0,ds3(),0) S3() -> 0 if(ds3() < 0,-ds3()/max(Sin3,0.001),0) diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/README.md b/Examples/signal-processing/spimageconvolution/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/README.md rename to Examples/signal-processing/spimageconvolution/README.md diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/metadata.yaml b/Examples/signal-processing/spimageconvolution/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/metadata.yaml rename to Examples/signal-processing/spimageconvolution/metadata.yaml index ba7722e..d9560f0 100644 --- a/Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/metadata.yaml +++ b/Examples/signal-processing/spimageconvolution/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/sp_image_convolution.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["ml-signal","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/sp_image_convolution.bngl b/Examples/signal-processing/spimageconvolution/sp_image_convolution.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/sp_image_convolution.bngl rename to Examples/signal-processing/spimageconvolution/sp_image_convolution.bngl diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/README.md b/Examples/signal-processing/spkalmanfilter/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/README.md rename to Examples/signal-processing/spkalmanfilter/README.md diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/metadata.yaml b/Examples/signal-processing/spkalmanfilter/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/metadata.yaml rename to Examples/signal-processing/spkalmanfilter/metadata.yaml index 4d5dc58..9204517 100644 --- a/Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/metadata.yaml +++ b/Examples/signal-processing/spkalmanfilter/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/sp_kalman_filter.bngl" playground: visible: false - gallery_category: "computer-science" + gallery_categories: ["ml-signal","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/sp_kalman_filter.bngl b/Examples/signal-processing/spkalmanfilter/sp_kalman_filter.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/sp_kalman_filter.bngl rename to Examples/signal-processing/spkalmanfilter/sp_kalman_filter.bngl diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/README.md b/Examples/synbio/synbiobandpassfilter/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/README.md rename to Examples/synbio/synbiobandpassfilter/README.md diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/metadata.yaml b/Examples/synbio/synbiobandpassfilter/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/metadata.yaml rename to Examples/synbio/synbiobandpassfilter/metadata.yaml index 2725a4f..7826482 100644 --- a/Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/metadata.yaml +++ b/Examples/synbio/synbiobandpassfilter/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/synbio_band_pass_filter.bngl" playground: visible: false - gallery_category: "synthetic-biology" + gallery_categories: ["synbio","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter.bngl b/Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter.bngl rename to Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter.bngl diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/README.md b/Examples/synbio/synbiocountermolecular/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/README.md rename to Examples/synbio/synbiocountermolecular/README.md diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/metadata.yaml b/Examples/synbio/synbiocountermolecular/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/metadata.yaml rename to Examples/synbio/synbiocountermolecular/metadata.yaml index d5f6699..e19dc1e 100644 --- a/Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/metadata.yaml +++ b/Examples/synbio/synbiocountermolecular/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/synbio_counter_molecular.bngl" playground: visible: false - gallery_category: "synthetic-biology" + gallery_categories: ["synbio","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl b/Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl rename to Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl diff --git a/Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/README.md b/Examples/synbio/synbioedgedetector/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/README.md rename to Examples/synbio/synbioedgedetector/README.md diff --git a/Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/metadata.yaml b/Examples/synbio/synbioedgedetector/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/metadata.yaml rename to Examples/synbio/synbioedgedetector/metadata.yaml index 404d439..0c782e2 100644 --- a/Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/metadata.yaml +++ b/Examples/synbio/synbioedgedetector/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/synbio_edge_detector.bngl" playground: visible: false - gallery_category: "synthetic-biology" + gallery_categories: ["synbio","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl b/Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl rename to Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/README.md b/Examples/synbio/synbiologicgatesenzymatic/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/README.md rename to Examples/synbio/synbiologicgatesenzymatic/README.md diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/metadata.yaml b/Examples/synbio/synbiologicgatesenzymatic/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/metadata.yaml rename to Examples/synbio/synbiologicgatesenzymatic/metadata.yaml index e978abd..d03229d 100644 --- a/Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/metadata.yaml +++ b/Examples/synbio/synbiologicgatesenzymatic/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/synbio_logic_gates_enzymatic.bngl" playground: visible: false - gallery_category: "synthetic-biology" + gallery_categories: ["synbio","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl b/Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl rename to Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/README.md b/Examples/synbio/synbiooscillatorsynchronization/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/README.md rename to Examples/synbio/synbiooscillatorsynchronization/README.md diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/metadata.yaml b/Examples/synbio/synbiooscillatorsynchronization/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/metadata.yaml rename to Examples/synbio/synbiooscillatorsynchronization/metadata.yaml index 584ff33..04ac40d 100644 --- a/Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/metadata.yaml +++ b/Examples/synbio/synbiooscillatorsynchronization/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/synbio_oscillator_synchronization.bngl" playground: visible: false - gallery_category: "synthetic-biology" + gallery_categories: ["synbio","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl b/Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl rename to Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl diff --git a/Contributed/BNGPlayground_Examples/wacky/wackyalchemystone/README.md b/Examples/wacky/wackyalchemystone/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/wacky/wackyalchemystone/README.md rename to Examples/wacky/wackyalchemystone/README.md diff --git a/Contributed/BNGPlayground_Examples/wacky/wackyalchemystone/metadata.yaml b/Examples/wacky/wackyalchemystone/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/wacky/wackyalchemystone/metadata.yaml rename to Examples/wacky/wackyalchemystone/metadata.yaml index d4b4301..ed32f38 100644 --- a/Contributed/BNGPlayground_Examples/wacky/wackyalchemystone/metadata.yaml +++ b/Examples/wacky/wackyalchemystone/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/wacky_alchemy_stone.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["synbio","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/wacky/wackyalchemystone/wacky_alchemy_stone.bngl b/Examples/wacky/wackyalchemystone/wacky_alchemy_stone.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/wacky/wackyalchemystone/wacky_alchemy_stone.bngl rename to Examples/wacky/wackyalchemystone/wacky_alchemy_stone.bngl diff --git a/Contributed/BNGPlayground_Examples/wacky/wackyblackhole/README.md b/Examples/wacky/wackyblackhole/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/wacky/wackyblackhole/README.md rename to Examples/wacky/wackyblackhole/README.md diff --git a/Contributed/BNGPlayground_Examples/wacky/wackyblackhole/metadata.yaml b/Examples/wacky/wackyblackhole/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Examples/wacky/wackyblackhole/metadata.yaml rename to Examples/wacky/wackyblackhole/metadata.yaml index 80b6f1b..c8c34c6 100644 --- a/Contributed/BNGPlayground_Examples/wacky/wackyblackhole/metadata.yaml +++ b/Examples/wacky/wackyblackhole/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/wacky_black_hole.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/wacky/wackyblackhole/wacky_black_hole.bngl b/Examples/wacky/wackyblackhole/wacky_black_hole.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/wacky/wackyblackhole/wacky_black_hole.bngl rename to Examples/wacky/wackyblackhole/wacky_black_hole.bngl diff --git a/Contributed/BNGPlayground_Examples/wacky/wackybouncingball/README.md b/Examples/wacky/wackybouncingball/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/wacky/wackybouncingball/README.md rename to Examples/wacky/wackybouncingball/README.md diff --git a/Contributed/BNGPlayground_Examples/wacky/wackybouncingball/metadata.yaml b/Examples/wacky/wackybouncingball/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/wacky/wackybouncingball/metadata.yaml rename to Examples/wacky/wackybouncingball/metadata.yaml index 05d9352..e68148e 100644 --- a/Contributed/BNGPlayground_Examples/wacky/wackybouncingball/metadata.yaml +++ b/Examples/wacky/wackybouncingball/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/wacky_bouncing_ball.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["physics","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/wacky/wackybouncingball/wacky_bouncing_ball.bngl b/Examples/wacky/wackybouncingball/wacky_bouncing_ball.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/wacky/wackybouncingball/wacky_bouncing_ball.bngl rename to Examples/wacky/wackybouncingball/wacky_bouncing_ball.bngl diff --git a/Contributed/BNGPlayground_Examples/wacky/wackytrafficjamasep/README.md b/Examples/wacky/wackytrafficjamasep/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/wacky/wackytrafficjamasep/README.md rename to Examples/wacky/wackytrafficjamasep/README.md diff --git a/Contributed/BNGPlayground_Examples/wacky/wackytrafficjamasep/metadata.yaml b/Examples/wacky/wackytrafficjamasep/metadata.yaml similarity index 93% rename from Contributed/BNGPlayground_Examples/wacky/wackytrafficjamasep/metadata.yaml rename to Examples/wacky/wackytrafficjamasep/metadata.yaml index 57712ae..157fa14 100644 --- a/Contributed/BNGPlayground_Examples/wacky/wackytrafficjamasep/metadata.yaml +++ b/Examples/wacky/wackytrafficjamasep/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/wacky_traffic_jam_asep.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["physics","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/wacky/wackytrafficjamasep/wacky_traffic_jam_asep.bngl b/Examples/wacky/wackytrafficjamasep/wacky_traffic_jam_asep.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/wacky/wackytrafficjamasep/wacky_traffic_jam_asep.bngl rename to Examples/wacky/wackytrafficjamasep/wacky_traffic_jam_asep.bngl diff --git a/Contributed/BNGPlayground_Examples/wacky/wackyzombieinfection/README.md b/Examples/wacky/wackyzombieinfection/README.md similarity index 100% rename from Contributed/BNGPlayground_Examples/wacky/wackyzombieinfection/README.md rename to Examples/wacky/wackyzombieinfection/README.md diff --git a/Contributed/BNGPlayground_Examples/wacky/wackyzombieinfection/metadata.yaml b/Examples/wacky/wackyzombieinfection/metadata.yaml similarity index 92% rename from Contributed/BNGPlayground_Examples/wacky/wackyzombieinfection/metadata.yaml rename to Examples/wacky/wackyzombieinfection/metadata.yaml index 01b3200..39a91d9 100644 --- a/Contributed/BNGPlayground_Examples/wacky/wackyzombieinfection/metadata.yaml +++ b/Examples/wacky/wackyzombieinfection/metadata.yaml @@ -19,6 +19,6 @@ source: source_path: "example-models/wacky_zombie_infection.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["ecology","test-models"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Examples/wacky/wackyzombieinfection/wacky_zombie_infection.bngl b/Examples/wacky/wackyzombieinfection/wacky_zombie_infection.bngl similarity index 100% rename from Contributed/BNGPlayground_Examples/wacky/wackyzombieinfection/wacky_zombie_infection.bngl rename to Examples/wacky/wackyzombieinfection/wacky_zombie_infection.bngl diff --git a/Published/An2009/metadata.yaml b/Published/An2009/metadata.yaml index 4bdf97e..f949b5b 100644 --- a/Published/An2009/metadata.yaml +++ b/Published/An2009/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/immune-signaling/An_2009.bngl" playground: visible: true - gallery_category: "immunology" + gallery_categories: ["immunology"] featured: false difficulty: "intermediate" diff --git a/Published/Barua2007/metadata.yaml b/Published/Barua2007/metadata.yaml index c8d45e8..5eaeff0 100644 --- a/Published/Barua2007/metadata.yaml +++ b/Published/Barua2007/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Barua_2007.bngl" playground: visible: true - gallery_category: "signaling" + gallery_categories: ["cancer"] featured: false difficulty: "intermediate" diff --git a/Published/Barua2009/metadata.yaml b/Published/Barua2009/metadata.yaml index b9172fa..3fb621b 100644 --- a/Published/Barua2009/metadata.yaml +++ b/Published/Barua2009/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Barua_2009.bngl" playground: visible: true - gallery_category: "signaling" + gallery_categories: ["cancer"] featured: false difficulty: "intermediate" diff --git a/Published/Barua2013/metadata.yaml b/Published/Barua2013/metadata.yaml index 123da78..7f3df0e 100644 --- a/Published/Barua2013/metadata.yaml +++ b/Published/Barua2013/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/cell-regulation/Barua_2013.bngl" playground: visible: true - gallery_category: "regulation" + gallery_categories: [] featured: false difficulty: "intermediate" diff --git a/Published/BaruaBCR2012/metadata.yaml b/Published/BaruaBCR2012/metadata.yaml index f85b0d9..f910fe3 100644 --- a/Published/BaruaBCR2012/metadata.yaml +++ b/Published/BaruaBCR2012/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/immune-signaling/BaruaBCR_2012.bngl" playground: visible: false - gallery_category: "immunology" + gallery_categories: ["immunology"] featured: false difficulty: "advanced" diff --git a/Published/BaruaFceRI2012/metadata.yaml b/Published/BaruaFceRI2012/metadata.yaml index 148a704..4a4b33e 100644 --- a/Published/BaruaFceRI2012/metadata.yaml +++ b/Published/BaruaFceRI2012/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/immune-signaling/BaruaFceRI_2012.bngl" playground: visible: false - gallery_category: "immunology" + gallery_categories: ["immunology"] featured: false difficulty: "advanced" diff --git a/Published/Blinov2006/metadata.yaml b/Published/Blinov2006/metadata.yaml index e0cf624..8717506 100644 --- a/Published/Blinov2006/metadata.yaml +++ b/Published/Blinov2006/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Blinov_2006.bngl" playground: visible: true - gallery_category: "signaling" + gallery_categories: ["cell-cycle"] featured: false difficulty: "intermediate" diff --git a/Published/Blinovegfr/metadata.yaml b/Published/Blinovegfr/metadata.yaml index ff4c244..bf60149 100644 --- a/Published/Blinovegfr/metadata.yaml +++ b/Published/Blinovegfr/metadata.yaml @@ -4,7 +4,7 @@ description: "EGFR signaling model" tags: ["published", "nfsim", "blinov", "egfr", "egf", "grb2", "shc", "simulate_nf"] category: "signaling" compatibility: - bng2_compatible: false + bng2_compatible: true simulation_methods: ["nf"] uses_compartments: true uses_energy: false @@ -17,6 +17,6 @@ source: source_path: "published-models/growth-factor-signaling/Blinov_egfr.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer"] featured: false difficulty: "advanced" diff --git a/Published/Blinovran/metadata.yaml b/Published/Blinovran/metadata.yaml index e92f3b2..2143b98 100644 --- a/Published/Blinovran/metadata.yaml +++ b/Published/Blinovran/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/cell-regulation/Blinov_ran.bngl" playground: visible: false - gallery_category: "regulation" + gallery_categories: ["cell-cycle"] featured: false difficulty: "advanced" diff --git a/Published/Chattaraj2021/metadata.yaml b/Published/Chattaraj2021/metadata.yaml index 3092abb..4a2b65f 100644 --- a/Published/Chattaraj2021/metadata.yaml +++ b/Published/Chattaraj2021/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Chattaraj_2021.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["neuroscience"] featured: false difficulty: "advanced" diff --git a/Published/CheemalavaguJAKSTAT/metadata.yaml b/Published/CheemalavaguJAKSTAT/metadata.yaml index 5689cd4..b1aa6a3 100644 --- a/Published/CheemalavaguJAKSTAT/metadata.yaml +++ b/Published/CheemalavaguJAKSTAT/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/literature/Cheemalavagu_JAK_STAT.bngl" playground: visible: true - gallery_category: "other" + gallery_categories: ["immunology"] featured: false difficulty: "intermediate" diff --git a/Published/ChylekTCR2014/metadata.yaml b/Published/ChylekTCR2014/metadata.yaml index 9de38d0..f91b398 100644 --- a/Published/ChylekTCR2014/metadata.yaml +++ b/Published/ChylekTCR2014/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/immune-signaling/ChylekTCR_2014.bngl" playground: visible: false - gallery_category: "immunology" + gallery_categories: ["immunology"] featured: false difficulty: "advanced" diff --git a/Published/Dolan2015/metadata.yaml b/Published/Dolan2015/metadata.yaml index 3f6c2b6..ed93027 100644 --- a/Published/Dolan2015/metadata.yaml +++ b/Published/Dolan2015/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/literature/Dolan_2015.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["metabolism"] featured: false difficulty: "advanced" diff --git a/Published/Dushek2011/metadata.yaml b/Published/Dushek2011/metadata.yaml index a246a37..f54c701 100644 --- a/Published/Dushek2011/metadata.yaml +++ b/Published/Dushek2011/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Dushek_2011.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology"] featured: false difficulty: "advanced" diff --git a/Published/Dushek2014/metadata.yaml b/Published/Dushek2014/metadata.yaml index 956b96f..43ea73d 100644 --- a/Published/Dushek2014/metadata.yaml +++ b/Published/Dushek2014/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Dushek_2014.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology"] featured: false difficulty: "advanced" diff --git a/Published/Erdem2021/metadata.yaml b/Published/Erdem2021/metadata.yaml index 69b2fe0..0d70fdb 100644 --- a/Published/Erdem2021/metadata.yaml +++ b/Published/Erdem2021/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Erdem_2021.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["metabolism"] featured: false difficulty: "advanced" diff --git a/Published/Faeder2003/metadata.yaml b/Published/Faeder2003/metadata.yaml index b8403f7..1d7353d 100644 --- a/Published/Faeder2003/metadata.yaml +++ b/Published/Faeder2003/metadata.yaml @@ -4,12 +4,12 @@ description: "FceRI signaling" tags: ["published", "immunology", "faeder", "2003", "lig", "lyn", "syk", "rec"] category: "immunology" compatibility: - bng2_compatible: false + bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "published" original_format: "bngl" @@ -17,6 +17,6 @@ source: source_path: "published-models/immune-signaling/Faeder_2003.bngl" playground: visible: true - gallery_category: "immunology" + gallery_categories: ["immunology"] featured: false difficulty: "advanced" diff --git a/Published/Hat2016/metadata.yaml b/Published/Hat2016/metadata.yaml index d7afdc6..8e37c76 100644 --- a/Published/Hat2016/metadata.yaml +++ b/Published/Hat2016/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/cell-regulation/Hat_2016.bngl" playground: visible: true - gallery_category: "regulation" + gallery_categories: ["cell-cycle","multistage"] featured: false difficulty: "intermediate" diff --git a/Contributed/Hlavacek2018Egg/BioNetFit_files/egg.bngl b/Published/Hlavacek2018Egg/BioNetFit_files/egg.bngl similarity index 100% rename from Contributed/Hlavacek2018Egg/BioNetFit_files/egg.bngl rename to Published/Hlavacek2018Egg/BioNetFit_files/egg.bngl diff --git a/Contributed/Hlavacek2018Egg/BioNetFit_files/egg.exp b/Published/Hlavacek2018Egg/BioNetFit_files/egg.exp similarity index 100% rename from Contributed/Hlavacek2018Egg/BioNetFit_files/egg.exp rename to Published/Hlavacek2018Egg/BioNetFit_files/egg.exp diff --git a/Contributed/Hlavacek2018Egg/BioNetFit_files/egg_boot.conf b/Published/Hlavacek2018Egg/BioNetFit_files/egg_boot.conf similarity index 100% rename from Contributed/Hlavacek2018Egg/BioNetFit_files/egg_boot.conf rename to Published/Hlavacek2018Egg/BioNetFit_files/egg_boot.conf diff --git a/Contributed/Hlavacek2018Egg/BioNetFit_files/egg_fit.conf b/Published/Hlavacek2018Egg/BioNetFit_files/egg_fit.conf similarity index 100% rename from Contributed/Hlavacek2018Egg/BioNetFit_files/egg_fit.conf rename to Published/Hlavacek2018Egg/BioNetFit_files/egg_fit.conf diff --git a/Contributed/Hlavacek2018Egg/README.md b/Published/Hlavacek2018Egg/README.md similarity index 100% rename from Contributed/Hlavacek2018Egg/README.md rename to Published/Hlavacek2018Egg/README.md diff --git a/Contributed/Hlavacek2018Egg/egg.bngl b/Published/Hlavacek2018Egg/egg.bngl similarity index 100% rename from Contributed/Hlavacek2018Egg/egg.bngl rename to Published/Hlavacek2018Egg/egg.bngl diff --git a/Published/Hlavacek2018Egg/metadata.yaml b/Published/Hlavacek2018Egg/metadata.yaml new file mode 100644 index 0000000..98808fd --- /dev/null +++ b/Published/Hlavacek2018Egg/metadata.yaml @@ -0,0 +1,19 @@ +id: Hlavacek2018Egg_egg +name: Hlavacek2018Egg +description: End of permute change log +tags: ["a0__free", "a1__free", "a2__free", "b1__free", "b2__free", "c0__free", "c1__free", "c2__free", "d1__free", "d2__free", "a0", "a1", "a2", "b1", "b2", "c0", "c1", "c2", "d1", "d2", "period", "t", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Hlavacek2018Elephant/BioNetFit_files/elephant.bngl b/Published/Hlavacek2018Elephant/BioNetFit_files/elephant.bngl similarity index 100% rename from Contributed/Hlavacek2018Elephant/BioNetFit_files/elephant.bngl rename to Published/Hlavacek2018Elephant/BioNetFit_files/elephant.bngl diff --git a/Contributed/Hlavacek2018Elephant/BioNetFit_files/elephant.exp b/Published/Hlavacek2018Elephant/BioNetFit_files/elephant.exp similarity index 100% rename from Contributed/Hlavacek2018Elephant/BioNetFit_files/elephant.exp rename to Published/Hlavacek2018Elephant/BioNetFit_files/elephant.exp diff --git a/Contributed/Hlavacek2018Elephant/BioNetFit_files/elephant_fit.conf b/Published/Hlavacek2018Elephant/BioNetFit_files/elephant_fit.conf similarity index 100% rename from Contributed/Hlavacek2018Elephant/BioNetFit_files/elephant_fit.conf rename to Published/Hlavacek2018Elephant/BioNetFit_files/elephant_fit.conf diff --git a/Contributed/Hlavacek2018Elephant/README.md b/Published/Hlavacek2018Elephant/README.md similarity index 100% rename from Contributed/Hlavacek2018Elephant/README.md rename to Published/Hlavacek2018Elephant/README.md diff --git a/Contributed/Hlavacek2018Elephant/elephant_EFA.bngl b/Published/Hlavacek2018Elephant/elephant_EFA.bngl similarity index 100% rename from Contributed/Hlavacek2018Elephant/elephant_EFA.bngl rename to Published/Hlavacek2018Elephant/elephant_EFA.bngl diff --git a/Contributed/Hlavacek2018Elephant/elephant_fit.bngl b/Published/Hlavacek2018Elephant/elephant_fit.bngl similarity index 100% rename from Contributed/Hlavacek2018Elephant/elephant_fit.bngl rename to Published/Hlavacek2018Elephant/elephant_fit.bngl diff --git a/Published/Hlavacek2018Elephant/metadata.yaml b/Published/Hlavacek2018Elephant/metadata.yaml new file mode 100644 index 0000000..0c16dce --- /dev/null +++ b/Published/Hlavacek2018Elephant/metadata.yaml @@ -0,0 +1,19 @@ +id: Hlavacek2018Elephant_elephant_EFA +name: Hlavacek2018Elephant +description: BNGL model: elephant_EFA +tags: ["a0", "a1", "a2", "a3", "a4", "a5", "a6", "a7", "a8", "a9", "a10", "a11", "a12", "a13", "a14", "a15", "a16", "a17", "a18", "a19", "a20", "b0", "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17", "b18", "b19", "b20", "c0", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "c8", "c9", "c10", "c11", "c12", "c13", "c14", "c15", "c16", "c17", "c18", "c19", "c20", "d0", "d1", "d2", "d3", "d4", "d5", "d6", "d7", "d8", "d9", "d10", "d11", "d12", "d13", "d14", "d15", "d16", "d17", "d18", "d19", "d20", "period", "t", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Hlavacek2018Restructuration/README.md b/Published/Hlavacek2018Restructuration/README.md similarity index 100% rename from Contributed/Hlavacek2018Restructuration/README.md rename to Published/Hlavacek2018Restructuration/README.md diff --git a/Contributed/Hlavacek2018Restructuration/after_bunching.bngl b/Published/Hlavacek2018Restructuration/after_bunching.bngl similarity index 100% rename from Contributed/Hlavacek2018Restructuration/after_bunching.bngl rename to Published/Hlavacek2018Restructuration/after_bunching.bngl diff --git a/Contributed/Hlavacek2018Restructuration/after_decoupling.bngl b/Published/Hlavacek2018Restructuration/after_decoupling.bngl similarity index 100% rename from Contributed/Hlavacek2018Restructuration/after_decoupling.bngl rename to Published/Hlavacek2018Restructuration/after_decoupling.bngl diff --git a/Contributed/Hlavacek2018Restructuration/after_scaling.bngl b/Published/Hlavacek2018Restructuration/after_scaling.bngl similarity index 100% rename from Contributed/Hlavacek2018Restructuration/after_scaling.bngl rename to Published/Hlavacek2018Restructuration/after_scaling.bngl diff --git a/Contributed/Hlavacek2018Restructuration/before_bunching.bngl b/Published/Hlavacek2018Restructuration/before_bunching.bngl similarity index 100% rename from Contributed/Hlavacek2018Restructuration/before_bunching.bngl rename to Published/Hlavacek2018Restructuration/before_bunching.bngl diff --git a/Contributed/Hlavacek2018Restructuration/before_decoupling.bngl b/Published/Hlavacek2018Restructuration/before_decoupling.bngl similarity index 100% rename from Contributed/Hlavacek2018Restructuration/before_decoupling.bngl rename to Published/Hlavacek2018Restructuration/before_decoupling.bngl diff --git a/Contributed/Hlavacek2018Restructuration/before_scaling.bngl b/Published/Hlavacek2018Restructuration/before_scaling.bngl similarity index 100% rename from Contributed/Hlavacek2018Restructuration/before_scaling.bngl rename to Published/Hlavacek2018Restructuration/before_scaling.bngl diff --git a/Contributed/Hlavacek2018Restructuration/check_scaling.bngl b/Published/Hlavacek2018Restructuration/check_scaling.bngl similarity index 100% rename from Contributed/Hlavacek2018Restructuration/check_scaling.bngl rename to Published/Hlavacek2018Restructuration/check_scaling.bngl diff --git a/Published/Hlavacek2018Restructuration/metadata.yaml b/Published/Hlavacek2018Restructuration/metadata.yaml new file mode 100644 index 0000000..00f6fdf --- /dev/null +++ b/Published/Hlavacek2018Restructuration/metadata.yaml @@ -0,0 +1,19 @@ +id: Hlavacek2018Restructuration_after_bunching +name: Hlavacek2018Restructuration +description: BNGL model: after_bunching +tags: ["na", "vecf", "egftot", "egfrtot", "kd", "kr", "kpx", "kmx", "kp", "kdp", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/JaruszewiczBlonska2023/metadata.yaml b/Published/JaruszewiczBlonska2023/metadata.yaml index 498640f..b469a53 100644 --- a/Published/JaruszewiczBlonska2023/metadata.yaml +++ b/Published/JaruszewiczBlonska2023/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/immune-signaling/Jaruszewicz-Blonska_2023.bngl" playground: visible: true - gallery_category: "immunology" + gallery_categories: ["immunology"] featured: false difficulty: "intermediate" diff --git a/Published/Jung2017/metadata.yaml b/Published/Jung2017/metadata.yaml index eecc4e6..bba84b0 100644 --- a/Published/Jung2017/metadata.yaml +++ b/Published/Jung2017/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Jung_2017.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["neuroscience"] featured: false difficulty: "advanced" diff --git a/Published/Kesseler2013/metadata.yaml b/Published/Kesseler2013/metadata.yaml index bb5daec..86b76e0 100644 --- a/Published/Kesseler2013/metadata.yaml +++ b/Published/Kesseler2013/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Kesseler_2013.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cell-cycle"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Validation/Korwek2023/Korwek_2023.bngl b/Published/Korwek2023/Korwek_2023.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/Korwek2023/Korwek_2023.bngl rename to Published/Korwek2023/Korwek_2023.bngl diff --git a/Contributed/BNGPlayground_Validation/Korwek2023/README.md b/Published/Korwek2023/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/Korwek2023/README.md rename to Published/Korwek2023/README.md diff --git a/Contributed/BNGPlayground_Validation/Korwek2023/metadata.yaml b/Published/Korwek2023/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/Korwek2023/metadata.yaml rename to Published/Korwek2023/metadata.yaml diff --git a/Published/Kozer2013/metadata.yaml b/Published/Kozer2013/metadata.yaml index e0167a2..b904460 100644 --- a/Published/Kozer2013/metadata.yaml +++ b/Published/Kozer2013/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Kozer_2013.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer"] featured: false difficulty: "advanced" diff --git a/Published/Kozer2014/metadata.yaml b/Published/Kozer2014/metadata.yaml index 20bcd9a..aaca3fe 100644 --- a/Published/Kozer2014/metadata.yaml +++ b/Published/Kozer2014/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Kozer_2014.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer"] featured: false difficulty: "advanced" diff --git a/Published/Lang2024/metadata.yaml b/Published/Lang2024/metadata.yaml index 248a891..fde4a07 100644 --- a/Published/Lang2024/metadata.yaml +++ b/Published/Lang2024/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/growth-factor-signaling/Lang_2024.bngl" playground: visible: true - gallery_category: "signaling" + gallery_categories: ["cell-cycle"] featured: false difficulty: "intermediate" diff --git a/Published/Ligon2014/metadata.yaml b/Published/Ligon2014/metadata.yaml index 85367e9..198fe7a 100644 --- a/Published/Ligon2014/metadata.yaml +++ b/Published/Ligon2014/metadata.yaml @@ -4,7 +4,7 @@ description: "Lipoplex delivery" tags: ["published", "nfsim", "ligon", "2014", "lext", "pit", "lint"] category: "signaling" compatibility: - bng2_compatible: false + bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false uses_energy: false @@ -17,6 +17,6 @@ source: source_path: "published-models/growth-factor-signaling/Ligon_2014.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer"] featured: false difficulty: "advanced" diff --git a/Published/Lin2019/metadata.yaml b/Published/Lin2019/metadata.yaml new file mode 100644 index 0000000..7e47ccf --- /dev/null +++ b/Published/Lin2019/metadata.yaml @@ -0,0 +1,19 @@ +id: Lin2019_ERK_model +name: ERK_model.bngl +description: filename: ERK_model.bngl +tags: ["egf", "erkpp_sos1_fb", "erkpp_mek_fb", "erkpp_raf1_fb", "lambda", "egfr_tot", "ras_tot", "sos_tot", "rasgap_tot", "raf_tot", "mek_tot", "erk_tot", "ekar3_tot", "erktr_tot", "a1", "d1", "b1", "u1a", "u1b", "b2a", "u2a", "b2b", "u2b", "k2a", "k2b", "b3", "u3", "k3", "a2", "d2", "p1", "q1", "p2", "q2", "p3", "q3", "p4", "q4", "q5", "p6", "q6", "a0_ekar3", "d0_ekar3", "a0_erktr", "d0_erktr", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode", "ssa"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/LinERK2019/metadata.yaml b/Published/LinERK2019/metadata.yaml index e287713..8c2ee39 100644 --- a/Published/LinERK2019/metadata.yaml +++ b/Published/LinERK2019/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/literature/Lin_ERK_2019.bngl" playground: visible: true - gallery_category: "other" + gallery_categories: ["developmental"] featured: false difficulty: "intermediate" diff --git a/Published/LinPrion2019/metadata.yaml b/Published/LinPrion2019/metadata.yaml index 1cc264c..ad5b740 100644 --- a/Published/LinPrion2019/metadata.yaml +++ b/Published/LinPrion2019/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/literature/Lin_Prion_2019.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["neuroscience"] featured: false difficulty: "advanced" diff --git a/Published/LinTCR2019/metadata.yaml b/Published/LinTCR2019/metadata.yaml index d4fcc09..9b72e6b 100644 --- a/Published/LinTCR2019/metadata.yaml +++ b/Published/LinTCR2019/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/literature/Lin_TCR_2019.bngl" playground: visible: true - gallery_category: "other" + gallery_categories: ["immunology"] featured: false difficulty: "intermediate" diff --git a/Published/Massole2023/metadata.yaml b/Published/Massole2023/metadata.yaml index 217131e..7827faf 100644 --- a/Published/Massole2023/metadata.yaml +++ b/Published/Massole2023/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Massole_2023.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["developmental"] featured: false difficulty: "advanced" diff --git a/Published/McMillan2021/metadata.yaml b/Published/McMillan2021/metadata.yaml index 66afb7e..5f911a8 100644 --- a/Published/McMillan2021/metadata.yaml +++ b/Published/McMillan2021/metadata.yaml @@ -4,12 +4,12 @@ description: "TNF signaling" tags: ["published", "nfsim", "mcmillan", "2021", "r0_tot", "t0_tot", "r", "t", "generate_network", "simulate_ode"] category: "signaling" compatibility: - bng2_compatible: false + bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "published" original_format: "bngl" @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/McMillan_2021.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["immunology"] featured: false difficulty: "advanced" diff --git a/Published/Mertins2023/metadata.yaml b/Published/Mertins2023/metadata.yaml index c7364b2..3f0ac83 100644 --- a/Published/Mertins2023/metadata.yaml +++ b/Published/Mertins2023/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/growth-factor-signaling/Mertins_2023.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer"] featured: false difficulty: "advanced" diff --git a/Published/Mitra2019/02-egfr/bnf1/InputFiles/metadata.yaml b/Published/Mitra2019/02-egfr/bnf1/InputFiles/metadata.yaml new file mode 100644 index 0000000..5e81019 --- /dev/null +++ b/Published/Mitra2019/02-egfr/bnf1/InputFiles/metadata.yaml @@ -0,0 +1,19 @@ +id: Mitra2019_02_egfr_bnf1_InputFiles_egfr +name: InputFiles +description: EGFR model +tags: ["signaling"] +category: signaling +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/02-egfr/metadata.yaml b/Published/Mitra2019/02-egfr/metadata.yaml new file mode 100644 index 0000000..8d4eaeb --- /dev/null +++ b/Published/Mitra2019/02-egfr/metadata.yaml @@ -0,0 +1,19 @@ +id: 02_egfr_egfr +name: 02-egfr +description: EGFR model +tags: ["signaling"] +category: signaling +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/03-fcerig/metadata.yaml b/Published/Mitra2019/03-fcerig/metadata.yaml new file mode 100644 index 0000000..cb9e95d --- /dev/null +++ b/Published/Mitra2019/03-fcerig/metadata.yaml @@ -0,0 +1,19 @@ +id: 03_fcerig_fceri_gamma2 +name: 03-fcerig +description: Added molecule type definition block so that the +tags: ["immunology"] +category: immunology +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/04-egfrnf/metadata.yaml b/Published/Mitra2019/04-egfrnf/metadata.yaml new file mode 100644 index 0000000..2e2f669 --- /dev/null +++ b/Published/Mitra2019/04-egfrnf/metadata.yaml @@ -0,0 +1,19 @@ +id: 04_egfrnf_egfr_nf +name: example2_starting_point.bngl +description: Filename: example2_starting_point.bngl +tags: ["f", "lt_nm", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "molecules"] +category: signaling +compatibility: + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/05-threestep/metadata.yaml b/Published/Mitra2019/05-threestep/metadata.yaml new file mode 100644 index 0000000..11faf00 --- /dev/null +++ b/Published/Mitra2019/05-threestep/metadata.yaml @@ -0,0 +1,19 @@ +id: 05_threestep_m1 +name: of a 3-step signaling cascade +description: Toy model of a 3-step signaling cascade +tags: ["k1", "k2", "k3", "ainit", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/06-degranulation/metadata.yaml b/Published/Mitra2019/06-degranulation/metadata.yaml new file mode 100644 index 0000000..19633eb --- /dev/null +++ b/Published/Mitra2019/06-degranulation/metadata.yaml @@ -0,0 +1,19 @@ +id: 06_degranulation_model_tofit +name: of IgE receptor signaling +description: A model of IgE receptor signaling +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/07-egg/metadata.yaml b/Published/Mitra2019/07-egg/metadata.yaml new file mode 100644 index 0000000..8d900bd --- /dev/null +++ b/Published/Mitra2019/07-egg/metadata.yaml @@ -0,0 +1,19 @@ +id: 07_egg_egg +name: 07-egg +description: BNGL model: egg +tags: ["a0", "a1", "a2", "b1", "b2", "c0", "c1", "c2", "d1", "d2", "period", "t", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/10-egfr/metadata.yaml b/Published/Mitra2019/10-egfr/metadata.yaml new file mode 100644 index 0000000..80c2386 --- /dev/null +++ b/Published/Mitra2019/10-egfr/metadata.yaml @@ -0,0 +1,19 @@ +id: 10_egfr_egfr_ode +name: example1.bngl +description: Filename: example1.bngl +tags: ["lt", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "alpha1", "alpha2", "alpha3", "alpha4", "molecules", "species"] +category: signaling +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/11-TLBR/metadata.yaml b/Published/Mitra2019/11-TLBR/metadata.yaml new file mode 100644 index 0000000..74cad65 --- /dev/null +++ b/Published/Mitra2019/11-TLBR/metadata.yaml @@ -0,0 +1,19 @@ +id: 11_TLBR_tlbr +name: 11-TLBR +description: BNGL model: tlbr +tags: ["alpha", "molecules", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/12-TCR/metadata.yaml b/Published/Mitra2019/12-TCR/metadata.yaml new file mode 100644 index 0000000..f012f6e --- /dev/null +++ b/Published/Mitra2019/12-TCR/metadata.yaml @@ -0,0 +1,19 @@ +id: 12_TCR_tcr +name: of T cell receptor signaling +description: A model of T cell receptor signaling +tags: ["immunology"] +category: immunology +compatibility: + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/13-receptor/metadata.yaml b/Published/Mitra2019/13-receptor/metadata.yaml new file mode 100644 index 0000000..7876568 --- /dev/null +++ b/Published/Mitra2019/13-receptor/metadata.yaml @@ -0,0 +1,19 @@ +id: 13_receptor_example5_starting_point +name: 13-receptor +description: A simple model +tags: ["ligand_ispresent", "molecules", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/14-receptor-nf/metadata.yaml b/Published/Mitra2019/14-receptor-nf/metadata.yaml new file mode 100644 index 0000000..453cb28 --- /dev/null +++ b/Published/Mitra2019/14-receptor-nf/metadata.yaml @@ -0,0 +1,19 @@ +id: 14_receptor_nf_receptor_nf +name: of ligand/receptor binding and receptor phosphorylation. +description: A simple model of ligand/receptor binding and receptor phosphorylation. +tags: ["molecules", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/15-igf1r/metadata.yaml b/Published/Mitra2019/15-igf1r/metadata.yaml new file mode 100644 index 0000000..eaa977d --- /dev/null +++ b/Published/Mitra2019/15-igf1r/metadata.yaml @@ -0,0 +1,19 @@ +id: 15_igf1r_IGF1R_fit_all +name: 15-igf1r +description: Author: William S. Hlavacek +tags: ["dilution", "a1_permpers", "a2_permpers", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/17-egfr-ssa/metadata.yaml b/Published/Mitra2019/17-egfr-ssa/metadata.yaml new file mode 100644 index 0000000..ea3c02a --- /dev/null +++ b/Published/Mitra2019/17-egfr-ssa/metadata.yaml @@ -0,0 +1,19 @@ +id: 17_egfr_ssa_egfr +name: 17-egfr-ssa +description: EGFR model +tags: ["signaling"] +category: signaling +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/18-mapk/metadata.yaml b/Published/Mitra2019/18-mapk/metadata.yaml new file mode 100644 index 0000000..c0360c8 --- /dev/null +++ b/Published/Mitra2019/18-mapk/metadata.yaml @@ -0,0 +1,19 @@ +id: 18_mapk_Scaff_22_ground +name: 18-mapk +description: For "ground truth" model, use median values such that hierarchy H1 occurs, as shown in Table 3. +tags: ["signaling"] +category: signaling +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/19-raf-constraint/metadata.yaml b/Published/Mitra2019/19-raf-constraint/metadata.yaml new file mode 100644 index 0000000..6899a68 --- /dev/null +++ b/Published/Mitra2019/19-raf-constraint/metadata.yaml @@ -0,0 +1,19 @@ +id: 19_raf_constraint_RAFi +name: 19-raf-constraint +description: BNGL model: RAFi +tags: ["k1", "k2", "k3", "k5", "kf1", "kf2", "kf3", "kf4", "kf5", "kf6", "rtot", "ifree", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/20-raf-constraint4/metadata.yaml b/Published/Mitra2019/20-raf-constraint4/metadata.yaml new file mode 100644 index 0000000..27072fe --- /dev/null +++ b/Published/Mitra2019/20-raf-constraint4/metadata.yaml @@ -0,0 +1,19 @@ +id: 20_raf_constraint4_RAFi +name: 20-raf-constraint4 +description: BNGL model: RAFi +tags: ["k1", "k2", "k3", "k5", "kf1", "kf2", "kf3", "kf4", "kf5", "kf6", "rtot", "ifree", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/24-jnk/metadata.yaml b/Published/Mitra2019/24-jnk/metadata.yaml new file mode 100644 index 0000000..f2c51fc --- /dev/null +++ b/Published/Mitra2019/24-jnk/metadata.yaml @@ -0,0 +1,19 @@ +id: 24_jnk_JNKmodel_180724_bnf +name: 24-jnk +description: BNGL model: JNKmodel_180724_bnf +tags: ["scale_t", "ani", "k3_zakbyu1", "k1_u1tozak", "d3_zak", "d1_zak", "k3_mkk4byzak", "k1_zaktomkk4", "d3_mkk4", "d1_mkk4", "k3_mkk7byzak", "k1_zaktomkk7", "f3_mkk7byzak", "d3_mkk7", "d1_mkk7", "k3_jnkbymkk4", "k1_mkk4tojnk", "k3_jnkbymkk7", "k1_mkk7tojnk", "f3_jnkbymkk7", "d3_jnk", "d1_jnk", "k3_mkk7byjnk", "k1_jnktomkk7", "inh_jnk", "d3_mkk7byjnkpt", "d1_jnkpttomkk7", "f1_zaktomkk7p", "k1_zaktojnk", "k3_mkk4byakt", "k1_akttomkk4", "k3_mkk7byakt", "k1_akttomkk7", "d3_mkk4byaktpt", "d1_aktpttomkk4", "d3_mkk7byaktpt", "d1_aktpttomkk7", "scale_ppmkk4", "scale_ppmkk7", "scale_ppjnk", "pakt", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/26-tcr-sens/metadata.yaml b/Published/Mitra2019/26-tcr-sens/metadata.yaml new file mode 100644 index 0000000..f3c37ff --- /dev/null +++ b/Published/Mitra2019/26-tcr-sens/metadata.yaml @@ -0,0 +1,19 @@ +id: 26_tcr_sens_tcr_sens_tofit +name: for the Manz/Groves 2011 data +description: Modification of Mukhopadhyay/Dushek 2013 model for the Manz/Groves 2011 data +tags: ["immunology"] +category: immunology +compatibility: + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/28-mapk/metadata.yaml b/Published/Mitra2019/28-mapk/metadata.yaml new file mode 100644 index 0000000..51c8c28 --- /dev/null +++ b/Published/Mitra2019/28-mapk/metadata.yaml @@ -0,0 +1,19 @@ +id: 28_mapk_ensemble_tofit +name: translated into BNGL +description: Ensemble model translated into BNGL +tags: ["signaling"] +category: signaling +compatibility: + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/30-jobs/metadata.yaml b/Published/Mitra2019/30-jobs/metadata.yaml new file mode 100644 index 0000000..c923871 --- /dev/null +++ b/Published/Mitra2019/30-jobs/metadata.yaml @@ -0,0 +1,19 @@ +id: 30_jobs_jobs_ground +name: 30-jobs +description: NFsim simulation of the job market +tags: ["other"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Mitra2019/31-elephant/metadata.yaml b/Published/Mitra2019/31-elephant/metadata.yaml new file mode 100644 index 0000000..69006b1 --- /dev/null +++ b/Published/Mitra2019/31-elephant/metadata.yaml @@ -0,0 +1,19 @@ +id: 31_elephant_elephant +name: 31-elephant +description: BNGL model: elephant +tags: ["a0", "a1", "a2", "a3", "a4", "a5", "a6", "a7", "a8", "a9", "a10", "a11", "a12", "a13", "a14", "a15", "a16", "a17", "a18", "a19", "a20", "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17", "b18", "b19", "b20", "c0", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "c8", "c9", "c10", "c11", "c12", "c13", "c14", "c15", "c16", "c17", "c18", "c19", "c20", "d1", "d2", "d3", "d4", "d5", "d6", "d7", "d8", "d9", "d10", "d11", "d12", "d13", "d14", "d15", "d16", "d17", "d18", "d19", "d20", "tmax", "t", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Likelihood/README.md b/Published/Mitra2019Likelihood/README.md similarity index 100% rename from Contributed/Mitra2019Likelihood/README.md rename to Published/Mitra2019Likelihood/README.md diff --git a/Published/Mitra2019Likelihood/metadata.yaml b/Published/Mitra2019Likelihood/metadata.yaml new file mode 100644 index 0000000..f36e183 --- /dev/null +++ b/Published/Mitra2019Likelihood/metadata.yaml @@ -0,0 +1,67 @@ +id: model_ground +name: model_ground.bngl +description: filename: model_ground.bngl +tags: + - x_tot__free + - k_xoff__free + - k_xon__free + - kase__free + - kdegx__free + - kdegran__free + - km_ship1__free + - km_syk__free + - km_x__free + - koff__free + - kp_ship1__free + - kp_syk__free + - kp_x__free + - kpten__free + - ksynth1__free + - pase__free + - f + - na + - t + - vchannel + - nchannel + - vcyt + - ag_tot_0 + - ag_conc1 + - r_tot + - syk_tot + - ship1_tot + - kon + - koff + - kase + - pase + - kp_syk + - km_syk + - kp_ship1 + - km_ship1 + - ksynth1 + - kdeg1 + - kpten + - h_tot + - kdegran + - kdegx + - k_xon + - k_xoff + - kp_x + - km_x + - molecules +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: + - ode + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: + [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Likelihood/model_ground.bngl b/Published/Mitra2019Likelihood/model_ground.bngl similarity index 100% rename from Contributed/Mitra2019Likelihood/model_ground.bngl rename to Published/Mitra2019Likelihood/model_ground.bngl diff --git a/Contributed/Mitra2019Likelihood/problem16/degran-pt.conf b/Published/Mitra2019Likelihood/problem16/degran-pt.conf similarity index 100% rename from Contributed/Mitra2019Likelihood/problem16/degran-pt.conf rename to Published/Mitra2019Likelihood/problem16/degran-pt.conf diff --git a/Published/Mitra2019Likelihood/problem16/metadata.yaml b/Published/Mitra2019Likelihood/problem16/metadata.yaml new file mode 100644 index 0000000..e65d938 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem16/metadata.yaml @@ -0,0 +1,19 @@ +id: problem16_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Likelihood/problem16/model0_tofit.bngl b/Published/Mitra2019Likelihood/problem16/model0_tofit.bngl similarity index 100% rename from Contributed/Mitra2019Likelihood/problem16/model0_tofit.bngl rename to Published/Mitra2019Likelihood/problem16/model0_tofit.bngl diff --git a/Contributed/Mitra2019Likelihood/problem16/p1_5.prop b/Published/Mitra2019Likelihood/problem16/p1_5.prop similarity index 100% rename from Contributed/Mitra2019Likelihood/problem16/p1_5.prop rename to Published/Mitra2019Likelihood/problem16/p1_5.prop diff --git a/Contributed/Mitra2019Likelihood/problem16_3cat/degran-pt.conf b/Published/Mitra2019Likelihood/problem16_3cat/degran-pt.conf similarity index 100% rename from Contributed/Mitra2019Likelihood/problem16_3cat/degran-pt.conf rename to Published/Mitra2019Likelihood/problem16_3cat/degran-pt.conf diff --git a/Published/Mitra2019Likelihood/problem16_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem16_3cat/metadata.yaml new file mode 100644 index 0000000..0b33b20 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem16_3cat/metadata.yaml @@ -0,0 +1,19 @@ +id: problem16_3cat_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Likelihood/problem16_3cat/model0_tofit.bngl b/Published/Mitra2019Likelihood/problem16_3cat/model0_tofit.bngl similarity index 100% rename from Contributed/Mitra2019Likelihood/problem16_3cat/model0_tofit.bngl rename to Published/Mitra2019Likelihood/problem16_3cat/model0_tofit.bngl diff --git a/Contributed/Mitra2019Likelihood/problem16_3cat/p1_5.prop b/Published/Mitra2019Likelihood/problem16_3cat/p1_5.prop similarity index 100% rename from Contributed/Mitra2019Likelihood/problem16_3cat/p1_5.prop rename to Published/Mitra2019Likelihood/problem16_3cat/p1_5.prop diff --git a/Contributed/Mitra2019Likelihood/problem32/degran-pt.conf b/Published/Mitra2019Likelihood/problem32/degran-pt.conf similarity index 100% rename from Contributed/Mitra2019Likelihood/problem32/degran-pt.conf rename to Published/Mitra2019Likelihood/problem32/degran-pt.conf diff --git a/Published/Mitra2019Likelihood/problem32/metadata.yaml b/Published/Mitra2019Likelihood/problem32/metadata.yaml new file mode 100644 index 0000000..1014c66 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem32/metadata.yaml @@ -0,0 +1,19 @@ +id: problem32_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Likelihood/problem32/model0_tofit.bngl b/Published/Mitra2019Likelihood/problem32/model0_tofit.bngl similarity index 100% rename from Contributed/Mitra2019Likelihood/problem32/model0_tofit.bngl rename to Published/Mitra2019Likelihood/problem32/model0_tofit.bngl diff --git a/Contributed/Mitra2019Likelihood/problem32/p1_5.prop b/Published/Mitra2019Likelihood/problem32/p1_5.prop similarity index 100% rename from Contributed/Mitra2019Likelihood/problem32/p1_5.prop rename to Published/Mitra2019Likelihood/problem32/p1_5.prop diff --git a/Contributed/Mitra2019Likelihood/problem32_3cat/degran-pt.conf b/Published/Mitra2019Likelihood/problem32_3cat/degran-pt.conf similarity index 100% rename from Contributed/Mitra2019Likelihood/problem32_3cat/degran-pt.conf rename to Published/Mitra2019Likelihood/problem32_3cat/degran-pt.conf diff --git a/Published/Mitra2019Likelihood/problem32_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem32_3cat/metadata.yaml new file mode 100644 index 0000000..a4aab66 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem32_3cat/metadata.yaml @@ -0,0 +1,19 @@ +id: problem32_3cat_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Likelihood/problem32_3cat/model0_tofit.bngl b/Published/Mitra2019Likelihood/problem32_3cat/model0_tofit.bngl similarity index 100% rename from Contributed/Mitra2019Likelihood/problem32_3cat/model0_tofit.bngl rename to Published/Mitra2019Likelihood/problem32_3cat/model0_tofit.bngl diff --git a/Contributed/Mitra2019Likelihood/problem32_3cat/p1_5.prop b/Published/Mitra2019Likelihood/problem32_3cat/p1_5.prop similarity index 100% rename from Contributed/Mitra2019Likelihood/problem32_3cat/p1_5.prop rename to Published/Mitra2019Likelihood/problem32_3cat/p1_5.prop diff --git a/Contributed/Mitra2019Likelihood/problem4/degran-pt.conf b/Published/Mitra2019Likelihood/problem4/degran-pt.conf similarity index 100% rename from Contributed/Mitra2019Likelihood/problem4/degran-pt.conf rename to Published/Mitra2019Likelihood/problem4/degran-pt.conf diff --git a/Published/Mitra2019Likelihood/problem4/metadata.yaml b/Published/Mitra2019Likelihood/problem4/metadata.yaml new file mode 100644 index 0000000..ed346e4 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem4/metadata.yaml @@ -0,0 +1,19 @@ +id: problem4_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Likelihood/problem4/model0_tofit.bngl b/Published/Mitra2019Likelihood/problem4/model0_tofit.bngl similarity index 100% rename from Contributed/Mitra2019Likelihood/problem4/model0_tofit.bngl rename to Published/Mitra2019Likelihood/problem4/model0_tofit.bngl diff --git a/Contributed/Mitra2019Likelihood/problem4/p1_5.prop b/Published/Mitra2019Likelihood/problem4/p1_5.prop similarity index 100% rename from Contributed/Mitra2019Likelihood/problem4/p1_5.prop rename to Published/Mitra2019Likelihood/problem4/p1_5.prop diff --git a/Contributed/Mitra2019Likelihood/problem4_3cat/degran-pt.conf b/Published/Mitra2019Likelihood/problem4_3cat/degran-pt.conf similarity index 100% rename from Contributed/Mitra2019Likelihood/problem4_3cat/degran-pt.conf rename to Published/Mitra2019Likelihood/problem4_3cat/degran-pt.conf diff --git a/Published/Mitra2019Likelihood/problem4_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem4_3cat/metadata.yaml new file mode 100644 index 0000000..87229b8 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem4_3cat/metadata.yaml @@ -0,0 +1,19 @@ +id: problem4_3cat_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Likelihood/problem4_3cat/model0_tofit.bngl b/Published/Mitra2019Likelihood/problem4_3cat/model0_tofit.bngl similarity index 100% rename from Contributed/Mitra2019Likelihood/problem4_3cat/model0_tofit.bngl rename to Published/Mitra2019Likelihood/problem4_3cat/model0_tofit.bngl diff --git a/Contributed/Mitra2019Likelihood/problem4_3cat/p1_5.prop b/Published/Mitra2019Likelihood/problem4_3cat/p1_5.prop similarity index 100% rename from Contributed/Mitra2019Likelihood/problem4_3cat/p1_5.prop rename to Published/Mitra2019Likelihood/problem4_3cat/p1_5.prop diff --git a/Contributed/Mitra2019Likelihood/problem64/degran-pt.conf b/Published/Mitra2019Likelihood/problem64/degran-pt.conf similarity index 100% rename from Contributed/Mitra2019Likelihood/problem64/degran-pt.conf rename to Published/Mitra2019Likelihood/problem64/degran-pt.conf diff --git a/Published/Mitra2019Likelihood/problem64/metadata.yaml b/Published/Mitra2019Likelihood/problem64/metadata.yaml new file mode 100644 index 0000000..ecab0a2 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem64/metadata.yaml @@ -0,0 +1,19 @@ +id: problem64_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Likelihood/problem64/model0_tofit.bngl b/Published/Mitra2019Likelihood/problem64/model0_tofit.bngl similarity index 100% rename from Contributed/Mitra2019Likelihood/problem64/model0_tofit.bngl rename to Published/Mitra2019Likelihood/problem64/model0_tofit.bngl diff --git a/Contributed/Mitra2019Likelihood/problem64/p1_5.prop b/Published/Mitra2019Likelihood/problem64/p1_5.prop similarity index 100% rename from Contributed/Mitra2019Likelihood/problem64/p1_5.prop rename to Published/Mitra2019Likelihood/problem64/p1_5.prop diff --git a/Contributed/Mitra2019Likelihood/problem64_3cat/degran-pt.conf b/Published/Mitra2019Likelihood/problem64_3cat/degran-pt.conf similarity index 100% rename from Contributed/Mitra2019Likelihood/problem64_3cat/degran-pt.conf rename to Published/Mitra2019Likelihood/problem64_3cat/degran-pt.conf diff --git a/Published/Mitra2019Likelihood/problem64_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem64_3cat/metadata.yaml new file mode 100644 index 0000000..4a27752 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem64_3cat/metadata.yaml @@ -0,0 +1,19 @@ +id: problem64_3cat_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Likelihood/problem64_3cat/model0_tofit.bngl b/Published/Mitra2019Likelihood/problem64_3cat/model0_tofit.bngl similarity index 100% rename from Contributed/Mitra2019Likelihood/problem64_3cat/model0_tofit.bngl rename to Published/Mitra2019Likelihood/problem64_3cat/model0_tofit.bngl diff --git a/Contributed/Mitra2019Likelihood/problem64_3cat/p1_5.prop b/Published/Mitra2019Likelihood/problem64_3cat/p1_5.prop similarity index 100% rename from Contributed/Mitra2019Likelihood/problem64_3cat/p1_5.prop rename to Published/Mitra2019Likelihood/problem64_3cat/p1_5.prop diff --git a/Contributed/Mitra2019Likelihood/problem8/degran-pt.conf b/Published/Mitra2019Likelihood/problem8/degran-pt.conf similarity index 100% rename from Contributed/Mitra2019Likelihood/problem8/degran-pt.conf rename to Published/Mitra2019Likelihood/problem8/degran-pt.conf diff --git a/Published/Mitra2019Likelihood/problem8/metadata.yaml b/Published/Mitra2019Likelihood/problem8/metadata.yaml new file mode 100644 index 0000000..49757c2 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem8/metadata.yaml @@ -0,0 +1,19 @@ +id: problem8_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Likelihood/problem8/model0_tofit.bngl b/Published/Mitra2019Likelihood/problem8/model0_tofit.bngl similarity index 100% rename from Contributed/Mitra2019Likelihood/problem8/model0_tofit.bngl rename to Published/Mitra2019Likelihood/problem8/model0_tofit.bngl diff --git a/Contributed/Mitra2019Likelihood/problem8/p1_5.prop b/Published/Mitra2019Likelihood/problem8/p1_5.prop similarity index 100% rename from Contributed/Mitra2019Likelihood/problem8/p1_5.prop rename to Published/Mitra2019Likelihood/problem8/p1_5.prop diff --git a/Contributed/Mitra2019Likelihood/problem8_3cat/degran-pt.conf b/Published/Mitra2019Likelihood/problem8_3cat/degran-pt.conf similarity index 100% rename from Contributed/Mitra2019Likelihood/problem8_3cat/degran-pt.conf rename to Published/Mitra2019Likelihood/problem8_3cat/degran-pt.conf diff --git a/Published/Mitra2019Likelihood/problem8_3cat/metadata.yaml b/Published/Mitra2019Likelihood/problem8_3cat/metadata.yaml new file mode 100644 index 0000000..93ac8bb --- /dev/null +++ b/Published/Mitra2019Likelihood/problem8_3cat/metadata.yaml @@ -0,0 +1,19 @@ +id: problem8_3cat_model0_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Likelihood/problem8_3cat/model0_tofit.bngl b/Published/Mitra2019Likelihood/problem8_3cat/model0_tofit.bngl similarity index 100% rename from Contributed/Mitra2019Likelihood/problem8_3cat/model0_tofit.bngl rename to Published/Mitra2019Likelihood/problem8_3cat/model0_tofit.bngl diff --git a/Contributed/Mitra2019Likelihood/problem8_3cat/p1_5.prop b/Published/Mitra2019Likelihood/problem8_3cat/p1_5.prop similarity index 100% rename from Contributed/Mitra2019Likelihood/problem8_3cat/p1_5.prop rename to Published/Mitra2019Likelihood/problem8_3cat/p1_5.prop diff --git a/Contributed/Mitra2019Likelihood/problem_quant/degran-pt.conf b/Published/Mitra2019Likelihood/problem_quant/degran-pt.conf similarity index 100% rename from Contributed/Mitra2019Likelihood/problem_quant/degran-pt.conf rename to Published/Mitra2019Likelihood/problem_quant/degran-pt.conf diff --git a/Published/Mitra2019Likelihood/problem_quant/metadata.yaml b/Published/Mitra2019Likelihood/problem_quant/metadata.yaml new file mode 100644 index 0000000..3d21f85 --- /dev/null +++ b/Published/Mitra2019Likelihood/problem_quant/metadata.yaml @@ -0,0 +1,19 @@ +id: problem_quant_model_tofit +name: model.bngl +description: filename: model.bngl +tags: ["f", "na", "t", "vchannel", "nchannel", "vcyt", "ag_tot_0", "ag_conc1", "r_tot", "syk_tot", "ship1_tot", "kon", "koff", "kase", "pase", "kp_syk", "km_syk", "kp_ship1", "km_ship1", "ksynth1", "kdeg1", "kpten", "h_tot", "kdegran", "kdegx", "k_xon", "k_xoff", "kp_x", "km_x", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Likelihood/problem_quant/model_tofit.bngl b/Published/Mitra2019Likelihood/problem_quant/model_tofit.bngl similarity index 100% rename from Contributed/Mitra2019Likelihood/problem_quant/model_tofit.bngl rename to Published/Mitra2019Likelihood/problem_quant/model_tofit.bngl diff --git a/Contributed/Mitra2019Likelihood/problem_quant/p1_5.exp b/Published/Mitra2019Likelihood/problem_quant/p1_5.exp similarity index 100% rename from Contributed/Mitra2019Likelihood/problem_quant/p1_5.exp rename to Published/Mitra2019Likelihood/problem_quant/p1_5.exp diff --git a/Contributed/Mitra2019Likelihood/problem_quant/p3_120.exp b/Published/Mitra2019Likelihood/problem_quant/p3_120.exp similarity index 100% rename from Contributed/Mitra2019Likelihood/problem_quant/p3_120.exp rename to Published/Mitra2019Likelihood/problem_quant/p3_120.exp diff --git a/Contributed/Mitra2019Likelihood/problem_quant/p3_240.exp b/Published/Mitra2019Likelihood/problem_quant/p3_240.exp similarity index 100% rename from Contributed/Mitra2019Likelihood/problem_quant/p3_240.exp rename to Published/Mitra2019Likelihood/problem_quant/p3_240.exp diff --git a/Contributed/Mitra2019Likelihood/problem_quant/p3_30.exp b/Published/Mitra2019Likelihood/problem_quant/p3_30.exp similarity index 100% rename from Contributed/Mitra2019Likelihood/problem_quant/p3_30.exp rename to Published/Mitra2019Likelihood/problem_quant/p3_30.exp diff --git a/Contributed/Mitra2019Likelihood/problem_quant/p3_5.exp b/Published/Mitra2019Likelihood/problem_quant/p3_5.exp similarity index 100% rename from Contributed/Mitra2019Likelihood/problem_quant/p3_5.exp rename to Published/Mitra2019Likelihood/problem_quant/p3_5.exp diff --git a/Contributed/Mitra2019Likelihood/problem_quant/p3_60.exp b/Published/Mitra2019Likelihood/problem_quant/p3_60.exp similarity index 100% rename from Contributed/Mitra2019Likelihood/problem_quant/p3_60.exp rename to Published/Mitra2019Likelihood/problem_quant/p3_60.exp diff --git a/Contributed/Mitra2019Rab/README.md b/Published/Mitra2019Rab/README.md similarity index 100% rename from Contributed/Mitra2019Rab/README.md rename to Published/Mitra2019Rab/README.md diff --git a/Published/Mitra2019Rab/metadata.yaml b/Published/Mitra2019Rab/metadata.yaml new file mode 100644 index 0000000..f9a4af3 --- /dev/null +++ b/Published/Mitra2019Rab/metadata.yaml @@ -0,0 +1,72 @@ +id: rab_mon1ccz1_ox +name: rab_mon1ccz1_ox.bngl +description: filename:rab_mon1ccz1_ox.bngl +tags: + - kd_rabgef1__free + - d_hill__free + - d_threshold__free + - k_deg__free + - k_dephos__free + - k_deub__free + - k_extract__free + - k_insert__free + - k_recyc__free + - k_synth__free + - k_to_endo__free + - kcat_rab5__free + - kcat_rab7__free + - kf_rab5_mon1__free + - kf_rab5_rabep1__free + - kf_ptyr_sh2__free + - kr_kub_uim__free + - kr_rab5_mon1__free + - kr_rab5_rabep1__free + - kr_ptyr_sh2__free + - py_basal_coef__free + - py_half_coef__free + - py_hill_coef__free + - py_scale_coef__free + - r_hill__free + - r_threshold__free + - ub_basal_coef__free + - ub_half_coef__free + - ub_hill_coef__free + - ub_scale_coef__free + - rab5_expr + - rab7_expr + - mon1_expr + - ccz1_expr + - kf_mon1_ccz1 + - kr_mon1_ccz1 + - egf_conc_ngml + - ub_hill_coef + - ub_half_coef + - ub_basal_coef + - ub_scale_coef + - py_hill_coef + - py_half_coef + - py_basal_coef + - py_scale_coef + - gtp_to_gdp_ratio + - kcatgtp_rab5 + - k_gdp_gef_eff + - kcatgtp_rab7 + - molecules + - 0 +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: + - ode + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: + [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Rab/pybnf_files/data_highegf3.exp b/Published/Mitra2019Rab/pybnf_files/data_highegf3.exp similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/data_highegf3.exp rename to Published/Mitra2019Rab/pybnf_files/data_highegf3.exp diff --git a/Contributed/Mitra2019Rab/pybnf_files/data_highegf3_rab5_ox.exp b/Published/Mitra2019Rab/pybnf_files/data_highegf3_rab5_ox.exp similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/data_highegf3_rab5_ox.exp rename to Published/Mitra2019Rab/pybnf_files/data_highegf3_rab5_ox.exp diff --git a/Contributed/Mitra2019Rab/pybnf_files/data_highegf3_rab7_ox.exp b/Published/Mitra2019Rab/pybnf_files/data_highegf3_rab7_ox.exp similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/data_highegf3_rab7_ox.exp rename to Published/Mitra2019Rab/pybnf_files/data_highegf3_rab7_ox.exp diff --git a/Contributed/Mitra2019Rab/pybnf_files/data_lowegf2.exp b/Published/Mitra2019Rab/pybnf_files/data_lowegf2.exp similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/data_lowegf2.exp rename to Published/Mitra2019Rab/pybnf_files/data_lowegf2.exp diff --git a/Contributed/Mitra2019Rab/pybnf_files/data_lowegf2_mon1ccz1_ox.exp b/Published/Mitra2019Rab/pybnf_files/data_lowegf2_mon1ccz1_ox.exp similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/data_lowegf2_mon1ccz1_ox.exp rename to Published/Mitra2019Rab/pybnf_files/data_lowegf2_mon1ccz1_ox.exp diff --git a/Contributed/Mitra2019Rab/pybnf_files/data_lowegf2_rab5_ox.exp b/Published/Mitra2019Rab/pybnf_files/data_lowegf2_rab5_ox.exp similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/data_lowegf2_rab5_ox.exp rename to Published/Mitra2019Rab/pybnf_files/data_lowegf2_rab5_ox.exp diff --git a/Contributed/Mitra2019Rab/pybnf_files/data_lowegf2_rab7_ox.exp b/Published/Mitra2019Rab/pybnf_files/data_lowegf2_rab7_ox.exp similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/data_lowegf2_rab7_ox.exp rename to Published/Mitra2019Rab/pybnf_files/data_lowegf2_rab7_ox.exp diff --git a/Contributed/Mitra2019Rab/pybnf_files/egfr_ss_norm2.exp b/Published/Mitra2019Rab/pybnf_files/egfr_ss_norm2.exp similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/egfr_ss_norm2.exp rename to Published/Mitra2019Rab/pybnf_files/egfr_ss_norm2.exp diff --git a/Published/Mitra2019Rab/pybnf_files/metadata.yaml b/Published/Mitra2019Rab/pybnf_files/metadata.yaml new file mode 100644 index 0000000..036cae4 --- /dev/null +++ b/Published/Mitra2019Rab/pybnf_files/metadata.yaml @@ -0,0 +1,19 @@ +id: pybnf_files_rab_mon1ccz1_ox +name: rab_mon1ccz1_ox.bngl +description: filename:rab_mon1ccz1_ox.bngl +tags: ["rab5_expr", "rab7_expr", "mon1_expr", "ccz1_expr", "kf_mon1_ccz1", "kr_mon1_ccz1", "egf_conc_ngml", "ub_hill_coef", "ub_half_coef", "ub_basal_coef", "ub_scale_coef", "py_hill_coef", "py_half_coef", "py_basal_coef", "py_scale_coef", "gtp_to_gdp_ratio", "kcatgtp_rab5", "k_gdp_gef_eff", "kcatgtp_rab7", "molecules", "0"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Contributed/Mitra2019Rab/pybnf_files/rab.conf b/Published/Mitra2019Rab/pybnf_files/rab.conf similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/rab.conf rename to Published/Mitra2019Rab/pybnf_files/rab.conf diff --git a/Contributed/Mitra2019Rab/pybnf_files/rab_mon1ccz1_ox.bngl b/Published/Mitra2019Rab/pybnf_files/rab_mon1ccz1_ox.bngl similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/rab_mon1ccz1_ox.bngl rename to Published/Mitra2019Rab/pybnf_files/rab_mon1ccz1_ox.bngl diff --git a/Contributed/Mitra2019Rab/pybnf_files/rab_rab5_ox.bngl b/Published/Mitra2019Rab/pybnf_files/rab_rab5_ox.bngl similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/rab_rab5_ox.bngl rename to Published/Mitra2019Rab/pybnf_files/rab_rab5_ox.bngl diff --git a/Contributed/Mitra2019Rab/pybnf_files/rab_rab7_ox.bngl b/Published/Mitra2019Rab/pybnf_files/rab_rab7_ox.bngl similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/rab_rab7_ox.bngl rename to Published/Mitra2019Rab/pybnf_files/rab_rab7_ox.bngl diff --git a/Contributed/Mitra2019Rab/pybnf_files/rab_wt.bngl b/Published/Mitra2019Rab/pybnf_files/rab_wt.bngl similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/rab_wt.bngl rename to Published/Mitra2019Rab/pybnf_files/rab_wt.bngl diff --git a/Contributed/Mitra2019Rab/pybnf_files/transfer.exp b/Published/Mitra2019Rab/pybnf_files/transfer.exp similarity index 100% rename from Contributed/Mitra2019Rab/pybnf_files/transfer.exp rename to Published/Mitra2019Rab/pybnf_files/transfer.exp diff --git a/Contributed/Mitra2019Rab/rab_mon1ccz1_ox.bngl b/Published/Mitra2019Rab/rab_mon1ccz1_ox.bngl similarity index 100% rename from Contributed/Mitra2019Rab/rab_mon1ccz1_ox.bngl rename to Published/Mitra2019Rab/rab_mon1ccz1_ox.bngl diff --git a/Contributed/Mitra2019Rab/rab_rab5_ox.bngl b/Published/Mitra2019Rab/rab_rab5_ox.bngl similarity index 100% rename from Contributed/Mitra2019Rab/rab_rab5_ox.bngl rename to Published/Mitra2019Rab/rab_rab5_ox.bngl diff --git a/Contributed/Mitra2019Rab/rab_rab7_ox.bngl b/Published/Mitra2019Rab/rab_rab7_ox.bngl similarity index 100% rename from Contributed/Mitra2019Rab/rab_rab7_ox.bngl rename to Published/Mitra2019Rab/rab_rab7_ox.bngl diff --git a/Contributed/Mitra2019Rab/rab_wt.bngl b/Published/Mitra2019Rab/rab_wt.bngl similarity index 100% rename from Contributed/Mitra2019Rab/rab_wt.bngl rename to Published/Mitra2019Rab/rab_wt.bngl diff --git a/Published/ModelZAP/metadata.yaml b/Published/ModelZAP/metadata.yaml index 96c46ab..4b45d42 100644 --- a/Published/ModelZAP/metadata.yaml +++ b/Published/ModelZAP/metadata.yaml @@ -4,7 +4,7 @@ description: "ZAP-70 recruitment" tags: ["published", "immunology", "nfsim", "model", "zap", "kon", "a", "cbl", "cd16", "lck", "ligand", "zeta", "dead"] category: "immunology" compatibility: - bng2_compatible: false + bng2_compatible: true simulation_methods: ["nf"] uses_compartments: false uses_energy: false @@ -17,6 +17,6 @@ source: source_path: "published-models/immune-signaling/Model_ZAP.bngl" playground: visible: false - gallery_category: "immunology" + gallery_categories: ["immunology"] featured: false difficulty: "advanced" diff --git a/Published/Mukhopadhyay2013/metadata.yaml b/Published/Mukhopadhyay2013/metadata.yaml index 504df46..b2fbb7f 100644 --- a/Published/Mukhopadhyay2013/metadata.yaml +++ b/Published/Mukhopadhyay2013/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/immune-signaling/Mukhopadhyay_2013.bngl" playground: visible: false - gallery_category: "immunology" + gallery_categories: ["immunology"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_PublicRuntime/MyrtleBeachConwayNorthMyrtleBeachSCNC/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl b/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl similarity index 100% rename from Contributed/BNGPlayground_PublicRuntime/MyrtleBeachConwayNorthMyrtleBeachSCNC/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl rename to Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl diff --git a/Contributed/BNGPlayground_PublicRuntime/MyrtleBeachConwayNorthMyrtleBeachSCNC/README.md b/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/README.md similarity index 100% rename from Contributed/BNGPlayground_PublicRuntime/MyrtleBeachConwayNorthMyrtleBeachSCNC/README.md rename to Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/README.md diff --git a/Contributed/BNGPlayground_PublicRuntime/MyrtleBeachConwayNorthMyrtleBeachSCNC/metadata.yaml b/Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_PublicRuntime/MyrtleBeachConwayNorthMyrtleBeachSCNC/metadata.yaml rename to Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/metadata.yaml diff --git a/Published/Nag2009/metadata.yaml b/Published/Nag2009/metadata.yaml index f8c3f18..3c34784 100644 --- a/Published/Nag2009/metadata.yaml +++ b/Published/Nag2009/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Nag_2009.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer"] featured: false difficulty: "advanced" diff --git a/Published/Nosbisch2022/metadata.yaml b/Published/Nosbisch2022/metadata.yaml index ac2b240..0c755c1 100644 --- a/Published/Nosbisch2022/metadata.yaml +++ b/Published/Nosbisch2022/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Nosbisch_2022.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer"] featured: false difficulty: "advanced" diff --git a/Published/Ordyan2020/CaMKIIholo/metadata.yaml b/Published/Ordyan2020/CaMKIIholo/metadata.yaml index 138d472..dfcbd0d 100644 --- a/Published/Ordyan2020/CaMKIIholo/metadata.yaml +++ b/Published/Ordyan2020/CaMKIIholo/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/Ordyan_2020/CaMKII_holo.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: [] featured: false difficulty: "advanced" diff --git a/PyBioNetGen/HIVdynamics/pt303/README.md b/Published/PyBioNetGen/HIVdynamics/pt303/README.md similarity index 100% rename from PyBioNetGen/HIVdynamics/pt303/README.md rename to Published/PyBioNetGen/HIVdynamics/pt303/README.md diff --git a/PyBioNetGen/HIVdynamics/pt303/metadata.yaml b/Published/PyBioNetGen/HIVdynamics/pt303/metadata.yaml similarity index 100% rename from PyBioNetGen/HIVdynamics/pt303/metadata.yaml rename to Published/PyBioNetGen/HIVdynamics/pt303/metadata.yaml diff --git a/PyBioNetGen/HIVdynamics/pt303/pt303.bngl b/Published/PyBioNetGen/HIVdynamics/pt303/pt303.bngl similarity index 100% rename from PyBioNetGen/HIVdynamics/pt303/pt303.bngl rename to Published/PyBioNetGen/HIVdynamics/pt303/pt303.bngl diff --git a/PyBioNetGen/HIVdynamics/pt403/README.md b/Published/PyBioNetGen/HIVdynamics/pt403/README.md similarity index 100% rename from PyBioNetGen/HIVdynamics/pt403/README.md rename to Published/PyBioNetGen/HIVdynamics/pt403/README.md diff --git a/PyBioNetGen/HIVdynamics/pt403/metadata.yaml b/Published/PyBioNetGen/HIVdynamics/pt403/metadata.yaml similarity index 100% rename from PyBioNetGen/HIVdynamics/pt403/metadata.yaml rename to Published/PyBioNetGen/HIVdynamics/pt403/metadata.yaml diff --git a/PyBioNetGen/HIVdynamics/pt403/pt403.bngl b/Published/PyBioNetGen/HIVdynamics/pt403/pt403.bngl similarity index 100% rename from PyBioNetGen/HIVdynamics/pt403/pt403.bngl rename to Published/PyBioNetGen/HIVdynamics/pt403/pt403.bngl diff --git a/PyBioNetGen/HIVdynamics/pt409/README.md b/Published/PyBioNetGen/HIVdynamics/pt409/README.md similarity index 100% rename from PyBioNetGen/HIVdynamics/pt409/README.md rename to Published/PyBioNetGen/HIVdynamics/pt409/README.md diff --git a/PyBioNetGen/HIVdynamics/pt409/metadata.yaml b/Published/PyBioNetGen/HIVdynamics/pt409/metadata.yaml similarity index 100% rename from PyBioNetGen/HIVdynamics/pt409/metadata.yaml rename to Published/PyBioNetGen/HIVdynamics/pt409/metadata.yaml diff --git a/PyBioNetGen/HIVdynamics/pt409/pt409.bngl b/Published/PyBioNetGen/HIVdynamics/pt409/pt409.bngl similarity index 100% rename from PyBioNetGen/HIVdynamics/pt409/pt409.bngl rename to Published/PyBioNetGen/HIVdynamics/pt409/pt409.bngl diff --git a/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/IGF1R_Model_receptor_activation_bnf.bngl b/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/IGF1R_Model_receptor_activation_bnf.bngl similarity index 100% rename from PyBioNetGen/core/IGF1RModelreceptoractivationbnf/IGF1R_Model_receptor_activation_bnf.bngl rename to Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/IGF1R_Model_receptor_activation_bnf.bngl diff --git a/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/README.md b/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/README.md similarity index 100% rename from PyBioNetGen/core/IGF1RModelreceptoractivationbnf/README.md rename to Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/README.md diff --git a/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/metadata.yaml b/Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/metadata.yaml similarity index 100% rename from PyBioNetGen/core/IGF1RModelreceptoractivationbnf/metadata.yaml rename to Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/metadata.yaml diff --git a/PyBioNetGen/core/RAFi/RAFi.bngl b/Published/PyBioNetGen/core/RAFi/RAFi.bngl similarity index 100% rename from PyBioNetGen/core/RAFi/RAFi.bngl rename to Published/PyBioNetGen/core/RAFi/RAFi.bngl diff --git a/PyBioNetGen/core/RAFi/README.md b/Published/PyBioNetGen/core/RAFi/README.md similarity index 100% rename from PyBioNetGen/core/RAFi/README.md rename to Published/PyBioNetGen/core/RAFi/README.md diff --git a/PyBioNetGen/core/RAFi/metadata.yaml b/Published/PyBioNetGen/core/RAFi/metadata.yaml similarity index 100% rename from PyBioNetGen/core/RAFi/metadata.yaml rename to Published/PyBioNetGen/core/RAFi/metadata.yaml diff --git a/PyBioNetGen/core/RAFiground/RAFi_ground.bngl b/Published/PyBioNetGen/core/RAFiground/RAFi_ground.bngl similarity index 100% rename from PyBioNetGen/core/RAFiground/RAFi_ground.bngl rename to Published/PyBioNetGen/core/RAFiground/RAFi_ground.bngl diff --git a/PyBioNetGen/core/RAFiground/README.md b/Published/PyBioNetGen/core/RAFiground/README.md similarity index 100% rename from PyBioNetGen/core/RAFiground/README.md rename to Published/PyBioNetGen/core/RAFiground/README.md diff --git a/PyBioNetGen/core/RAFiground/metadata.yaml b/Published/PyBioNetGen/core/RAFiground/metadata.yaml similarity index 100% rename from PyBioNetGen/core/RAFiground/metadata.yaml rename to Published/PyBioNetGen/core/RAFiground/metadata.yaml diff --git a/PyBioNetGen/core/degranulationmodel/README.md b/Published/PyBioNetGen/core/degranulationmodel/README.md similarity index 100% rename from PyBioNetGen/core/degranulationmodel/README.md rename to Published/PyBioNetGen/core/degranulationmodel/README.md diff --git a/PyBioNetGen/core/degranulationmodel/degranulation_model.bngl b/Published/PyBioNetGen/core/degranulationmodel/degranulation_model.bngl similarity index 100% rename from PyBioNetGen/core/degranulationmodel/degranulation_model.bngl rename to Published/PyBioNetGen/core/degranulationmodel/degranulation_model.bngl diff --git a/PyBioNetGen/core/degranulationmodel/metadata.yaml b/Published/PyBioNetGen/core/degranulationmodel/metadata.yaml similarity index 94% rename from PyBioNetGen/core/degranulationmodel/metadata.yaml rename to Published/PyBioNetGen/core/degranulationmodel/metadata.yaml index ebae83b..6b5f68d 100644 --- a/PyBioNetGen/core/degranulationmodel/metadata.yaml +++ b/Published/PyBioNetGen/core/degranulationmodel/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/PyBNG/degranulation_model.bngl" playground: visible: true - gallery_category: "other" + gallery_categories: ["immunology"] featured: false difficulty: "intermediate" diff --git a/PyBioNetGen/core/egfr/README.md b/Published/PyBioNetGen/core/egfr/README.md similarity index 100% rename from PyBioNetGen/core/egfr/README.md rename to Published/PyBioNetGen/core/egfr/README.md diff --git a/PyBioNetGen/core/egfr/egfr.bngl b/Published/PyBioNetGen/core/egfr/egfr.bngl similarity index 100% rename from PyBioNetGen/core/egfr/egfr.bngl rename to Published/PyBioNetGen/core/egfr/egfr.bngl diff --git a/PyBioNetGen/core/egfr/metadata.yaml b/Published/PyBioNetGen/core/egfr/metadata.yaml similarity index 100% rename from PyBioNetGen/core/egfr/metadata.yaml rename to Published/PyBioNetGen/core/egfr/metadata.yaml diff --git a/PyBioNetGen/core/egfrground/README.md b/Published/PyBioNetGen/core/egfrground/README.md similarity index 100% rename from PyBioNetGen/core/egfrground/README.md rename to Published/PyBioNetGen/core/egfrground/README.md diff --git a/PyBioNetGen/core/egfrground/egfr_ground.bngl b/Published/PyBioNetGen/core/egfrground/egfr_ground.bngl similarity index 100% rename from PyBioNetGen/core/egfrground/egfr_ground.bngl rename to Published/PyBioNetGen/core/egfrground/egfr_ground.bngl diff --git a/PyBioNetGen/core/egfrground/metadata.yaml b/Published/PyBioNetGen/core/egfrground/metadata.yaml similarity index 100% rename from PyBioNetGen/core/egfrground/metadata.yaml rename to Published/PyBioNetGen/core/egfrground/metadata.yaml diff --git a/PyBioNetGen/core/egfrnf/README.md b/Published/PyBioNetGen/core/egfrnf/README.md similarity index 100% rename from PyBioNetGen/core/egfrnf/README.md rename to Published/PyBioNetGen/core/egfrnf/README.md diff --git a/PyBioNetGen/core/egfrnf/egfr_nf.bngl b/Published/PyBioNetGen/core/egfrnf/egfr_nf.bngl similarity index 100% rename from PyBioNetGen/core/egfrnf/egfr_nf.bngl rename to Published/PyBioNetGen/core/egfrnf/egfr_nf.bngl diff --git a/PyBioNetGen/core/egfrnf/metadata.yaml b/Published/PyBioNetGen/core/egfrnf/metadata.yaml similarity index 100% rename from PyBioNetGen/core/egfrnf/metadata.yaml rename to Published/PyBioNetGen/core/egfrnf/metadata.yaml diff --git a/PyBioNetGen/core/egfrode/README.md b/Published/PyBioNetGen/core/egfrode/README.md similarity index 100% rename from PyBioNetGen/core/egfrode/README.md rename to Published/PyBioNetGen/core/egfrode/README.md diff --git a/PyBioNetGen/core/egfrode/egfr_ode.bngl b/Published/PyBioNetGen/core/egfrode/egfr_ode.bngl similarity index 100% rename from PyBioNetGen/core/egfrode/egfr_ode.bngl rename to Published/PyBioNetGen/core/egfrode/egfr_ode.bngl diff --git a/PyBioNetGen/core/egfrode/metadata.yaml b/Published/PyBioNetGen/core/egfrode/metadata.yaml similarity index 94% rename from PyBioNetGen/core/egfrode/metadata.yaml rename to Published/PyBioNetGen/core/egfrode/metadata.yaml index 33962a5..f2096c0 100644 --- a/PyBioNetGen/core/egfrode/metadata.yaml +++ b/Published/PyBioNetGen/core/egfrode/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/PyBNG/egfr_ode/egfr_ode.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["cancer"] featured: false difficulty: "advanced" diff --git a/PyBioNetGen/core/egfrode_published-models_PyBNG/README.md b/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/README.md similarity index 100% rename from PyBioNetGen/core/egfrode_published-models_PyBNG/README.md rename to Published/PyBioNetGen/core/egfrode_published-models_PyBNG/README.md diff --git a/PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode.bngl b/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode.bngl similarity index 100% rename from PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode.bngl rename to Published/PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode.bngl diff --git a/PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml b/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml similarity index 94% rename from PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml rename to Published/PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml index 94925b9..f8c53c9 100644 --- a/PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml +++ b/Published/PyBioNetGen/core/egfrode_published-models_PyBNG/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/PyBNG/egfr_ode.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["cancer"] featured: false difficulty: "advanced" diff --git a/PyBioNetGen/core/example1/README.md b/Published/PyBioNetGen/core/example1/README.md similarity index 100% rename from PyBioNetGen/core/example1/README.md rename to Published/PyBioNetGen/core/example1/README.md diff --git a/PyBioNetGen/core/example1/example1.bngl b/Published/PyBioNetGen/core/example1/example1.bngl similarity index 100% rename from PyBioNetGen/core/example1/example1.bngl rename to Published/PyBioNetGen/core/example1/example1.bngl diff --git a/PyBioNetGen/core/example1/metadata.yaml b/Published/PyBioNetGen/core/example1/metadata.yaml similarity index 100% rename from PyBioNetGen/core/example1/metadata.yaml rename to Published/PyBioNetGen/core/example1/metadata.yaml diff --git a/PyBioNetGen/core/example2startingpoint/README.md b/Published/PyBioNetGen/core/example2startingpoint/README.md similarity index 100% rename from PyBioNetGen/core/example2startingpoint/README.md rename to Published/PyBioNetGen/core/example2startingpoint/README.md diff --git a/PyBioNetGen/core/example2startingpoint/example2_starting_point.bngl b/Published/PyBioNetGen/core/example2startingpoint/example2_starting_point.bngl similarity index 100% rename from PyBioNetGen/core/example2startingpoint/example2_starting_point.bngl rename to Published/PyBioNetGen/core/example2startingpoint/example2_starting_point.bngl diff --git a/PyBioNetGen/core/example2startingpoint/metadata.yaml b/Published/PyBioNetGen/core/example2startingpoint/metadata.yaml similarity index 100% rename from PyBioNetGen/core/example2startingpoint/metadata.yaml rename to Published/PyBioNetGen/core/example2startingpoint/metadata.yaml diff --git a/PyBioNetGen/core/fcerigamma2/README.md b/Published/PyBioNetGen/core/fcerigamma2/README.md similarity index 100% rename from PyBioNetGen/core/fcerigamma2/README.md rename to Published/PyBioNetGen/core/fcerigamma2/README.md diff --git a/PyBioNetGen/core/fcerigamma2/fceri_gamma2.bngl b/Published/PyBioNetGen/core/fcerigamma2/fceri_gamma2.bngl similarity index 100% rename from PyBioNetGen/core/fcerigamma2/fceri_gamma2.bngl rename to Published/PyBioNetGen/core/fcerigamma2/fceri_gamma2.bngl diff --git a/PyBioNetGen/core/fcerigamma2/metadata.yaml b/Published/PyBioNetGen/core/fcerigamma2/metadata.yaml similarity index 95% rename from PyBioNetGen/core/fcerigamma2/metadata.yaml rename to Published/PyBioNetGen/core/fcerigamma2/metadata.yaml index 2f6e283..b53c12d 100644 --- a/PyBioNetGen/core/fcerigamma2/metadata.yaml +++ b/Published/PyBioNetGen/core/fcerigamma2/metadata.yaml @@ -9,7 +9,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "published" original_format: "bngl" diff --git a/PyBioNetGen/core/fcerigamma2groundtruth/README.md b/Published/PyBioNetGen/core/fcerigamma2groundtruth/README.md similarity index 100% rename from PyBioNetGen/core/fcerigamma2groundtruth/README.md rename to Published/PyBioNetGen/core/fcerigamma2groundtruth/README.md diff --git a/PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth.bngl b/Published/PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth.bngl similarity index 100% rename from PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth.bngl rename to Published/PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth.bngl diff --git a/PyBioNetGen/core/fcerigamma2groundtruth/metadata.yaml b/Published/PyBioNetGen/core/fcerigamma2groundtruth/metadata.yaml similarity index 100% rename from PyBioNetGen/core/fcerigamma2groundtruth/metadata.yaml rename to Published/PyBioNetGen/core/fcerigamma2groundtruth/metadata.yaml diff --git a/PyBioNetGen/core/model/README.md b/Published/PyBioNetGen/core/model/README.md similarity index 100% rename from PyBioNetGen/core/model/README.md rename to Published/PyBioNetGen/core/model/README.md diff --git a/PyBioNetGen/core/model/metadata.yaml b/Published/PyBioNetGen/core/model/metadata.yaml similarity index 100% rename from PyBioNetGen/core/model/metadata.yaml rename to Published/PyBioNetGen/core/model/metadata.yaml diff --git a/PyBioNetGen/core/model/model.bngl b/Published/PyBioNetGen/core/model/model.bngl similarity index 100% rename from PyBioNetGen/core/model/model.bngl rename to Published/PyBioNetGen/core/model/model.bngl diff --git a/PyBioNetGen/core/model_Degranulation_aMCMC/README.md b/Published/PyBioNetGen/core/model_Degranulation_aMCMC/README.md similarity index 100% rename from PyBioNetGen/core/model_Degranulation_aMCMC/README.md rename to Published/PyBioNetGen/core/model_Degranulation_aMCMC/README.md diff --git a/PyBioNetGen/core/model_Degranulation_aMCMC/metadata.yaml b/Published/PyBioNetGen/core/model_Degranulation_aMCMC/metadata.yaml similarity index 100% rename from PyBioNetGen/core/model_Degranulation_aMCMC/metadata.yaml rename to Published/PyBioNetGen/core/model_Degranulation_aMCMC/metadata.yaml diff --git a/PyBioNetGen/core/model_Degranulation_aMCMC/model.bngl b/Published/PyBioNetGen/core/model_Degranulation_aMCMC/model.bngl similarity index 100% rename from PyBioNetGen/core/model_Degranulation_aMCMC/model.bngl rename to Published/PyBioNetGen/core/model_Degranulation_aMCMC/model.bngl diff --git a/PyBioNetGen/core/modeltofit/README.md b/Published/PyBioNetGen/core/modeltofit/README.md similarity index 100% rename from PyBioNetGen/core/modeltofit/README.md rename to Published/PyBioNetGen/core/modeltofit/README.md diff --git a/PyBioNetGen/core/modeltofit/metadata.yaml b/Published/PyBioNetGen/core/modeltofit/metadata.yaml similarity index 100% rename from PyBioNetGen/core/modeltofit/metadata.yaml rename to Published/PyBioNetGen/core/modeltofit/metadata.yaml diff --git a/PyBioNetGen/core/modeltofit/model_tofit.bngl b/Published/PyBioNetGen/core/modeltofit/model_tofit.bngl similarity index 100% rename from PyBioNetGen/core/modeltofit/model_tofit.bngl rename to Published/PyBioNetGen/core/modeltofit/model_tofit.bngl diff --git a/PyBioNetGen/core/parabola/README.md b/Published/PyBioNetGen/core/parabola/README.md similarity index 100% rename from PyBioNetGen/core/parabola/README.md rename to Published/PyBioNetGen/core/parabola/README.md diff --git a/PyBioNetGen/core/parabola/metadata.yaml b/Published/PyBioNetGen/core/parabola/metadata.yaml similarity index 100% rename from PyBioNetGen/core/parabola/metadata.yaml rename to Published/PyBioNetGen/core/parabola/metadata.yaml diff --git a/PyBioNetGen/core/parabola/parabola.bngl b/Published/PyBioNetGen/core/parabola/parabola.bngl similarity index 100% rename from PyBioNetGen/core/parabola/parabola.bngl rename to Published/PyBioNetGen/core/parabola/parabola.bngl diff --git a/PyBioNetGen/core/parabola_demo/README.md b/Published/PyBioNetGen/core/parabola_demo/README.md similarity index 100% rename from PyBioNetGen/core/parabola_demo/README.md rename to Published/PyBioNetGen/core/parabola_demo/README.md diff --git a/PyBioNetGen/core/parabola_demo/metadata.yaml b/Published/PyBioNetGen/core/parabola_demo/metadata.yaml similarity index 100% rename from PyBioNetGen/core/parabola_demo/metadata.yaml rename to Published/PyBioNetGen/core/parabola_demo/metadata.yaml diff --git a/PyBioNetGen/core/parabola_demo/parabola.bngl b/Published/PyBioNetGen/core/parabola_demo/parabola.bngl similarity index 100% rename from PyBioNetGen/core/parabola_demo/parabola.bngl rename to Published/PyBioNetGen/core/parabola_demo/parabola.bngl diff --git a/PyBioNetGen/core/parabolaground/README.md b/Published/PyBioNetGen/core/parabolaground/README.md similarity index 100% rename from PyBioNetGen/core/parabolaground/README.md rename to Published/PyBioNetGen/core/parabolaground/README.md diff --git a/PyBioNetGen/core/parabolaground/metadata.yaml b/Published/PyBioNetGen/core/parabolaground/metadata.yaml similarity index 100% rename from PyBioNetGen/core/parabolaground/metadata.yaml rename to Published/PyBioNetGen/core/parabolaground/metadata.yaml diff --git a/PyBioNetGen/core/parabolaground/parabola_ground.bngl b/Published/PyBioNetGen/core/parabolaground/parabola_ground.bngl similarity index 100% rename from PyBioNetGen/core/parabolaground/parabola_ground.bngl rename to Published/PyBioNetGen/core/parabolaground/parabola_ground.bngl diff --git a/PyBioNetGen/core/polynomial/README.md b/Published/PyBioNetGen/core/polynomial/README.md similarity index 100% rename from PyBioNetGen/core/polynomial/README.md rename to Published/PyBioNetGen/core/polynomial/README.md diff --git a/PyBioNetGen/core/polynomial/metadata.yaml b/Published/PyBioNetGen/core/polynomial/metadata.yaml similarity index 100% rename from PyBioNetGen/core/polynomial/metadata.yaml rename to Published/PyBioNetGen/core/polynomial/metadata.yaml diff --git a/PyBioNetGen/core/polynomial/polynomial.bngl b/Published/PyBioNetGen/core/polynomial/polynomial.bngl similarity index 100% rename from PyBioNetGen/core/polynomial/polynomial.bngl rename to Published/PyBioNetGen/core/polynomial/polynomial.bngl diff --git a/PyBioNetGen/core/polynomialground/README.md b/Published/PyBioNetGen/core/polynomialground/README.md similarity index 100% rename from PyBioNetGen/core/polynomialground/README.md rename to Published/PyBioNetGen/core/polynomialground/README.md diff --git a/PyBioNetGen/core/polynomialground/metadata.yaml b/Published/PyBioNetGen/core/polynomialground/metadata.yaml similarity index 100% rename from PyBioNetGen/core/polynomialground/metadata.yaml rename to Published/PyBioNetGen/core/polynomialground/metadata.yaml diff --git a/PyBioNetGen/core/polynomialground/polynomial_ground.bngl b/Published/PyBioNetGen/core/polynomialground/polynomial_ground.bngl similarity index 100% rename from PyBioNetGen/core/polynomialground/polynomial_ground.bngl rename to Published/PyBioNetGen/core/polynomialground/polynomial_ground.bngl diff --git a/PyBioNetGen/core/receptor/README.md b/Published/PyBioNetGen/core/receptor/README.md similarity index 100% rename from PyBioNetGen/core/receptor/README.md rename to Published/PyBioNetGen/core/receptor/README.md diff --git a/PyBioNetGen/core/receptor/metadata.yaml b/Published/PyBioNetGen/core/receptor/metadata.yaml similarity index 100% rename from PyBioNetGen/core/receptor/metadata.yaml rename to Published/PyBioNetGen/core/receptor/metadata.yaml diff --git a/PyBioNetGen/core/receptor/receptor.bngl b/Published/PyBioNetGen/core/receptor/receptor.bngl similarity index 100% rename from PyBioNetGen/core/receptor/receptor.bngl rename to Published/PyBioNetGen/core/receptor/receptor.bngl diff --git a/PyBioNetGen/core/receptornf/README.md b/Published/PyBioNetGen/core/receptornf/README.md similarity index 100% rename from PyBioNetGen/core/receptornf/README.md rename to Published/PyBioNetGen/core/receptornf/README.md diff --git a/PyBioNetGen/core/receptornf/metadata.yaml b/Published/PyBioNetGen/core/receptornf/metadata.yaml similarity index 100% rename from PyBioNetGen/core/receptornf/metadata.yaml rename to Published/PyBioNetGen/core/receptornf/metadata.yaml diff --git a/PyBioNetGen/core/receptornf/receptor_nf.bngl b/Published/PyBioNetGen/core/receptornf/receptor_nf.bngl similarity index 100% rename from PyBioNetGen/core/receptornf/receptor_nf.bngl rename to Published/PyBioNetGen/core/receptornf/receptor_nf.bngl diff --git a/PyBioNetGen/core/tcr/README.md b/Published/PyBioNetGen/core/tcr/README.md similarity index 100% rename from PyBioNetGen/core/tcr/README.md rename to Published/PyBioNetGen/core/tcr/README.md diff --git a/PyBioNetGen/core/tcr/metadata.yaml b/Published/PyBioNetGen/core/tcr/metadata.yaml similarity index 100% rename from PyBioNetGen/core/tcr/metadata.yaml rename to Published/PyBioNetGen/core/tcr/metadata.yaml diff --git a/PyBioNetGen/core/tcr/tcr.bngl b/Published/PyBioNetGen/core/tcr/tcr.bngl similarity index 100% rename from PyBioNetGen/core/tcr/tcr.bngl rename to Published/PyBioNetGen/core/tcr/tcr.bngl diff --git a/PyBioNetGen/core/tlbr/README.md b/Published/PyBioNetGen/core/tlbr/README.md similarity index 100% rename from PyBioNetGen/core/tlbr/README.md rename to Published/PyBioNetGen/core/tlbr/README.md diff --git a/PyBioNetGen/core/tlbr/metadata.yaml b/Published/PyBioNetGen/core/tlbr/metadata.yaml similarity index 93% rename from PyBioNetGen/core/tlbr/metadata.yaml rename to Published/PyBioNetGen/core/tlbr/metadata.yaml index c9b8638..64f5111 100644 --- a/PyBioNetGen/core/tlbr/metadata.yaml +++ b/Published/PyBioNetGen/core/tlbr/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/PyBNG/tlbr/tlbr.bngl" playground: visible: false - gallery_category: "other" + gallery_categories: ["immunology"] featured: false difficulty: "advanced" diff --git a/PyBioNetGen/core/tlbr/tlbr.bngl b/Published/PyBioNetGen/core/tlbr/tlbr.bngl similarity index 100% rename from PyBioNetGen/core/tlbr/tlbr.bngl rename to Published/PyBioNetGen/core/tlbr/tlbr.bngl diff --git a/PyBioNetGen/tests/ErrNoFrees/ErrNoFrees.bngl b/Published/PyBioNetGen/tests/ErrNoFrees/ErrNoFrees.bngl similarity index 100% rename from PyBioNetGen/tests/ErrNoFrees/ErrNoFrees.bngl rename to Published/PyBioNetGen/tests/ErrNoFrees/ErrNoFrees.bngl diff --git a/PyBioNetGen/tests/ErrNoFrees/README.md b/Published/PyBioNetGen/tests/ErrNoFrees/README.md similarity index 100% rename from PyBioNetGen/tests/ErrNoFrees/README.md rename to Published/PyBioNetGen/tests/ErrNoFrees/README.md diff --git a/PyBioNetGen/tests/ErrNoFrees/metadata.yaml b/Published/PyBioNetGen/tests/ErrNoFrees/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/ErrNoFrees/metadata.yaml rename to Published/PyBioNetGen/tests/ErrNoFrees/metadata.yaml diff --git a/PyBioNetGen/tests/LilyIgE/LilyIgE.bngl b/Published/PyBioNetGen/tests/LilyIgE/LilyIgE.bngl similarity index 100% rename from PyBioNetGen/tests/LilyIgE/LilyIgE.bngl rename to Published/PyBioNetGen/tests/LilyIgE/LilyIgE.bngl diff --git a/PyBioNetGen/tests/LilyIgE/README.md b/Published/PyBioNetGen/tests/LilyIgE/README.md similarity index 100% rename from PyBioNetGen/tests/LilyIgE/README.md rename to Published/PyBioNetGen/tests/LilyIgE/README.md diff --git a/PyBioNetGen/tests/LilyIgE/metadata.yaml b/Published/PyBioNetGen/tests/LilyIgE/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/LilyIgE/metadata.yaml rename to Published/PyBioNetGen/tests/LilyIgE/metadata.yaml diff --git a/PyBioNetGen/tests/NFmodel/NFmodel.bngl b/Published/PyBioNetGen/tests/NFmodel/NFmodel.bngl similarity index 100% rename from PyBioNetGen/tests/NFmodel/NFmodel.bngl rename to Published/PyBioNetGen/tests/NFmodel/NFmodel.bngl diff --git a/PyBioNetGen/tests/NFmodel/README.md b/Published/PyBioNetGen/tests/NFmodel/README.md similarity index 100% rename from PyBioNetGen/tests/NFmodel/README.md rename to Published/PyBioNetGen/tests/NFmodel/README.md diff --git a/PyBioNetGen/tests/NFmodel/metadata.yaml b/Published/PyBioNetGen/tests/NFmodel/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/NFmodel/metadata.yaml rename to Published/PyBioNetGen/tests/NFmodel/metadata.yaml diff --git a/PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere.bngl b/Published/PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere.bngl similarity index 100% rename from PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere.bngl rename to Published/PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere.bngl diff --git a/PyBioNetGen/tests/ParamsEverywhere/README.md b/Published/PyBioNetGen/tests/ParamsEverywhere/README.md similarity index 100% rename from PyBioNetGen/tests/ParamsEverywhere/README.md rename to Published/PyBioNetGen/tests/ParamsEverywhere/README.md diff --git a/PyBioNetGen/tests/ParamsEverywhere/metadata.yaml b/Published/PyBioNetGen/tests/ParamsEverywhere/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/ParamsEverywhere/metadata.yaml rename to Published/PyBioNetGen/tests/ParamsEverywhere/metadata.yaml diff --git a/PyBioNetGen/tests/Simple/README.md b/Published/PyBioNetGen/tests/Simple/README.md similarity index 100% rename from PyBioNetGen/tests/Simple/README.md rename to Published/PyBioNetGen/tests/Simple/README.md diff --git a/PyBioNetGen/tests/Simple/Simple.bngl b/Published/PyBioNetGen/tests/Simple/Simple.bngl similarity index 100% rename from PyBioNetGen/tests/Simple/Simple.bngl rename to Published/PyBioNetGen/tests/Simple/Simple.bngl diff --git a/PyBioNetGen/tests/Simple/metadata.yaml b/Published/PyBioNetGen/tests/Simple/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/Simple/metadata.yaml rename to Published/PyBioNetGen/tests/Simple/metadata.yaml diff --git a/PyBioNetGen/tests/SimpleAddActions/README.md b/Published/PyBioNetGen/tests/SimpleAddActions/README.md similarity index 100% rename from PyBioNetGen/tests/SimpleAddActions/README.md rename to Published/PyBioNetGen/tests/SimpleAddActions/README.md diff --git a/PyBioNetGen/tests/SimpleAddActions/Simple_AddActions.bngl b/Published/PyBioNetGen/tests/SimpleAddActions/Simple_AddActions.bngl similarity index 100% rename from PyBioNetGen/tests/SimpleAddActions/Simple_AddActions.bngl rename to Published/PyBioNetGen/tests/SimpleAddActions/Simple_AddActions.bngl diff --git a/PyBioNetGen/tests/SimpleAddActions/metadata.yaml b/Published/PyBioNetGen/tests/SimpleAddActions/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/SimpleAddActions/metadata.yaml rename to Published/PyBioNetGen/tests/SimpleAddActions/metadata.yaml diff --git a/PyBioNetGen/tests/SimpleAnswer/README.md b/Published/PyBioNetGen/tests/SimpleAnswer/README.md similarity index 100% rename from PyBioNetGen/tests/SimpleAnswer/README.md rename to Published/PyBioNetGen/tests/SimpleAnswer/README.md diff --git a/PyBioNetGen/tests/SimpleAnswer/Simple_Answer.bngl b/Published/PyBioNetGen/tests/SimpleAnswer/Simple_Answer.bngl similarity index 100% rename from PyBioNetGen/tests/SimpleAnswer/Simple_Answer.bngl rename to Published/PyBioNetGen/tests/SimpleAnswer/Simple_Answer.bngl diff --git a/PyBioNetGen/tests/SimpleAnswer/metadata.yaml b/Published/PyBioNetGen/tests/SimpleAnswer/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/SimpleAnswer/metadata.yaml rename to Published/PyBioNetGen/tests/SimpleAnswer/metadata.yaml diff --git a/PyBioNetGen/tests/SimpleGenOnly/README.md b/Published/PyBioNetGen/tests/SimpleGenOnly/README.md similarity index 100% rename from PyBioNetGen/tests/SimpleGenOnly/README.md rename to Published/PyBioNetGen/tests/SimpleGenOnly/README.md diff --git a/PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly.bngl b/Published/PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly.bngl similarity index 100% rename from PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly.bngl rename to Published/PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly.bngl diff --git a/PyBioNetGen/tests/SimpleGenOnly/metadata.yaml b/Published/PyBioNetGen/tests/SimpleGenOnly/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/SimpleGenOnly/metadata.yaml rename to Published/PyBioNetGen/tests/SimpleGenOnly/metadata.yaml diff --git a/PyBioNetGen/tests/Simplenogen/README.md b/Published/PyBioNetGen/tests/Simplenogen/README.md similarity index 100% rename from PyBioNetGen/tests/Simplenogen/README.md rename to Published/PyBioNetGen/tests/Simplenogen/README.md diff --git a/PyBioNetGen/tests/Simplenogen/Simple_nogen.bngl b/Published/PyBioNetGen/tests/Simplenogen/Simple_nogen.bngl similarity index 100% rename from PyBioNetGen/tests/Simplenogen/Simple_nogen.bngl rename to Published/PyBioNetGen/tests/Simplenogen/Simple_nogen.bngl diff --git a/PyBioNetGen/tests/Simplenogen/metadata.yaml b/Published/PyBioNetGen/tests/Simplenogen/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/Simplenogen/metadata.yaml rename to Published/PyBioNetGen/tests/Simplenogen/metadata.yaml diff --git a/PyBioNetGen/tests/Tricky/README.md b/Published/PyBioNetGen/tests/Tricky/README.md similarity index 100% rename from PyBioNetGen/tests/Tricky/README.md rename to Published/PyBioNetGen/tests/Tricky/README.md diff --git a/PyBioNetGen/tests/Tricky/Tricky.bngl b/Published/PyBioNetGen/tests/Tricky/Tricky.bngl similarity index 100% rename from PyBioNetGen/tests/Tricky/Tricky.bngl rename to Published/PyBioNetGen/tests/Tricky/Tricky.bngl diff --git a/PyBioNetGen/tests/Tricky/metadata.yaml b/Published/PyBioNetGen/tests/Tricky/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/Tricky/metadata.yaml rename to Published/PyBioNetGen/tests/Tricky/metadata.yaml diff --git a/PyBioNetGen/tests/TrickyUS/README.md b/Published/PyBioNetGen/tests/TrickyUS/README.md similarity index 100% rename from PyBioNetGen/tests/TrickyUS/README.md rename to Published/PyBioNetGen/tests/TrickyUS/README.md diff --git a/PyBioNetGen/tests/TrickyUS/TrickyUS.bngl b/Published/PyBioNetGen/tests/TrickyUS/TrickyUS.bngl similarity index 100% rename from PyBioNetGen/tests/TrickyUS/TrickyUS.bngl rename to Published/PyBioNetGen/tests/TrickyUS/TrickyUS.bngl diff --git a/PyBioNetGen/tests/TrickyUS/metadata.yaml b/Published/PyBioNetGen/tests/TrickyUS/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/TrickyUS/metadata.yaml rename to Published/PyBioNetGen/tests/TrickyUS/metadata.yaml diff --git a/PyBioNetGen/tests/actionssyntax/README.md b/Published/PyBioNetGen/tests/actionssyntax/README.md similarity index 100% rename from PyBioNetGen/tests/actionssyntax/README.md rename to Published/PyBioNetGen/tests/actionssyntax/README.md diff --git a/PyBioNetGen/tests/actionssyntax/actions_syntax.bngl b/Published/PyBioNetGen/tests/actionssyntax/actions_syntax.bngl similarity index 100% rename from PyBioNetGen/tests/actionssyntax/actions_syntax.bngl rename to Published/PyBioNetGen/tests/actionssyntax/actions_syntax.bngl diff --git a/PyBioNetGen/tests/actionssyntax/metadata.yaml b/Published/PyBioNetGen/tests/actionssyntax/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/actionssyntax/metadata.yaml rename to Published/PyBioNetGen/tests/actionssyntax/metadata.yaml diff --git a/PyBioNetGen/tests/bngerror/README.md b/Published/PyBioNetGen/tests/bngerror/README.md similarity index 100% rename from PyBioNetGen/tests/bngerror/README.md rename to Published/PyBioNetGen/tests/bngerror/README.md diff --git a/PyBioNetGen/tests/bngerror/bng_error.bngl b/Published/PyBioNetGen/tests/bngerror/bng_error.bngl similarity index 100% rename from PyBioNetGen/tests/bngerror/bng_error.bngl rename to Published/PyBioNetGen/tests/bngerror/bng_error.bngl diff --git a/PyBioNetGen/tests/bngerror/metadata.yaml b/Published/PyBioNetGen/tests/bngerror/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/bngerror/metadata.yaml rename to Published/PyBioNetGen/tests/bngerror/metadata.yaml diff --git a/PyBioNetGen/tests/egg/README.md b/Published/PyBioNetGen/tests/egg/README.md similarity index 100% rename from PyBioNetGen/tests/egg/README.md rename to Published/PyBioNetGen/tests/egg/README.md diff --git a/PyBioNetGen/tests/egg/egg.bngl b/Published/PyBioNetGen/tests/egg/egg.bngl similarity index 100% rename from PyBioNetGen/tests/egg/egg.bngl rename to Published/PyBioNetGen/tests/egg/egg.bngl diff --git a/PyBioNetGen/tests/egg/metadata.yaml b/Published/PyBioNetGen/tests/egg/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/egg/metadata.yaml rename to Published/PyBioNetGen/tests/egg/metadata.yaml diff --git a/PyBioNetGen/tests/freemissing/README.md b/Published/PyBioNetGen/tests/freemissing/README.md similarity index 100% rename from PyBioNetGen/tests/freemissing/README.md rename to Published/PyBioNetGen/tests/freemissing/README.md diff --git a/PyBioNetGen/tests/freemissing/free_missing.bngl b/Published/PyBioNetGen/tests/freemissing/free_missing.bngl similarity index 100% rename from PyBioNetGen/tests/freemissing/free_missing.bngl rename to Published/PyBioNetGen/tests/freemissing/free_missing.bngl diff --git a/PyBioNetGen/tests/freemissing/metadata.yaml b/Published/PyBioNetGen/tests/freemissing/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/freemissing/metadata.yaml rename to Published/PyBioNetGen/tests/freemissing/metadata.yaml diff --git a/PyBioNetGen/tests/nofrees/README.md b/Published/PyBioNetGen/tests/nofrees/README.md similarity index 100% rename from PyBioNetGen/tests/nofrees/README.md rename to Published/PyBioNetGen/tests/nofrees/README.md diff --git a/PyBioNetGen/tests/nofrees/metadata.yaml b/Published/PyBioNetGen/tests/nofrees/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/nofrees/metadata.yaml rename to Published/PyBioNetGen/tests/nofrees/metadata.yaml diff --git a/PyBioNetGen/tests/nofrees/no_frees.bngl b/Published/PyBioNetGen/tests/nofrees/no_frees.bngl similarity index 100% rename from PyBioNetGen/tests/nofrees/no_frees.bngl rename to Published/PyBioNetGen/tests/nofrees/no_frees.bngl diff --git a/PyBioNetGen/tests/nogeneratenetwork/README.md b/Published/PyBioNetGen/tests/nogeneratenetwork/README.md similarity index 100% rename from PyBioNetGen/tests/nogeneratenetwork/README.md rename to Published/PyBioNetGen/tests/nogeneratenetwork/README.md diff --git a/PyBioNetGen/tests/nogeneratenetwork/metadata.yaml b/Published/PyBioNetGen/tests/nogeneratenetwork/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/nogeneratenetwork/metadata.yaml rename to Published/PyBioNetGen/tests/nogeneratenetwork/metadata.yaml diff --git a/PyBioNetGen/tests/nogeneratenetwork/no_generate_network.bngl b/Published/PyBioNetGen/tests/nogeneratenetwork/no_generate_network.bngl similarity index 100% rename from PyBioNetGen/tests/nogeneratenetwork/no_generate_network.bngl rename to Published/PyBioNetGen/tests/nogeneratenetwork/no_generate_network.bngl diff --git a/PyBioNetGen/tests/nosuffix/README.md b/Published/PyBioNetGen/tests/nosuffix/README.md similarity index 100% rename from PyBioNetGen/tests/nosuffix/README.md rename to Published/PyBioNetGen/tests/nosuffix/README.md diff --git a/PyBioNetGen/tests/nosuffix/metadata.yaml b/Published/PyBioNetGen/tests/nosuffix/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/nosuffix/metadata.yaml rename to Published/PyBioNetGen/tests/nosuffix/metadata.yaml diff --git a/PyBioNetGen/tests/nosuffix/no_suffix.bngl b/Published/PyBioNetGen/tests/nosuffix/no_suffix.bngl similarity index 100% rename from PyBioNetGen/tests/nosuffix/no_suffix.bngl rename to Published/PyBioNetGen/tests/nosuffix/no_suffix.bngl diff --git a/PyBioNetGen/tests/parabola/README.md b/Published/PyBioNetGen/tests/parabola/README.md similarity index 100% rename from PyBioNetGen/tests/parabola/README.md rename to Published/PyBioNetGen/tests/parabola/README.md diff --git a/PyBioNetGen/tests/parabola/metadata.yaml b/Published/PyBioNetGen/tests/parabola/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/parabola/metadata.yaml rename to Published/PyBioNetGen/tests/parabola/metadata.yaml diff --git a/PyBioNetGen/tests/parabola/parabola.bngl b/Published/PyBioNetGen/tests/parabola/parabola.bngl similarity index 100% rename from PyBioNetGen/tests/parabola/parabola.bngl rename to Published/PyBioNetGen/tests/parabola/parabola.bngl diff --git a/PyBioNetGen/tests/parabola2/README.md b/Published/PyBioNetGen/tests/parabola2/README.md similarity index 100% rename from PyBioNetGen/tests/parabola2/README.md rename to Published/PyBioNetGen/tests/parabola2/README.md diff --git a/PyBioNetGen/tests/parabola2/metadata.yaml b/Published/PyBioNetGen/tests/parabola2/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/parabola2/metadata.yaml rename to Published/PyBioNetGen/tests/parabola2/metadata.yaml diff --git a/PyBioNetGen/tests/parabola2/parabola2.bngl b/Published/PyBioNetGen/tests/parabola2/parabola2.bngl similarity index 100% rename from PyBioNetGen/tests/parabola2/parabola2.bngl rename to Published/PyBioNetGen/tests/parabola2/parabola2.bngl diff --git a/PyBioNetGen/tests/parabola_bngl_files/README.md b/Published/PyBioNetGen/tests/parabola_bngl_files/README.md similarity index 100% rename from PyBioNetGen/tests/parabola_bngl_files/README.md rename to Published/PyBioNetGen/tests/parabola_bngl_files/README.md diff --git a/PyBioNetGen/tests/parabola_bngl_files/metadata.yaml b/Published/PyBioNetGen/tests/parabola_bngl_files/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/parabola_bngl_files/metadata.yaml rename to Published/PyBioNetGen/tests/parabola_bngl_files/metadata.yaml diff --git a/PyBioNetGen/tests/parabola_bngl_files/parabola.bngl b/Published/PyBioNetGen/tests/parabola_bngl_files/parabola.bngl similarity index 100% rename from PyBioNetGen/tests/parabola_bngl_files/parabola.bngl rename to Published/PyBioNetGen/tests/parabola_bngl_files/parabola.bngl diff --git a/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/README.md b/Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/README.md similarity index 100% rename from PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/README.md rename to Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/README.md diff --git a/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/metadata.yaml b/Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/metadata.yaml rename to Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/metadata.yaml diff --git a/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola.bngl b/Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola.bngl similarity index 100% rename from PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola.bngl rename to Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola.bngl diff --git a/PyBioNetGen/tests/polynomial/README.md b/Published/PyBioNetGen/tests/polynomial/README.md similarity index 100% rename from PyBioNetGen/tests/polynomial/README.md rename to Published/PyBioNetGen/tests/polynomial/README.md diff --git a/PyBioNetGen/tests/polynomial/metadata.yaml b/Published/PyBioNetGen/tests/polynomial/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/polynomial/metadata.yaml rename to Published/PyBioNetGen/tests/polynomial/metadata.yaml diff --git a/PyBioNetGen/tests/polynomial/polynomial.bngl b/Published/PyBioNetGen/tests/polynomial/polynomial.bngl similarity index 100% rename from PyBioNetGen/tests/polynomial/polynomial.bngl rename to Published/PyBioNetGen/tests/polynomial/polynomial.bngl diff --git a/PyBioNetGen/tests/polynomial_full_tests_T6-check/README.md b/Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/README.md similarity index 100% rename from PyBioNetGen/tests/polynomial_full_tests_T6-check/README.md rename to Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/README.md diff --git a/PyBioNetGen/tests/polynomial_full_tests_T6-check/metadata.yaml b/Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/polynomial_full_tests_T6-check/metadata.yaml rename to Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/metadata.yaml diff --git a/PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial.bngl b/Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial.bngl similarity index 100% rename from PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial.bngl rename to Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial.bngl diff --git a/PyBioNetGen/tests/receptornf/README.md b/Published/PyBioNetGen/tests/receptornf/README.md similarity index 100% rename from PyBioNetGen/tests/receptornf/README.md rename to Published/PyBioNetGen/tests/receptornf/README.md diff --git a/PyBioNetGen/tests/receptornf/metadata.yaml b/Published/PyBioNetGen/tests/receptornf/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/receptornf/metadata.yaml rename to Published/PyBioNetGen/tests/receptornf/metadata.yaml diff --git a/PyBioNetGen/tests/receptornf/receptor_nf.bngl b/Published/PyBioNetGen/tests/receptornf/receptor_nf.bngl similarity index 100% rename from PyBioNetGen/tests/receptornf/receptor_nf.bngl rename to Published/PyBioNetGen/tests/receptornf/receptor_nf.bngl diff --git a/PyBioNetGen/tests/simplenfseed/README.md b/Published/PyBioNetGen/tests/simplenfseed/README.md similarity index 100% rename from PyBioNetGen/tests/simplenfseed/README.md rename to Published/PyBioNetGen/tests/simplenfseed/README.md diff --git a/PyBioNetGen/tests/simplenfseed/metadata.yaml b/Published/PyBioNetGen/tests/simplenfseed/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/simplenfseed/metadata.yaml rename to Published/PyBioNetGen/tests/simplenfseed/metadata.yaml diff --git a/PyBioNetGen/tests/simplenfseed/simple_nf_seed.bngl b/Published/PyBioNetGen/tests/simplenfseed/simple_nf_seed.bngl similarity index 100% rename from PyBioNetGen/tests/simplenfseed/simple_nf_seed.bngl rename to Published/PyBioNetGen/tests/simplenfseed/simple_nf_seed.bngl diff --git a/PyBioNetGen/tests/trivial/README.md b/Published/PyBioNetGen/tests/trivial/README.md similarity index 100% rename from PyBioNetGen/tests/trivial/README.md rename to Published/PyBioNetGen/tests/trivial/README.md diff --git a/PyBioNetGen/tests/trivial/metadata.yaml b/Published/PyBioNetGen/tests/trivial/metadata.yaml similarity index 100% rename from PyBioNetGen/tests/trivial/metadata.yaml rename to Published/PyBioNetGen/tests/trivial/metadata.yaml diff --git a/PyBioNetGen/tests/trivial/trivial.bngl b/Published/PyBioNetGen/tests/trivial/trivial.bngl similarity index 100% rename from PyBioNetGen/tests/trivial/trivial.bngl rename to Published/PyBioNetGen/tests/trivial/trivial.bngl diff --git a/Published/Rulebasedegfrtutorial/metadata.yaml b/Published/Rulebasedegfrtutorial/metadata.yaml index 730e135..3671927 100644 --- a/Published/Rulebasedegfrtutorial/metadata.yaml +++ b/Published/Rulebasedegfrtutorial/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/growth-factor-signaling/Rule_based_egfr_tutorial.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer"] featured: false difficulty: "advanced" diff --git a/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/metadata.yaml b/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/metadata.yaml new file mode 100644 index 0000000..085bf49 --- /dev/null +++ b/Published/Salazar-Cavazos2019/PyBNF-fitting-setup/metadata.yaml @@ -0,0 +1,19 @@ +id: PyBNF_fitting_setup_190127_CHO_EGFR_forBNF +name: PyBNF-fitting-setup +description: BNGL model: 190127_CHO_EGFR_forBNF +tags: ["kdephosy1068_f", "kdephosy1173_f", "kphos_f", "grb2_f", "ratio_kdephosy1173", "ratio_kphosy1173", "offrate_f", "onrate_f", "kdephosy1068_pre", "kdephosy1173_pre", "kdephosyn_pre", "kphosy1068_pre", "kphosy1173_pre", "kphosyn_pre", "kdephosy1068", "kdephosy1173", "kdephosyn", "kphosy1068", "kphosy1173", "kphosyn", "ratio_kphos_receiver", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Salazar-Cavazos2019/metadata.yaml b/Published/Salazar-Cavazos2019/metadata.yaml new file mode 100644 index 0000000..f32e34b --- /dev/null +++ b/Published/Salazar-Cavazos2019/metadata.yaml @@ -0,0 +1,19 @@ +id: Salazar_Cavazos2019_190127_CHO_EGFR_best_fit +name: Salazar-Cavazos2019 +description: BNGL model: 190127_CHO_EGFR_best-fit +tags: ["grb2_total__free", "shc1_total__free", "kdephosy1068__free", "kdephosyn__free", "ratio_kpkd_y1068__free", "ratio_kpkd_yn__free", "kdephosy1068_f", "kdephosy1173_f", "kphos_f", "grb2_f", "ratio_kdephosy1173", "ratio_kphosy1173", "offrate_f", "onrate_f", "kdephosy1068_pre", "kdephosy1173_pre", "kdephosyn_pre", "kphosy1068_pre", "kphosy1173_pre", "kphosyn_pre", "kdephosy1068", "kdephosy1173", "kdephosyn", "kphosy1068", "kphosy1173", "kphosyn", "ratio_kphos_receiver", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Thomas2016/example1_BNFfiles/metadata.yaml b/Published/Thomas2016/example1_BNFfiles/metadata.yaml new file mode 100644 index 0000000..f314871 --- /dev/null +++ b/Published/Thomas2016/example1_BNFfiles/metadata.yaml @@ -0,0 +1,19 @@ +id: example1_BNFfiles_example1 +name: example1_starting_point.bngl +description: Filename: example1_starting_point.bngl +tags: ["lt", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "alpha1", "alpha2", "alpha3", "alpha4", "molecules", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Thomas2016/example2_BNFfiles/metadata.yaml b/Published/Thomas2016/example2_BNFfiles/metadata.yaml new file mode 100644 index 0000000..8572dee --- /dev/null +++ b/Published/Thomas2016/example2_BNFfiles/metadata.yaml @@ -0,0 +1,19 @@ +id: example2_BNFfiles_example2 +name: example2_starting_point.bngl +description: Filename: example2_starting_point.bngl +tags: ["f", "lt_nm", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "molecules"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Thomas2016/example3_BNFfiles/metadata.yaml b/Published/Thomas2016/example3_BNFfiles/metadata.yaml new file mode 100644 index 0000000..1e96950 --- /dev/null +++ b/Published/Thomas2016/example3_BNFfiles/metadata.yaml @@ -0,0 +1,19 @@ +id: example3_BNFfiles_example3 +name: example3 BNFfiles +description: BNGL model: example3 +tags: ["alpha", "molecules", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Thomas2016/example4_BNFfiles/metadata.yaml b/Published/Thomas2016/example4_BNFfiles/metadata.yaml new file mode 100644 index 0000000..0fb8c64 --- /dev/null +++ b/Published/Thomas2016/example4_BNFfiles/metadata.yaml @@ -0,0 +1,19 @@ +id: example4_BNFfiles_example4 +name: in BNGL. For a description of BNGL, see: +description: Supplementary File A in File S1 +tags: ["other"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["nf"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Thomas2016/example5_BNFfiles/metadata.yaml b/Published/Thomas2016/example5_BNFfiles/metadata.yaml new file mode 100644 index 0000000..e7175e0 --- /dev/null +++ b/Published/Thomas2016/example5_BNFfiles/metadata.yaml @@ -0,0 +1,19 @@ +id: example5_BNFfiles_example5 +name: example5 BNFfiles +description: A simple model +tags: ["ligand_ispresent", "molecules", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Thomas2016/example6_BNFfiles/metadata.yaml b/Published/Thomas2016/example6_BNFfiles/metadata.yaml new file mode 100644 index 0000000..4130d68 --- /dev/null +++ b/Published/Thomas2016/example6_BNFfiles/metadata.yaml @@ -0,0 +1,19 @@ +id: example6_BNFfiles_example6 +name: example6 BNFfiles +description: A simple model +tags: ["molecules", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: true + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: false +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Thomas2016/metadata.yaml b/Published/Thomas2016/metadata.yaml new file mode 100644 index 0000000..7e11e6a --- /dev/null +++ b/Published/Thomas2016/metadata.yaml @@ -0,0 +1,19 @@ +id: Thomas2016_example1_fit +name: example1_starting_point.bngl +description: Filename: example1_starting_point.bngl +tags: ["chi_r__free__", "k_c__free__", "k_o__free__", "kaf__free__", "kar__free__", "alpha1_pre__free__", "alpha2_pre__free__", "alpha3_pre__free__", "alpha4_pre__free__", "lt", "rt", "k11", "k11r", "k21", "k21r", "k22", "k22r", "l20", "l20r", "l21r", "l22r", "k_o", "k_c", "kaf", "kar", "kp", "kdp", "chi_r", "avg1", "avg2", "avg3", "avg4", "alpha1", "alpha2", "alpha3", "alpha4", "molecules", "species"] +category: other +compatibility: + bng2_compatible: true + nfsim_compatible: false + simulation_methods: ["ode"] + uses_compartments: false + uses_energy: false + uses_functions: true +source: + origin: published +playground: + visible: false + gallery_categories: [] + featured: false + difficulty: intermediate diff --git a/Published/Zhang2021/metadata.yaml b/Published/Zhang2021/metadata.yaml index 3022a5d..ce5c945 100644 --- a/Published/Zhang2021/metadata.yaml +++ b/Published/Zhang2021/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Zhang_2021.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["developmental"] featured: false difficulty: "advanced" diff --git a/Published/Zhang2023/metadata.yaml b/Published/Zhang2023/metadata.yaml index 00b1112..a2f4ec2 100644 --- a/Published/Zhang2023/metadata.yaml +++ b/Published/Zhang2023/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/Zhang_2023.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["developmental"] featured: false difficulty: "advanced" diff --git a/Published/fcerifyn/metadata.yaml b/Published/fcerifyn/metadata.yaml index da9e7e0..32dadef 100644 --- a/Published/fcerifyn/metadata.yaml +++ b/Published/fcerifyn/metadata.yaml @@ -4,12 +4,12 @@ description: "FceRI signaling" tags: ["published", "immunology", "fceri", "fyn", "lig", "lyn", "syk", "rec"] category: "immunology" compatibility: - bng2_compatible: false + bng2_compatible: true simulation_methods: ["ode"] uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "published" original_format: "bngl" @@ -17,6 +17,6 @@ source: source_path: "published-models/immune-signaling/fceri_fyn.bngl" playground: visible: false - gallery_category: "immunology" + gallery_categories: ["immunology"] featured: false difficulty: "advanced" diff --git a/Published/innateimmunity/metadata.yaml b/Published/innateimmunity/metadata.yaml index 41efafa..4d96b53 100644 --- a/Published/innateimmunity/metadata.yaml +++ b/Published/innateimmunity/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/immune-signaling/innate_immunity.bngl" playground: visible: true - gallery_category: "immunology" + gallery_categories: ["immunology"] featured: false difficulty: "intermediate" diff --git a/Published/mapkdimers/metadata.yaml b/Published/mapkdimers/metadata.yaml index 442ea85..507ffc1 100644 --- a/Published/mapkdimers/metadata.yaml +++ b/Published/mapkdimers/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/mapk-dimers.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer"] featured: false difficulty: "advanced" diff --git a/Published/mapkmonomers/metadata.yaml b/Published/mapkmonomers/metadata.yaml index c0cd06f..5cc66e2 100644 --- a/Published/mapkmonomers/metadata.yaml +++ b/Published/mapkmonomers/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/complex-models/mapk-monomers.bngl" playground: visible: false - gallery_category: "signaling" + gallery_categories: ["cancer"] featured: false difficulty: "advanced" diff --git a/Published/tlbr/metadata.yaml b/Published/tlbr/metadata.yaml index 5172522..cd87cbf 100644 --- a/Published/tlbr/metadata.yaml +++ b/Published/tlbr/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/immune-signaling/tlbr.bngl" playground: visible: false - gallery_category: "immunology" + gallery_categories: ["immunology"] featured: false difficulty: "advanced" diff --git a/Published/vilar2002/metadata.yaml b/Published/vilar2002/metadata.yaml index 519238f..ac90aab 100644 --- a/Published/vilar2002/metadata.yaml +++ b/Published/vilar2002/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/cell-regulation/vilar_2002.bngl" playground: visible: false - gallery_category: "regulation" + gallery_categories: ["cell-cycle"] featured: false difficulty: "advanced" diff --git a/Published/vilar2002b/metadata.yaml b/Published/vilar2002b/metadata.yaml index b18425c..5e2bfb1 100644 --- a/Published/vilar2002b/metadata.yaml +++ b/Published/vilar2002b/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/cell-regulation/vilar_2002b.bngl" playground: visible: true - gallery_category: "regulation" + gallery_categories: ["cell-cycle"] featured: false difficulty: "intermediate" diff --git a/Contributed/BNGPlayground_Validation/CaOscillateFunc/CaOscillate_Func.bngl b/Tutorials/CaOscillateFunc/CaOscillate_Func.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/CaOscillateFunc/CaOscillate_Func.bngl rename to Tutorials/CaOscillateFunc/CaOscillate_Func.bngl diff --git a/Contributed/BNGPlayground_Validation/CaOscillateFunc/README.md b/Tutorials/CaOscillateFunc/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/CaOscillateFunc/README.md rename to Tutorials/CaOscillateFunc/README.md diff --git a/Contributed/BNGPlayground_Validation/CaOscillateFunc/metadata.yaml b/Tutorials/CaOscillateFunc/metadata.yaml similarity index 94% rename from Contributed/BNGPlayground_Validation/CaOscillateFunc/metadata.yaml rename to Tutorials/CaOscillateFunc/metadata.yaml index 2c13e47..a35afa2 100644 --- a/Contributed/BNGPlayground_Validation/CaOscillateFunc/metadata.yaml +++ b/Tutorials/CaOscillateFunc/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/validation/CaOscillate_Func.bngl" playground: visible: true - gallery_category: "validation" + gallery_categories: [] featured: false difficulty: "intermediate" diff --git a/Contributed/BNGPlayground_Validation/CaOscillateSat/CaOscillate_Sat.bngl b/Tutorials/CaOscillateSat/CaOscillate_Sat.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/CaOscillateSat/CaOscillate_Sat.bngl rename to Tutorials/CaOscillateSat/CaOscillate_Sat.bngl diff --git a/Contributed/BNGPlayground_Validation/CaOscillateSat/README.md b/Tutorials/CaOscillateSat/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/CaOscillateSat/README.md rename to Tutorials/CaOscillateSat/README.md diff --git a/Contributed/BNGPlayground_Validation/CaOscillateSat/metadata.yaml b/Tutorials/CaOscillateSat/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/CaOscillateSat/metadata.yaml rename to Tutorials/CaOscillateSat/metadata.yaml diff --git a/Tutorials/General/chemistry/metadata.yaml b/Tutorials/General/chemistry/metadata.yaml index 7b639a5..f3cec57 100644 --- a/Tutorials/General/chemistry/metadata.yaml +++ b/Tutorials/General/chemistry/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/tutorials/chemistry.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/General/polymer/metadata.yaml b/Tutorials/General/polymer/metadata.yaml index 9e985a7..60e9885 100644 --- a/Tutorials/General/polymer/metadata.yaml +++ b/Tutorials/General/polymer/metadata.yaml @@ -4,7 +4,7 @@ description: "Polymerization model" tags: ["published", "tutorials", "nfsim", "polymer", "a", "b", "c", "simulate_nf"] category: "tutorial" compatibility: - bng2_compatible: false + bng2_compatible: true simulation_methods: ["nf"] uses_compartments: true uses_energy: false @@ -17,6 +17,6 @@ source: source_path: "published-models/tutorials/polymer.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/General/polymerdraft/metadata.yaml b/Tutorials/General/polymerdraft/metadata.yaml index 1f957b0..ab4a178 100644 --- a/Tutorials/General/polymerdraft/metadata.yaml +++ b/Tutorials/General/polymerdraft/metadata.yaml @@ -4,7 +4,7 @@ description: "Polymerization (draft)" tags: ["published", "tutorials", "nfsim", "polymer", "draft", "a", "b", "c", "simulate_nf"] category: "tutorial" compatibility: - bng2_compatible: false + bng2_compatible: true simulation_methods: ["nf"] uses_compartments: true uses_energy: false @@ -17,6 +17,6 @@ source: source_path: "published-models/tutorials/polymer_draft.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/General/quasiequilibrium/metadata.yaml b/Tutorials/General/quasiequilibrium/metadata.yaml index eb2aa3a..ce39e33 100644 --- a/Tutorials/General/quasiequilibrium/metadata.yaml +++ b/Tutorials/General/quasiequilibrium/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/toy-models/quasi_equilibrium.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["tutorials","native-tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/General/simple/metadata.yaml b/Tutorials/General/simple/metadata.yaml index 0d75d97..1b28cf6 100644 --- a/Tutorials/General/simple/metadata.yaml +++ b/Tutorials/General/simple/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/tutorials/simple.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/General/toy1/metadata.yaml b/Tutorials/General/toy1/metadata.yaml index eb5b533..78534b1 100644 --- a/Tutorials/General/toy1/metadata.yaml +++ b/Tutorials/General/toy1/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/tutorials/toy1.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/General/toy2/metadata.yaml b/Tutorials/General/toy2/metadata.yaml index 1436eed..54c7082 100644 --- a/Tutorials/General/toy2/metadata.yaml +++ b/Tutorials/General/toy2/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/tutorials/toy2.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["tutorials"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Validation/Haugh2b/Haugh2b.bngl b/Tutorials/Haugh2b/Haugh2b.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/Haugh2b/Haugh2b.bngl rename to Tutorials/Haugh2b/Haugh2b.bngl diff --git a/Contributed/BNGPlayground_Validation/Haugh2b/README.md b/Tutorials/Haugh2b/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/Haugh2b/README.md rename to Tutorials/Haugh2b/README.md diff --git a/Contributed/BNGPlayground_Validation/Haugh2b/metadata.yaml b/Tutorials/Haugh2b/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/Haugh2b/metadata.yaml rename to Tutorials/Haugh2b/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/Kiefhaberemodel/Kiefhaber_emodel.bngl b/Tutorials/Kiefhaberemodel/Kiefhaber_emodel.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/Kiefhaberemodel/Kiefhaber_emodel.bngl rename to Tutorials/Kiefhaberemodel/Kiefhaber_emodel.bngl diff --git a/Contributed/BNGPlayground_Validation/Kiefhaberemodel/README.md b/Tutorials/Kiefhaberemodel/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/Kiefhaberemodel/README.md rename to Tutorials/Kiefhaberemodel/README.md diff --git a/Contributed/BNGPlayground_Validation/Kiefhaberemodel/metadata.yaml b/Tutorials/Kiefhaberemodel/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/Kiefhaberemodel/metadata.yaml rename to Tutorials/Kiefhaberemodel/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/Motivatingexample/Motivating_example.bngl b/Tutorials/Motivatingexample/Motivating_example.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/Motivatingexample/Motivating_example.bngl rename to Tutorials/Motivatingexample/Motivating_example.bngl diff --git a/Contributed/BNGPlayground_Validation/Motivatingexample/README.md b/Tutorials/Motivatingexample/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/Motivatingexample/README.md rename to Tutorials/Motivatingexample/README.md diff --git a/Contributed/BNGPlayground_Validation/Motivatingexample/metadata.yaml b/Tutorials/Motivatingexample/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/Motivatingexample/metadata.yaml rename to Tutorials/Motivatingexample/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/MotivatingexamplecBNGL/Motivating_example_cBNGL.bngl b/Tutorials/MotivatingexamplecBNGL/Motivating_example_cBNGL.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/MotivatingexamplecBNGL/Motivating_example_cBNGL.bngl rename to Tutorials/MotivatingexamplecBNGL/Motivating_example_cBNGL.bngl diff --git a/Contributed/BNGPlayground_Validation/MotivatingexamplecBNGL/README.md b/Tutorials/MotivatingexamplecBNGL/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/MotivatingexamplecBNGL/README.md rename to Tutorials/MotivatingexamplecBNGL/README.md diff --git a/Contributed/BNGPlayground_Validation/MotivatingexamplecBNGL/metadata.yaml b/Tutorials/MotivatingexamplecBNGL/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/MotivatingexamplecBNGL/metadata.yaml rename to Tutorials/MotivatingexamplecBNGL/metadata.yaml diff --git a/Tutorials/NativeTutorials/AB/metadata.yaml b/Tutorials/NativeTutorials/AB/metadata.yaml index 8c2e4b2..b0648ff 100644 --- a/Tutorials/NativeTutorials/AB/metadata.yaml +++ b/Tutorials/NativeTutorials/AB/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/AB/AB.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/ABC/metadata.yaml b/Tutorials/NativeTutorials/ABC/metadata.yaml index c8edb24..1e0c6e0 100644 --- a/Tutorials/NativeTutorials/ABC/metadata.yaml +++ b/Tutorials/NativeTutorials/ABC/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/ABC/ABC.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["metabolism","native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/ABCscan/metadata.yaml b/Tutorials/NativeTutorials/ABCscan/metadata.yaml index 94b8ec6..bf69d4b 100644 --- a/Tutorials/NativeTutorials/ABCscan/metadata.yaml +++ b/Tutorials/NativeTutorials/ABCscan/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/ABC/ABC_scan.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/ABCssa/metadata.yaml b/Tutorials/NativeTutorials/ABCssa/metadata.yaml index 5f008a2..6538b9d 100644 --- a/Tutorials/NativeTutorials/ABCssa/metadata.yaml +++ b/Tutorials/NativeTutorials/ABCssa/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/ABC/ABC_ssa.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/ABp/metadata.yaml b/Tutorials/NativeTutorials/ABp/metadata.yaml index bd5cc38..3166f63 100644 --- a/Tutorials/NativeTutorials/ABp/metadata.yaml +++ b/Tutorials/NativeTutorials/ABp/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/ABp/ABp.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["metabolism","native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/ABpapprox/metadata.yaml b/Tutorials/NativeTutorials/ABpapprox/metadata.yaml index b6dac54..fa5eaff 100644 --- a/Tutorials/NativeTutorials/ABpapprox/metadata.yaml +++ b/Tutorials/NativeTutorials/ABpapprox/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/ABp/ABp_approx.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/BAB/metadata.yaml b/Tutorials/NativeTutorials/BAB/metadata.yaml index a7de5c2..33124b3 100644 --- a/Tutorials/NativeTutorials/BAB/metadata.yaml +++ b/Tutorials/NativeTutorials/BAB/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/BAB/BAB.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/BABcoop/metadata.yaml b/Tutorials/NativeTutorials/BABcoop/metadata.yaml index 916a4cb..9bd00b1 100644 --- a/Tutorials/NativeTutorials/BABcoop/metadata.yaml +++ b/Tutorials/NativeTutorials/BABcoop/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/BAB/BAB_coop.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/BABscan/metadata.yaml b/Tutorials/NativeTutorials/BABscan/metadata.yaml index 6e2b416..4cb50c1 100644 --- a/Tutorials/NativeTutorials/BABscan/metadata.yaml +++ b/Tutorials/NativeTutorials/BABscan/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/BAB/BAB_scan.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/BLBR/metadata.yaml b/Tutorials/NativeTutorials/BLBR/metadata.yaml index c2375a1..d56a714 100644 --- a/Tutorials/NativeTutorials/BLBR/metadata.yaml +++ b/Tutorials/NativeTutorials/BLBR/metadata.yaml @@ -9,7 +9,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "tutorial" original_format: "bngl" diff --git a/Tutorials/NativeTutorials/Chyleklibrary/metadata.yaml b/Tutorials/NativeTutorials/Chyleklibrary/metadata.yaml index d2bbfab..d375931 100644 --- a/Tutorials/NativeTutorials/Chyleklibrary/metadata.yaml +++ b/Tutorials/NativeTutorials/Chyleklibrary/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/LargerModels/Chylek_library.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/CircadianOscillator/metadata.yaml b/Tutorials/NativeTutorials/CircadianOscillator/metadata.yaml index 00d3249..2d1bb8d 100644 --- a/Tutorials/NativeTutorials/CircadianOscillator/metadata.yaml +++ b/Tutorials/NativeTutorials/CircadianOscillator/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/SynDeg/CircadianOscillator.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["cell-cycle","native-tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/ComplexDegradation/metadata.yaml b/Tutorials/NativeTutorials/ComplexDegradation/metadata.yaml index f708516..04ebf11 100644 --- a/Tutorials/NativeTutorials/ComplexDegradation/metadata.yaml +++ b/Tutorials/NativeTutorials/ComplexDegradation/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/SynDeg/ComplexDegradation.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/Creamer2012/metadata.yaml b/Tutorials/NativeTutorials/Creamer2012/metadata.yaml index 7cf9f7d..fd58ecc 100644 --- a/Tutorials/NativeTutorials/Creamer2012/metadata.yaml +++ b/Tutorials/NativeTutorials/Creamer2012/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/LargerModels/Creamer_2012.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/FceRIji/metadata.yaml b/Tutorials/NativeTutorials/FceRIji/metadata.yaml index 71016fe..2addfe0 100644 --- a/Tutorials/NativeTutorials/FceRIji/metadata.yaml +++ b/Tutorials/NativeTutorials/FceRIji/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/LargerModels/FceRI_ji.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/FceRIviz/metadata.yaml b/Tutorials/NativeTutorials/FceRIviz/metadata.yaml index 909513d..2eb2af1 100644 --- a/Tutorials/NativeTutorials/FceRIviz/metadata.yaml +++ b/Tutorials/NativeTutorials/FceRIviz/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/Viz/FceRI_viz.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/GK/metadata.yaml b/Tutorials/NativeTutorials/GK/metadata.yaml index ca4469f..a5a674c 100644 --- a/Tutorials/NativeTutorials/GK/metadata.yaml +++ b/Tutorials/NativeTutorials/GK/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/ABp/GK.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["metabolism","native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/LR/metadata.yaml b/Tutorials/NativeTutorials/LR/metadata.yaml index bf7a637..670e47f 100644 --- a/Tutorials/NativeTutorials/LR/metadata.yaml +++ b/Tutorials/NativeTutorials/LR/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/CBNGL/LR.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/LRR/metadata.yaml b/Tutorials/NativeTutorials/LRR/metadata.yaml index a0f13b4..3a9da1f 100644 --- a/Tutorials/NativeTutorials/LRR/metadata.yaml +++ b/Tutorials/NativeTutorials/LRR/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/CBNGL/LRR.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/LRRcomp/metadata.yaml b/Tutorials/NativeTutorials/LRRcomp/metadata.yaml index 8d528a0..ceea271 100644 --- a/Tutorials/NativeTutorials/LRRcomp/metadata.yaml +++ b/Tutorials/NativeTutorials/LRRcomp/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/CBNGL/LRR_comp.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/LRcomp/metadata.yaml b/Tutorials/NativeTutorials/LRcomp/metadata.yaml index 0722f89..47204c6 100644 --- a/Tutorials/NativeTutorials/LRcomp/metadata.yaml +++ b/Tutorials/NativeTutorials/LRcomp/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/CBNGL/LR_comp.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/LV/metadata.yaml b/Tutorials/NativeTutorials/LV/metadata.yaml index 5587cd5..7fda679 100644 --- a/Tutorials/NativeTutorials/LV/metadata.yaml +++ b/Tutorials/NativeTutorials/LV/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/ABC/LV.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/LVcomp/metadata.yaml b/Tutorials/NativeTutorials/LVcomp/metadata.yaml index 1c4df77..ab19072 100644 --- a/Tutorials/NativeTutorials/LVcomp/metadata.yaml +++ b/Tutorials/NativeTutorials/LVcomp/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/CBNGL/LV_comp.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/Lisman/metadata.yaml b/Tutorials/NativeTutorials/Lisman/metadata.yaml index 54012a3..09a1be5 100644 --- a/Tutorials/NativeTutorials/Lisman/metadata.yaml +++ b/Tutorials/NativeTutorials/Lisman/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/ABp/Lisman.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["neuroscience","native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/Lismanbifurcate/metadata.yaml b/Tutorials/NativeTutorials/Lismanbifurcate/metadata.yaml index 5fb1898..5e5a68d 100644 --- a/Tutorials/NativeTutorials/Lismanbifurcate/metadata.yaml +++ b/Tutorials/NativeTutorials/Lismanbifurcate/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/ABp/Lisman_bifurcate.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["neuroscience","native-tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/Repressilator/metadata.yaml b/Tutorials/NativeTutorials/Repressilator/metadata.yaml index 7bf2d1a..10ea121 100644 --- a/Tutorials/NativeTutorials/Repressilator/metadata.yaml +++ b/Tutorials/NativeTutorials/Repressilator/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/SynDeg/Repressilator.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["cell-cycle","synbio","native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/SIR/metadata.yaml b/Tutorials/NativeTutorials/SIR/metadata.yaml index 2ddb901..555c05c 100644 --- a/Tutorials/NativeTutorials/SIR/metadata.yaml +++ b/Tutorials/NativeTutorials/SIR/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/ABC/SIR.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/Suderman2013/metadata.yaml b/Tutorials/NativeTutorials/Suderman2013/metadata.yaml index 136b325..8d8122a 100644 --- a/Tutorials/NativeTutorials/Suderman2013/metadata.yaml +++ b/Tutorials/NativeTutorials/Suderman2013/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/LargerModels/Suderman_2013.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/birthdeath/metadata.yaml b/Tutorials/NativeTutorials/birthdeath/metadata.yaml index 9079703..039e683 100644 --- a/Tutorials/NativeTutorials/birthdeath/metadata.yaml +++ b/Tutorials/NativeTutorials/birthdeath/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/SynDeg/birth-death.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/cBNGLsimple/metadata.yaml b/Tutorials/NativeTutorials/cBNGLsimple/metadata.yaml index a11e32c..b78f498 100644 --- a/Tutorials/NativeTutorials/cBNGLsimple/metadata.yaml +++ b/Tutorials/NativeTutorials/cBNGLsimple/metadata.yaml @@ -9,7 +9,7 @@ compatibility: uses_compartments: true uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "tutorial" original_format: "bngl" @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/CBNGL/cBNGL_simple.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/egfrsimple/metadata.yaml b/Tutorials/NativeTutorials/egfrsimple/metadata.yaml index 4068336..f296347 100644 --- a/Tutorials/NativeTutorials/egfrsimple/metadata.yaml +++ b/Tutorials/NativeTutorials/egfrsimple/metadata.yaml @@ -9,7 +9,7 @@ compatibility: uses_compartments: false uses_energy: false uses_functions: false - nfsim_compatible: false + nfsim_compatible: true source: origin: "tutorial" original_format: "bngl" @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/LargerModels/egfr_simple.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/organelletransport/metadata.yaml b/Tutorials/NativeTutorials/organelletransport/metadata.yaml index a35ba74..c8bd431 100644 --- a/Tutorials/NativeTutorials/organelletransport/metadata.yaml +++ b/Tutorials/NativeTutorials/organelletransport/metadata.yaml @@ -9,7 +9,7 @@ compatibility: uses_compartments: true uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "tutorial" original_format: "bngl" @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/CBNGL/organelle_transport.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/organelletransportstruct/metadata.yaml b/Tutorials/NativeTutorials/organelletransportstruct/metadata.yaml index a7512ad..7fbda96 100644 --- a/Tutorials/NativeTutorials/organelletransportstruct/metadata.yaml +++ b/Tutorials/NativeTutorials/organelletransportstruct/metadata.yaml @@ -9,7 +9,7 @@ compatibility: uses_compartments: true uses_energy: false uses_functions: true - nfsim_compatible: false + nfsim_compatible: true source: origin: "tutorial" original_format: "bngl" @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/CBNGL/organelle_transport_struct.bngl" playground: visible: true - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "intermediate" diff --git a/Tutorials/NativeTutorials/toggle/metadata.yaml b/Tutorials/NativeTutorials/toggle/metadata.yaml index baa4d0b..68257b0 100644 --- a/Tutorials/NativeTutorials/toggle/metadata.yaml +++ b/Tutorials/NativeTutorials/toggle/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/SynDeg/toggle.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["synbio","native-tutorials"] featured: false difficulty: "advanced" diff --git a/Tutorials/NativeTutorials/visualize/metadata.yaml b/Tutorials/NativeTutorials/visualize/metadata.yaml index 8ed981c..3af2581 100644 --- a/Tutorials/NativeTutorials/visualize/metadata.yaml +++ b/Tutorials/NativeTutorials/visualize/metadata.yaml @@ -17,6 +17,6 @@ source: source_path: "published-models/native-tutorials/Viz/visualize.bngl" playground: visible: false - gallery_category: "tutorial" + gallery_categories: ["native-tutorials"] featured: false difficulty: "advanced" diff --git a/Contributed/BNGPlayground_Validation/SHP2basemodel/README.md b/Tutorials/SHP2basemodel/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/SHP2basemodel/README.md rename to Tutorials/SHP2basemodel/README.md diff --git a/Contributed/BNGPlayground_Validation/SHP2basemodel/SHP2_base_model.bngl b/Tutorials/SHP2basemodel/SHP2_base_model.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/SHP2basemodel/SHP2_base_model.bngl rename to Tutorials/SHP2basemodel/SHP2_base_model.bngl diff --git a/Contributed/BNGPlayground_Validation/SHP2basemodel/metadata.yaml b/Tutorials/SHP2basemodel/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/SHP2basemodel/metadata.yaml rename to Tutorials/SHP2basemodel/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/catalysis/README.md b/Tutorials/catalysis/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/catalysis/README.md rename to Tutorials/catalysis/README.md diff --git a/Contributed/BNGPlayground_Validation/catalysis/catalysis.bngl b/Tutorials/catalysis/catalysis.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/catalysis/catalysis.bngl rename to Tutorials/catalysis/catalysis.bngl diff --git a/Contributed/BNGPlayground_Validation/catalysis/metadata.yaml b/Tutorials/catalysis/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/catalysis/metadata.yaml rename to Tutorials/catalysis/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/continue/README.md b/Tutorials/continue/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/continue/README.md rename to Tutorials/continue/README.md diff --git a/Contributed/BNGPlayground_Validation/continue/continue.bngl b/Tutorials/continue/continue.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/continue/continue.bngl rename to Tutorials/continue/continue.bngl diff --git a/Contributed/BNGPlayground_Validation/continue/metadata.yaml b/Tutorials/continue/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/continue/metadata.yaml rename to Tutorials/continue/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/egfrnet/README.md b/Tutorials/egfrnet/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/egfrnet/README.md rename to Tutorials/egfrnet/README.md diff --git a/Contributed/BNGPlayground_Validation/egfrnet/egfr_net.bngl b/Tutorials/egfrnet/egfr_net.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/egfrnet/egfr_net.bngl rename to Tutorials/egfrnet/egfr_net.bngl diff --git a/Contributed/BNGPlayground_Validation/egfrnet/metadata.yaml b/Tutorials/egfrnet/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/egfrnet/metadata.yaml rename to Tutorials/egfrnet/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/egfrnetred/README.md b/Tutorials/egfrnetred/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/egfrnetred/README.md rename to Tutorials/egfrnetred/README.md diff --git a/Contributed/BNGPlayground_Validation/egfrnetred/egfr_net_red.bngl b/Tutorials/egfrnetred/egfr_net_red.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/egfrnetred/egfr_net_red.bngl rename to Tutorials/egfrnetred/egfr_net_red.bngl diff --git a/Contributed/BNGPlayground_Validation/egfrnetred/metadata.yaml b/Tutorials/egfrnetred/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/egfrnetred/metadata.yaml rename to Tutorials/egfrnetred/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/egfrpath/README.md b/Tutorials/egfrpath/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/egfrpath/README.md rename to Tutorials/egfrpath/README.md diff --git a/Contributed/BNGPlayground_Validation/egfrpath/egfr_path.bngl b/Tutorials/egfrpath/egfr_path.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/egfrpath/egfr_path.bngl rename to Tutorials/egfrpath/egfr_path.bngl diff --git a/Contributed/BNGPlayground_Validation/egfrpath/metadata.yaml b/Tutorials/egfrpath/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/egfrpath/metadata.yaml rename to Tutorials/egfrpath/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/energyexample1/README.md b/Tutorials/energyexample1/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/energyexample1/README.md rename to Tutorials/energyexample1/README.md diff --git a/Contributed/BNGPlayground_Validation/energyexample1/energy_example1.bngl b/Tutorials/energyexample1/energy_example1.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/energyexample1/energy_example1.bngl rename to Tutorials/energyexample1/energy_example1.bngl diff --git a/Contributed/BNGPlayground_Validation/energyexample1/metadata.yaml b/Tutorials/energyexample1/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/energyexample1/metadata.yaml rename to Tutorials/energyexample1/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/example1/README.md b/Tutorials/example1/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/example1/README.md rename to Tutorials/example1/README.md diff --git a/Contributed/BNGPlayground_Validation/example1/example1.bngl b/Tutorials/example1/example1.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/example1/example1.bngl rename to Tutorials/example1/example1.bngl diff --git a/Contributed/BNGPlayground_Validation/example1/metadata.yaml b/Tutorials/example1/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/example1/metadata.yaml rename to Tutorials/example1/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/fcerijicomp/README.md b/Tutorials/fcerijicomp/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/fcerijicomp/README.md rename to Tutorials/fcerijicomp/README.md diff --git a/Contributed/BNGPlayground_Validation/fcerijicomp/fceri_ji_comp.bngl b/Tutorials/fcerijicomp/fceri_ji_comp.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/fcerijicomp/fceri_ji_comp.bngl rename to Tutorials/fcerijicomp/fceri_ji_comp.bngl diff --git a/Contributed/BNGPlayground_Validation/fcerijicomp/metadata.yaml b/Tutorials/fcerijicomp/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/fcerijicomp/metadata.yaml rename to Tutorials/fcerijicomp/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/heise/README.md b/Tutorials/heise/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/heise/README.md rename to Tutorials/heise/README.md diff --git a/Contributed/BNGPlayground_Validation/heise/heise.bngl b/Tutorials/heise/heise.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/heise/heise.bngl rename to Tutorials/heise/heise.bngl diff --git a/Contributed/BNGPlayground_Validation/heise/metadata.yaml b/Tutorials/heise/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/heise/metadata.yaml rename to Tutorials/heise/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/issue198short/README.md b/Tutorials/issue198short/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/issue198short/README.md rename to Tutorials/issue198short/README.md diff --git a/Contributed/BNGPlayground_Validation/issue198short/issue_198_short.bngl b/Tutorials/issue198short/issue_198_short.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/issue198short/issue_198_short.bngl rename to Tutorials/issue198short/issue_198_short.bngl diff --git a/Contributed/BNGPlayground_Validation/issue198short/metadata.yaml b/Tutorials/issue198short/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/issue198short/metadata.yaml rename to Tutorials/issue198short/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/localfunc/README.md b/Tutorials/localfunc/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/localfunc/README.md rename to Tutorials/localfunc/README.md diff --git a/Contributed/BNGPlayground_Validation/localfunc/localfunc.bngl b/Tutorials/localfunc/localfunc.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/localfunc/localfunc.bngl rename to Tutorials/localfunc/localfunc.bngl diff --git a/Contributed/BNGPlayground_Validation/localfunc/metadata.yaml b/Tutorials/localfunc/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/localfunc/metadata.yaml rename to Tutorials/localfunc/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/michment/README.md b/Tutorials/michment/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/michment/README.md rename to Tutorials/michment/README.md diff --git a/Contributed/BNGPlayground_Validation/michment/metadata.yaml b/Tutorials/michment/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/michment/metadata.yaml rename to Tutorials/michment/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/michment/michment.bngl b/Tutorials/michment/michment.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/michment/michment.bngl rename to Tutorials/michment/michment.bngl diff --git a/Contributed/BNGPlayground_Validation/michmentcont/README.md b/Tutorials/michmentcont/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/michmentcont/README.md rename to Tutorials/michmentcont/README.md diff --git a/Contributed/BNGPlayground_Validation/michmentcont/metadata.yaml b/Tutorials/michmentcont/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/michmentcont/metadata.yaml rename to Tutorials/michmentcont/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/michmentcont/michment_cont.bngl b/Tutorials/michmentcont/michment_cont.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/michmentcont/michment_cont.bngl rename to Tutorials/michmentcont/michment_cont.bngl diff --git a/Contributed/BNGPlayground_Validation/motor/README.md b/Tutorials/motor/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/motor/README.md rename to Tutorials/motor/README.md diff --git a/Contributed/BNGPlayground_Validation/motor/metadata.yaml b/Tutorials/motor/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/motor/metadata.yaml rename to Tutorials/motor/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/motor/motor.bngl b/Tutorials/motor/motor.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/motor/motor.bngl rename to Tutorials/motor/motor.bngl diff --git a/Contributed/BNGPlayground_Validation/mwc/README.md b/Tutorials/mwc/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/mwc/README.md rename to Tutorials/mwc/README.md diff --git a/Contributed/BNGPlayground_Validation/mwc/metadata.yaml b/Tutorials/mwc/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/mwc/metadata.yaml rename to Tutorials/mwc/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/mwc/mwc.bngl b/Tutorials/mwc/mwc.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/mwc/mwc.bngl rename to Tutorials/mwc/mwc.bngl diff --git a/Contributed/BNGPlayground_Validation/nfkb/README.md b/Tutorials/nfkb/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/nfkb/README.md rename to Tutorials/nfkb/README.md diff --git a/Contributed/BNGPlayground_Validation/nfkb/metadata.yaml b/Tutorials/nfkb/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/nfkb/metadata.yaml rename to Tutorials/nfkb/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/nfkb/nfkb.bngl b/Tutorials/nfkb/nfkb.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/nfkb/nfkb.bngl rename to Tutorials/nfkb/nfkb.bngl diff --git a/Contributed/BNGPlayground_Validation/nfkbillustratingprotocols/README.md b/Tutorials/nfkbillustratingprotocols/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/nfkbillustratingprotocols/README.md rename to Tutorials/nfkbillustratingprotocols/README.md diff --git a/Contributed/BNGPlayground_Validation/nfkbillustratingprotocols/metadata.yaml b/Tutorials/nfkbillustratingprotocols/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/nfkbillustratingprotocols/metadata.yaml rename to Tutorials/nfkbillustratingprotocols/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/nfkbillustratingprotocols/nfkb_illustrating_protocols.bngl b/Tutorials/nfkbillustratingprotocols/nfkb_illustrating_protocols.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/nfkbillustratingprotocols/nfkb_illustrating_protocols.bngl rename to Tutorials/nfkbillustratingprotocols/nfkb_illustrating_protocols.bngl diff --git a/Contributed/BNGPlayground_PublicRuntime/polymerfixed/README.md b/Tutorials/polymerfixed/README.md similarity index 100% rename from Contributed/BNGPlayground_PublicRuntime/polymerfixed/README.md rename to Tutorials/polymerfixed/README.md diff --git a/Contributed/BNGPlayground_PublicRuntime/polymerfixed/metadata.yaml b/Tutorials/polymerfixed/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_PublicRuntime/polymerfixed/metadata.yaml rename to Tutorials/polymerfixed/metadata.yaml diff --git a/Contributed/BNGPlayground_PublicRuntime/polymerfixed/polymer_fixed.bngl b/Tutorials/polymerfixed/polymer_fixed.bngl similarity index 100% rename from Contributed/BNGPlayground_PublicRuntime/polymerfixed/polymer_fixed.bngl rename to Tutorials/polymerfixed/polymer_fixed.bngl diff --git a/Contributed/BNGPlayground_Validation/recdim/README.md b/Tutorials/recdim/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/recdim/README.md rename to Tutorials/recdim/README.md diff --git a/Contributed/BNGPlayground_Validation/recdim/metadata.yaml b/Tutorials/recdim/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/recdim/metadata.yaml rename to Tutorials/recdim/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/recdim/rec_dim.bngl b/Tutorials/recdim/rec_dim.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/recdim/rec_dim.bngl rename to Tutorials/recdim/rec_dim.bngl diff --git a/Contributed/BNGPlayground_Validation/recdimcomp/README.md b/Tutorials/recdimcomp/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/recdimcomp/README.md rename to Tutorials/recdimcomp/README.md diff --git a/Contributed/BNGPlayground_Validation/recdimcomp/metadata.yaml b/Tutorials/recdimcomp/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/recdimcomp/metadata.yaml rename to Tutorials/recdimcomp/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/recdimcomp/rec_dim_comp.bngl b/Tutorials/recdimcomp/rec_dim_comp.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/recdimcomp/rec_dim_comp.bngl rename to Tutorials/recdimcomp/rec_dim_comp.bngl diff --git a/Contributed/BNGPlayground_PublicRuntime/simplenfsimtest/README.md b/Tutorials/simplenfsimtest/README.md similarity index 100% rename from Contributed/BNGPlayground_PublicRuntime/simplenfsimtest/README.md rename to Tutorials/simplenfsimtest/README.md diff --git a/Contributed/BNGPlayground_PublicRuntime/simplenfsimtest/metadata.yaml b/Tutorials/simplenfsimtest/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_PublicRuntime/simplenfsimtest/metadata.yaml rename to Tutorials/simplenfsimtest/metadata.yaml diff --git a/Contributed/BNGPlayground_PublicRuntime/simplenfsimtest/simple_nfsim_test.bngl b/Tutorials/simplenfsimtest/simple_nfsim_test.bngl similarity index 100% rename from Contributed/BNGPlayground_PublicRuntime/simplenfsimtest/simple_nfsim_test.bngl rename to Tutorials/simplenfsimtest/simple_nfsim_test.bngl diff --git a/Contributed/BNGPlayground_Validation/simplesbmlimport/README.md b/Tutorials/simplesbmlimport/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/simplesbmlimport/README.md rename to Tutorials/simplesbmlimport/README.md diff --git a/Contributed/BNGPlayground_Validation/simplesbmlimport/metadata.yaml b/Tutorials/simplesbmlimport/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/simplesbmlimport/metadata.yaml rename to Tutorials/simplesbmlimport/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/simplesbmlimport/simple_sbml_import.bngl b/Tutorials/simplesbmlimport/simple_sbml_import.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/simplesbmlimport/simple_sbml_import.bngl rename to Tutorials/simplesbmlimport/simple_sbml_import.bngl diff --git a/Contributed/BNGPlayground_Validation/simplesystem/README.md b/Tutorials/simplesystem/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/simplesystem/README.md rename to Tutorials/simplesystem/README.md diff --git a/Contributed/BNGPlayground_Validation/simplesystem/metadata.yaml b/Tutorials/simplesystem/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/simplesystem/metadata.yaml rename to Tutorials/simplesystem/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/simplesystem/simple_system.bngl b/Tutorials/simplesystem/simple_system.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/simplesystem/simple_system.bngl rename to Tutorials/simplesystem/simple_system.bngl diff --git a/Contributed/BNGPlayground_Validation/testANGsynthesissimple/README.md b/Tutorials/testANGsynthesissimple/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testANGsynthesissimple/README.md rename to Tutorials/testANGsynthesissimple/README.md diff --git a/Contributed/BNGPlayground_Validation/testANGsynthesissimple/metadata.yaml b/Tutorials/testANGsynthesissimple/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testANGsynthesissimple/metadata.yaml rename to Tutorials/testANGsynthesissimple/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testANGsynthesissimple/test_ANG_synthesis_simple.bngl b/Tutorials/testANGsynthesissimple/test_ANG_synthesis_simple.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testANGsynthesissimple/test_ANG_synthesis_simple.bngl rename to Tutorials/testANGsynthesissimple/test_ANG_synthesis_simple.bngl diff --git a/Contributed/BNGPlayground_Validation/testMM/README.md b/Tutorials/testMM/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testMM/README.md rename to Tutorials/testMM/README.md diff --git a/Contributed/BNGPlayground_Validation/testMM/metadata.yaml b/Tutorials/testMM/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testMM/metadata.yaml rename to Tutorials/testMM/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testMM/test_MM.bngl b/Tutorials/testMM/test_MM.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testMM/test_MM.bngl rename to Tutorials/testMM/test_MM.bngl diff --git a/Contributed/BNGPlayground_Validation/testfixed/README.md b/Tutorials/testfixed/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testfixed/README.md rename to Tutorials/testfixed/README.md diff --git a/Contributed/BNGPlayground_Validation/testfixed/metadata.yaml b/Tutorials/testfixed/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testfixed/metadata.yaml rename to Tutorials/testfixed/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testfixed/test_fixed.bngl b/Tutorials/testfixed/test_fixed.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testfixed/test_fixed.bngl rename to Tutorials/testfixed/test_fixed.bngl diff --git a/Contributed/BNGPlayground_Validation/testmratio/README.md b/Tutorials/testmratio/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testmratio/README.md rename to Tutorials/testmratio/README.md diff --git a/Contributed/BNGPlayground_Validation/testmratio/metadata.yaml b/Tutorials/testmratio/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testmratio/metadata.yaml rename to Tutorials/testmratio/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testmratio/test_mratio.bngl b/Tutorials/testmratio/test_mratio.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testmratio/test_mratio.bngl rename to Tutorials/testmratio/test_mratio.bngl diff --git a/Contributed/BNGPlayground_Validation/testnetworkgen/README.md b/Tutorials/testnetworkgen/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testnetworkgen/README.md rename to Tutorials/testnetworkgen/README.md diff --git a/Contributed/BNGPlayground_Validation/testnetworkgen/metadata.yaml b/Tutorials/testnetworkgen/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testnetworkgen/metadata.yaml rename to Tutorials/testnetworkgen/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testnetworkgen/test_network_gen.bngl b/Tutorials/testnetworkgen/test_network_gen.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testnetworkgen/test_network_gen.bngl rename to Tutorials/testnetworkgen/test_network_gen.bngl diff --git a/Contributed/BNGPlayground_Validation/testsat/README.md b/Tutorials/testsat/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testsat/README.md rename to Tutorials/testsat/README.md diff --git a/Contributed/BNGPlayground_Validation/testsat/metadata.yaml b/Tutorials/testsat/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testsat/metadata.yaml rename to Tutorials/testsat/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testsat/test_sat.bngl b/Tutorials/testsat/test_sat.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testsat/test_sat.bngl rename to Tutorials/testsat/test_sat.bngl diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/README.md b/Tutorials/testsynthesiscBNGLsimple/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/README.md rename to Tutorials/testsynthesiscBNGLsimple/README.md diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/metadata.yaml b/Tutorials/testsynthesiscBNGLsimple/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/metadata.yaml rename to Tutorials/testsynthesiscBNGLsimple/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl b/Tutorials/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl rename to Tutorials/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplex/README.md b/Tutorials/testsynthesiscomplex/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplex/README.md rename to Tutorials/testsynthesiscomplex/README.md diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplex/metadata.yaml b/Tutorials/testsynthesiscomplex/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplex/metadata.yaml rename to Tutorials/testsynthesiscomplex/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplex/test_synthesis_complex.bngl b/Tutorials/testsynthesiscomplex/test_synthesis_complex.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplex/test_synthesis_complex.bngl rename to Tutorials/testsynthesiscomplex/test_synthesis_complex.bngl diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplex0cBNGL/README.md b/Tutorials/testsynthesiscomplex0cBNGL/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplex0cBNGL/README.md rename to Tutorials/testsynthesiscomplex0cBNGL/README.md diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplex0cBNGL/metadata.yaml b/Tutorials/testsynthesiscomplex0cBNGL/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplex0cBNGL/metadata.yaml rename to Tutorials/testsynthesiscomplex0cBNGL/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl b/Tutorials/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl rename to Tutorials/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/README.md b/Tutorials/testsynthesiscomplexsourcecBNGL/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/README.md rename to Tutorials/testsynthesiscomplexsourcecBNGL/README.md diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/metadata.yaml b/Tutorials/testsynthesiscomplexsourcecBNGL/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/metadata.yaml rename to Tutorials/testsynthesiscomplexsourcecBNGL/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl b/Tutorials/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl rename to Tutorials/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl diff --git a/Contributed/BNGPlayground_Validation/testsynthesissimple/README.md b/Tutorials/testsynthesissimple/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesissimple/README.md rename to Tutorials/testsynthesissimple/README.md diff --git a/Contributed/BNGPlayground_Validation/testsynthesissimple/metadata.yaml b/Tutorials/testsynthesissimple/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesissimple/metadata.yaml rename to Tutorials/testsynthesissimple/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/testsynthesissimple/test_synthesis_simple.bngl b/Tutorials/testsynthesissimple/test_synthesis_simple.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/testsynthesissimple/test_synthesis_simple.bngl rename to Tutorials/testsynthesissimple/test_synthesis_simple.bngl diff --git a/Contributed/BNGPlayground_Validation/tlmr/README.md b/Tutorials/tlmr/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/tlmr/README.md rename to Tutorials/tlmr/README.md diff --git a/Contributed/BNGPlayground_Validation/tlmr/metadata.yaml b/Tutorials/tlmr/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/tlmr/metadata.yaml rename to Tutorials/tlmr/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/tlmr/tlmr.bngl b/Tutorials/tlmr/tlmr.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/tlmr/tlmr.bngl rename to Tutorials/tlmr/tlmr.bngl diff --git a/Contributed/BNGPlayground_Validation/toyjim/README.md b/Tutorials/toyjim/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/toyjim/README.md rename to Tutorials/toyjim/README.md diff --git a/Contributed/BNGPlayground_Validation/toyjim/metadata.yaml b/Tutorials/toyjim/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/toyjim/metadata.yaml rename to Tutorials/toyjim/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/toyjim/toy-jim.bngl b/Tutorials/toyjim/toy-jim.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/toyjim/toy-jim.bngl rename to Tutorials/toyjim/toy-jim.bngl diff --git a/Contributed/BNGPlayground_Validation/univsynth/README.md b/Tutorials/univsynth/README.md similarity index 100% rename from Contributed/BNGPlayground_Validation/univsynth/README.md rename to Tutorials/univsynth/README.md diff --git a/Contributed/BNGPlayground_Validation/univsynth/metadata.yaml b/Tutorials/univsynth/metadata.yaml similarity index 100% rename from Contributed/BNGPlayground_Validation/univsynth/metadata.yaml rename to Tutorials/univsynth/metadata.yaml diff --git a/Contributed/BNGPlayground_Validation/univsynth/univ_synth.bngl b/Tutorials/univsynth/univ_synth.bngl similarity index 100% rename from Contributed/BNGPlayground_Validation/univsynth/univ_synth.bngl rename to Tutorials/univsynth/univ_synth.bngl diff --git a/fix-test.js b/fix-test.js new file mode 100644 index 0000000..5e5173f --- /dev/null +++ b/fix-test.js @@ -0,0 +1,12 @@ +const fs = require('fs'); +let content = fs.readFileSync('scripts/generate-manifest.test.js', 'utf8'); + +// fix imports +content = content.replace(/<<<<<<< Updated upstream\nconst { buildEntry, parseMetadataYaml } = require\('\.\/generate-manifest\.js'\);\n=======\nconst { buildEntry, parseArgs } = require\('\.\/generate-manifest\.js'\);\n>>>>>>> Stashed changes/, "const { buildEntry, parseMetadataYaml, parseArgs } = require('./generate-manifest.js');"); + +// fix test sections +content = content.replace(/<<<<<<< Updated upstream/g, ""); +content = content.replace(/=======/g, ""); +content = content.replace(/>>>>>>> Stashed changes/g, ""); + +fs.writeFileSync('scripts/generate-manifest.test.js', content); diff --git a/gallery-assignments.json b/gallery-assignments.json new file mode 100644 index 0000000..9884710 --- /dev/null +++ b/gallery-assignments.json @@ -0,0 +1,2417 @@ +{ + "AB": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ABC": { + "gallery_categories": [ + "metabolism", + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ABC_scan": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "ABC_ssa": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ABp": { + "gallery_categories": [ + "metabolism", + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ABp_approx": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "An_2009": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "BAB": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "BAB_coop": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "BAB_scan": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "BaruaBCR_2012": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "BaruaFceRI_2012": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "Barua_2007": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "Barua_2009": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "Blinov_2006": { + "gallery_categories": [ + "cell-cycle" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "Blinov_egfr": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": true + }, + "Blinov_ran": { + "gallery_categories": [ + "cell-cycle" + ], + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": true + }, + "CaOscillate_Func": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "CaOscillate_Sat": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Chattaraj_2021": { + "gallery_categories": [ + "neuroscience" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "Cheemalavagu_JAK_STAT": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ChylekTCR_2014": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Chylek_library": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "CircadianOscillator": { + "gallery_categories": [ + "cell-cycle", + "native-tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "ComplexDegradation": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Creamer_2012": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Dolan_2015": { + "gallery_categories": [ + "metabolism" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": true + }, + "Dushek_2011": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Dushek_2014": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": true + }, + "Erdem_2021": { + "gallery_categories": [ + "metabolism" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": true + }, + "Faeder_2003": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": true + }, + "FceRI_ji": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "FceRI_viz": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "GK": { + "gallery_categories": [ + "metabolism", + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Hat_2016": { + "gallery_categories": [ + "cell-cycle", + "multistage" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "Haugh2b": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Jaruszewicz-Blonska_2023": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Jung_2017": { + "gallery_categories": [ + "neuroscience" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": true + }, + "Kesseler_2013": { + "gallery_categories": [ + "cell-cycle" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "Korwek_2023": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Kozer_2013": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": true + }, + "Kozer_2014": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": true + }, + "LR": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "LRR": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "LRR_comp": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "LR_comp": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "LV": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "LV_comp": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Lang_2024": { + "gallery_categories": [ + "cell-cycle" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Ligon_2014": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false + }, + "Lin_ERK_2019": { + "gallery_categories": [ + "developmental" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": true + }, + "Lin_Prion_2019": { + "gallery_categories": [ + "neuroscience" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": true + }, + "Lin_TCR_2019": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": true + }, + "Lisman": { + "gallery_categories": [ + "neuroscience", + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Lisman_bifurcate": { + "gallery_categories": [ + "neuroscience", + "native-tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "Massole_2023": { + "gallery_categories": [ + "developmental" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "McMillan_2021": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false + }, + "Mertins_2023": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": true + }, + "Model_ZAP": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": false + }, + "Motivating_example": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Motivating_example_cBNGL": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Mukhopadhyay_2013": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Nag_2009": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "Nosbisch_2022": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "Repressilator": { + "gallery_categories": [ + "cell-cycle", + "synbio", + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Rule_based_egfr_tutorial": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "SHP2_base_model": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "SIR": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Suderman_2013": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "Zhang_2021": { + "gallery_categories": [ + "developmental" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "Zhang_2023": { + "gallery_categories": [ + "developmental" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "akt-signaling": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "allosteric-activation": { + "gallery_categories": [ + "metabolism", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ampk-signaling": { + "gallery_categories": [ + "neuroscience", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "apoptosis-cascade": { + "gallery_categories": [ + "cell-cycle", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "auto-activation-loop": { + "gallery_categories": [ + "metabolism", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "autophagy-regulation": { + "gallery_categories": [ + "metabolism", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "bcr-signaling": { + "gallery_categories": [ + "immunology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "beta-adrenergic-response": { + "gallery_categories": [ + "neuroscience", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "birth-death": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "bistable-toggle-switch": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "blbr": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "blood-coagulation-thrombin": { + "gallery_categories": [ + "immunology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "bmp-signaling": { + "gallery_categories": [ + "developmental", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "brusselator-oscillator": { + "gallery_categories": [ + "physics", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "cBNGL_simple": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "calcineurin-nfat-pathway": { + "gallery_categories": [ + "neuroscience", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "calcium-spike-signaling": { + "gallery_categories": [ + "neuroscience", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "caspase-activation-loop": { + "gallery_categories": [ + "cell-cycle", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "catalysis": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "cd40-signaling": { + "gallery_categories": [ + "immunology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "cell-cycle-checkpoint": { + "gallery_categories": [ + "cell-cycle", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "checkpoint-kinase-signaling": { + "gallery_categories": [ + "cancer", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "chemistry": { + "gallery_categories": [ + "tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "chemotaxis-signal-transduction": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "circadian-oscillator": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "clock-bmal1-gene-circuit": { + "gallery_categories": [ + "cell-cycle", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "compartment_endocytosis": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "compartment_membrane_bound": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "compartment_nested_transport": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "compartment_nuclear_transport": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "compartment_organelle_exchange": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "competitive-enzyme-inhibition": { + "gallery_categories": [ + "metabolism", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "complement-activation-cascade": { + "gallery_categories": [ + "immunology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "contact-inhibition-hippo-yap": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "cooperative-binding": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "cs_diffie_hellman": { + "gallery_categories": [ + "cs", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "cs_hash_function": { + "gallery_categories": [ + "cs", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "cs_huffman": { + "gallery_categories": [ + "cs", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "cs_monte_carlo_pi": { + "gallery_categories": [ + "cs", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "cs_pagerank": { + "gallery_categories": [ + "cs", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "cs_pid_controller": { + "gallery_categories": [ + "cs", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "cs_regex_nfa": { + "gallery_categories": [ + "cs", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "degranulation_model": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "dna-damage-repair": { + "gallery_categories": [ + "cancer", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "dna-methylation-dynamics": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "dr5-apoptosis-signaling": { + "gallery_categories": [ + "cell-cycle", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "dual-site-phosphorylation": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "e2f-rb-cell-cycle-switch": { + "gallery_categories": [ + "cell-cycle", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "eco_coevolution_host_parasite": { + "gallery_categories": [ + "ecology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "eco_food_web_chaos_3sp": { + "gallery_categories": [ + "ecology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "eco_lotka_volterra_grid": { + "gallery_categories": [ + "ecology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "eco_mutualism_obligate": { + "gallery_categories": [ + "ecology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "eco_rock_paper_scissors_spatial": { + "gallery_categories": [ + "ecology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "egfr-signaling-pathway": { + "gallery_categories": [ + "cancer", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "egfr_net_red": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "egfr_ode": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "egfr_path": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "egfr_simple": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "eif2a-stress-response": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "endosomal-sorting-rab": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "energy_allostery_mwc": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "energy_catalysis_mm": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "energy_cooperativity_adh": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "energy_example1": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "energy_linear_chain": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "energy_transport_pump": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "er-stress-response": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "erk-nuclear-translocation": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "fceri_fyn": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": true + }, + "feature_functional_rates_volume": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "feature_global_functions_scan": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "feature_local_functions_explicit": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "feature_symmetry_factors_cyclic": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "feature_synthesis_degradation_ss": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "fgf-signaling-pathway": { + "gallery_categories": [ + "developmental", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "gas6-axl-signaling": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "gene-expression-toggle": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "genetic_bistability_energy": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "genetic_dna_replication_stochastic": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "genetic_goodwin_oscillator": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "genetic_translation_kinetics": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "genetic_turing_pattern_1d": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "glioblastoma-egfrviii-signaling": { + "gallery_categories": [ + "cancer", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "glycolysis-branch-point": { + "gallery_categories": [ + "metabolism", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "gm_game_of_life": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "gm_ray_marcher": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "gpcr-desensitization-arrestin": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "hedgehog-signaling-pathway": { + "gallery_categories": [ + "developmental", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "heise": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "hematopoietic-growth-factor": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "hif1a-degradation-loop": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "hif1a_degradation_loop": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "hypoxia-response-signaling": { + "gallery_categories": [ + "cancer", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "il1b-signaling": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "il6-jak-stat-pathway": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "immune-synapse-formation": { + "gallery_categories": [ + "immunology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "inflammasome-activation": { + "gallery_categories": [ + "immunology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "innate_immunity": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "inositol-phosphate-metabolism": { + "gallery_categories": [ + "neuroscience", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "insulin-glucose-homeostasis": { + "gallery_categories": [ + "metabolism", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "interferon-signaling": { + "gallery_categories": [ + "immunology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ire1a-xbp1-er-stress": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "issue_198_short": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "jak-stat-cytokine-signaling": { + "gallery_categories": [ + "immunology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "jnk-mapk-signaling": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "kir-channel-regulation": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "l-type-calcium-channel-dynamics": { + "gallery_categories": [ + "neuroscience", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "lac-operon-regulation": { + "gallery_categories": [ + "metabolism", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "lipid-mediated-pip3-signaling": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "localfunc": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "mapk-dimers": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "mapk-monomers": { + "gallery_categories": [ + "cancer" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "mapk-signaling-cascade": { + "gallery_categories": [ + "cancer", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "meta_formal_game_theory": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "meta_formal_molecular_clock": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "meta_formal_petri_net": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "michaelis-menten-kinetics": { + "gallery_categories": [ + "metabolism", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "michment": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ml_gradient_descent": { + "gallery_categories": [ + "ml-signal", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ml_hopfield": { + "gallery_categories": [ + "ml-signal", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ml_kmeans": { + "gallery_categories": [ + "ml-signal", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ml_q_learning": { + "gallery_categories": [ + "ml-signal", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ml_svm": { + "gallery_categories": [ + "ml-signal", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "motor": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "mt_arithmetic_compiler": { + "gallery_categories": [ + "cs", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "mt_bngl_interpreter": { + "gallery_categories": [ + "cs", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "mt_music_sequencer": { + "gallery_categories": [ + "cs", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "mt_pascal_triangle": { + "gallery_categories": [ + "cs", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "mt_quine": { + "gallery_categories": [ + "cs", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "mtor-signaling": { + "gallery_categories": [ + "neuroscience", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "mtorc2-signaling": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "mwc": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "myogenic-differentiation": { + "gallery_categories": [ + "developmental", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "negative-feedback-loop": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "neurotransmitter-release": { + "gallery_categories": [ + "neuroscience", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "nfkb": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "nfkb-feedback": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "nfsim_aggregation_gelation": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "nfsim_coarse_graining": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "nfsim_dynamic_compartments": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "nfsim_hybrid_particle_field": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "nfsim_ring_closure_polymer": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "nn_xor": { + "gallery_categories": [ + "ml-signal", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "no-cgmp-signaling": { + "gallery_categories": [ + "metabolism", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "notch-delta-lateral-inhibition": { + "gallery_categories": [ + "developmental", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "organelle_transport": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "organelle_transport_struct": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "oxidative-stress-response": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "p38-mapk-signaling": { + "gallery_categories": [ + "cancer", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "p53-mdm2-oscillator": { + "gallery_categories": [ + "cell-cycle", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "parp1-mediated-dna-repair": { + "gallery_categories": [ + "cell-cycle", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ph_lorenz_attractor": { + "gallery_categories": [ + "physics", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ph_nbody_gravity": { + "gallery_categories": [ + "physics", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ph_schrodinger": { + "gallery_categories": [ + "physics", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ph_wave_equation": { + "gallery_categories": [ + "physics", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "phosphorelay-chain": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "platelet-activation": { + "gallery_categories": [ + "immunology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "polymer": { + "gallery_categories": [ + "tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": true + }, + "polymer_draft": { + "gallery_categories": [ + "tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": true, + "excluded": true + }, + "predator-prey-dynamics": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "process_actin_treadmilling": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "process_autophagy_flux": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "process_cell_adhesion_strength": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "process_kinetic_proofreading_tcr": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "process_quorum_sensing_switch": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "quasi_equilibrium": { + "gallery_categories": [ + "tutorials", + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "quorum-sensing-circuit": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "rab-gtpase-cycle": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "rankl-rank-signaling": { + "gallery_categories": [ + "developmental", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "ras-gef-gap-cycle": { + "gallery_categories": [ + "cancer", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "repressilator-oscillator": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "retinoic-acid-signaling": { + "gallery_categories": [ + "developmental", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "rho-gtpase-actin-cytoskeleton": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "shp2-phosphatase-regulation": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "signal-amplification-cascade": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "simple": { + "gallery_categories": [ + "tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "simple-dimerization": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "simple_system": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "sir-epidemic-model": { + "gallery_categories": [ + "ecology", + "tutorials", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "smad-tgf-beta-signaling": { + "gallery_categories": [ + "developmental", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "sonic-hedgehog-gradient": { + "gallery_categories": [ + "developmental", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "sp_fourier_synthesizer": { + "gallery_categories": [ + "ml-signal", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "sp_image_convolution": { + "gallery_categories": [ + "ml-signal", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "sp_kalman_filter": { + "gallery_categories": [ + "ml-signal", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "stat3-mediated-transcription": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "stress-response-adaptation": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "synaptic-plasticity-ltp": { + "gallery_categories": [ + "neuroscience", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "synbio_band_pass_filter": { + "gallery_categories": [ + "synbio", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "synbio_counter_molecular": { + "gallery_categories": [ + "synbio", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "synbio_edge_detector": { + "gallery_categories": [ + "synbio", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "synbio_logic_gates_enzymatic": { + "gallery_categories": [ + "synbio", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "synbio_oscillator_synchronization": { + "gallery_categories": [ + "synbio", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "t-cell-activation": { + "gallery_categories": [ + "immunology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "test_ANG_synthesis_simple": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "test_MM": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "test_fixed": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "test_mratio": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "test_sat": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "test_synthesis_cBNGL_simple": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "test_synthesis_complex": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "test_synthesis_complex_0_cBNGL": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "test_synthesis_complex_source_cBNGL": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "test_synthesis_simple": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "tlbr": { + "gallery_categories": [ + "immunology" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "tlmr": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "tlr3-dsrna-sensing": { + "gallery_categories": [ + "immunology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "tnf-induced-apoptosis": { + "gallery_categories": [ + "cell-cycle", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "toggle": { + "gallery_categories": [ + "synbio", + "native-tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "toy-jim": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "toy1": { + "gallery_categories": [ + "tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "toy2": { + "gallery_categories": [ + "tutorials" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": true + }, + "two-component-system": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "univ_synth": { + "gallery_categories": [], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "vegf-angiogenesis": { + "gallery_categories": [ + "cancer", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "vilar_2002": { + "gallery_categories": [ + "cell-cycle" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "vilar_2002b": { + "gallery_categories": [ + "cell-cycle" + ], + "bng2_compatible": false, + "nfsim_compatible": false, + "excluded": false + }, + "viral-sensing-innate-immunity": { + "gallery_categories": [ + "immunology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "visualize": { + "gallery_categories": [ + "native-tutorials" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "wacky_alchemy_stone": { + "gallery_categories": [ + "synbio", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "wacky_black_hole": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "wacky_bouncing_ball": { + "gallery_categories": [ + "physics", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "wacky_traffic_jam_asep": { + "gallery_categories": [ + "physics", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "wacky_zombie_infection": { + "gallery_categories": [ + "ecology", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "wnt-beta-catenin-signaling": { + "gallery_categories": [ + "developmental", + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + }, + "wound-healing-pdgf-signaling": { + "gallery_categories": [ + "test-models" + ], + "bng2_compatible": true, + "nfsim_compatible": false, + "excluded": false + } +} \ No newline at end of file diff --git a/gallery-categories.yaml b/gallery-categories.yaml new file mode 100644 index 0000000..a691409 --- /dev/null +++ b/gallery-categories.yaml @@ -0,0 +1,83 @@ +# Gallery Category Definitions +# These define the static structure of the playground gallery + +categories: + - id: cancer + name: Cancer Biology + description: Oncogenic signaling pathways and cancer models + sortOrder: 0 + + - id: immunology + name: Immunology + description: Immune signaling models, TCR, BCR, Fc receptors + sortOrder: 1 + + - id: neuroscience + name: Neuroscience + description: Neuronal signaling, neural networks, synaptic models + sortOrder: 2 + + - id: cell-cycle + name: Cell Cycle + description: Cell division, cell cycle regulation models + sortOrder: 3 + + - id: metabolism + name: Metabolism + description: Metabolic networks, biochemical pathways + sortOrder: 4 + + - id: developmental + name: Developmental Biology + description: Developmental signaling, pattern formation + sortOrder: 5 + + - id: ecology + name: Ecology + description: Population dynamics, ecological networks + sortOrder: 6 + + - id: physics + name: Physics + description: Physical systems modeled with BNGL + sortOrder: 7 + + - id: cs + name: Computer Science + description: CS models, computational systems + sortOrder: 8 + + - id: ml-signal + name: ML / Signal Processing + description: Signal processing, machine learning models + sortOrder: 9 + + - id: synbio + name: Synthetic Biology + description: Synthetic gene circuits, engineered systems + sortOrder: 10 + + - id: published-models + name: Published Models + description: Peer-reviewed published models from literature + sortOrder: 11 + + - id: multistage + name: Multistage Models + description: Models with multiple stages or compartments + sortOrder: 12 + + - id: tutorials + name: Tutorials + description: Example models for learning BNGL + sortOrder: 13 + + - id: native-tutorials + name: Native Tutorials + description: Built-in tutorial models with guided steps + sortOrder: 14 + + - id: test-models + name: Test Models + description: Internal test and validation models + sortOrder: 15 diff --git a/gallery.generated.json b/gallery.generated.json new file mode 100644 index 0000000..5b3d7cb --- /dev/null +++ b/gallery.generated.json @@ -0,0 +1,1387 @@ +{ + "version": 1, + "generated": "2026-05-03T22:23:07.247Z", + "categories": [ + { + "id": "cancer", + "name": "Cancer Biology", + "description": "Oncogenic signaling pathways and cancer models", + "sortOrder": 0 + }, + { + "id": "immunology", + "name": "Immunology", + "description": "Immune signaling models, TCR, BCR, Fc receptors", + "sortOrder": 1 + }, + { + "id": "neuroscience", + "name": "Neuroscience", + "description": "Neuronal signaling, neural networks, synaptic models", + "sortOrder": 2 + }, + { + "id": "cell-cycle", + "name": "Cell Cycle", + "description": "Cell division, cell cycle regulation models", + "sortOrder": 3 + }, + { + "id": "metabolism", + "name": "Metabolism", + "description": "Metabolic networks, biochemical pathways", + "sortOrder": 4 + }, + { + "id": "developmental", + "name": "Developmental Biology", + "description": "Developmental signaling, pattern formation", + "sortOrder": 5 + }, + { + "id": "ecology", + "name": "Ecology", + "description": "Population dynamics, ecological networks", + "sortOrder": 6 + }, + { + "id": "physics", + "name": "Physics", + "description": "Physical systems modeled with BNGL", + "sortOrder": 7 + }, + { + "id": "cs", + "name": "Computer Science", + "description": "CS models, computational systems", + "sortOrder": 8 + }, + { + "id": "ml-signal", + "name": "ML / Signal Processing", + "description": "Signal processing, machine learning models", + "sortOrder": 9 + }, + { + "id": "synbio", + "name": "Synthetic Biology", + "description": "Synthetic gene circuits, engineered systems", + "sortOrder": 10 + }, + { + "id": "published-models", + "name": "Published Models", + "description": "Peer-reviewed published models from literature", + "sortOrder": 11 + }, + { + "id": "multistage", + "name": "Multistage Models", + "description": "Models with multiple stages or compartments", + "sortOrder": 12 + }, + { + "id": "tutorials", + "name": "Tutorials", + "description": "Example models for learning BNGL", + "sortOrder": 13 + }, + { + "id": "native-tutorials", + "name": "Native Tutorials", + "description": "Built-in tutorial models with guided steps", + "sortOrder": 14 + }, + { + "id": "test-models", + "name": "Test Models", + "description": "Internal test and validation models", + "sortOrder": 15 + } + ], + "assignments": { + "An_2009": [ + "immunology", + "published-models" + ], + "Barua_2007": [ + "cancer", + "published-models" + ], + "Barua_2009": [ + "cancer", + "published-models" + ], + "BaruaBCR_2012": [ + "immunology", + "published-models" + ], + "BaruaFceRI_2012": [ + "immunology", + "published-models" + ], + "Blinov_2006": [ + "cell-cycle", + "published-models" + ], + "Blinov_egfr": [ + "cancer", + "published-models" + ], + "Blinov_ran": [ + "cell-cycle", + "published-models" + ], + "Chattaraj_2021": [ + "neuroscience", + "published-models" + ], + "Cheemalavagu_JAK_STAT": [ + "immunology", + "published-models" + ], + "ChylekFceRI_2014": [ + "immunology", + "published-models" + ], + "ChylekTCR_2014": [ + "immunology", + "published-models" + ], + "Dembo_1978": [ + "physics", + "published-models" + ], + "Dolan_2015": [ + "metabolism", + "published-models" + ], + "Dushek_2011": [ + "immunology", + "published-models" + ], + "Dushek_2014": [ + "immunology", + "published-models" + ], + "Erdem_2021": [ + "metabolism", + "published-models" + ], + "Faeder_2003": [ + "immunology", + "published-models" + ], + "fceri_fyn": [ + "immunology", + "published-models" + ], + "Goldstein_1980": [ + "physics", + "published-models" + ], + "Harmon_2017": [ + "immunology", + "published-models" + ], + "Hat_2016": [ + "cell-cycle", + "multistage", + "published-models" + ], + "Hlavacek_1999": [ + "physics", + "published-models" + ], + "Hlavacek_2001": [ + "physics", + "published-models" + ], + "innate_immunity": [ + "immunology", + "published-models" + ], + "Jaruszewicz-Blonska_2023": [ + "immunology", + "published-models" + ], + "Jung_2017": [ + "neuroscience", + "published-models" + ], + "Kesseler_2013": [ + "cell-cycle", + "published-models" + ], + "Kozer_2013": [ + "cancer", + "published-models" + ], + "Kozer_2014": [ + "cancer", + "published-models" + ], + "Lang_2024": [ + "cell-cycle", + "published-models" + ], + "Ligon_2014": [ + "cancer", + "published-models" + ], + "Lin_ERK_2019": [ + "developmental", + "published-models" + ], + "Lin_Prion_2019": [ + "neuroscience", + "published-models" + ], + "Lin_TCR_2019": [ + "immunology", + "published-models" + ], + "Macken_1982": [ + "physics", + "published-models" + ], + "mapk-dimers": [ + "cancer", + "published-models" + ], + "mapk-monomers": [ + "cancer", + "published-models" + ], + "Massole_2023": [ + "developmental", + "published-models" + ], + "McMillan_2021": [ + "immunology", + "published-models" + ], + "Mertins_2023": [ + "cancer", + "published-models" + ], + "Model_ZAP": [ + "immunology", + "published-models" + ], + "Mukhopadhyay_2013": [ + "immunology", + "published-models" + ], + "Nag_2009": [ + "cancer", + "published-models" + ], + "Nosbisch_2022": [ + "cancer", + "published-models" + ], + "Posner_1995": [ + "physics", + "published-models" + ], + "Posner_2004": [ + "physics", + "published-models" + ], + "degranulation_model": [ + "immunology", + "published-models" + ], + "egfr_ode": [ + "cancer", + "published-models" + ], + "tlbr": [ + "immunology", + "published-models" + ], + "Rule_based_egfr_tutorial": [ + "cancer", + "published-models" + ], + "vilar_2002": [ + "cell-cycle", + "published-models" + ], + "vilar_2002b": [ + "cell-cycle", + "published-models" + ], + "Yang_2008": [ + "physics", + "published-models" + ], + "Zhang_2021": [ + "developmental", + "published-models" + ], + "Zhang_2023": [ + "developmental", + "published-models" + ], + "akt-signaling": [ + "test-models" + ], + "allosteric-activation": [ + "metabolism", + "test-models" + ], + "ampk-signaling": [ + "neuroscience", + "test-models" + ], + "apoptosis-cascade": [ + "cell-cycle", + "test-models" + ], + "auto-activation-loop": [ + "metabolism", + "test-models" + ], + "autophagy-regulation": [ + "metabolism", + "test-models" + ], + "bcr-signaling": [ + "immunology", + "test-models" + ], + "beta-adrenergic-response": [ + "neuroscience", + "test-models" + ], + "bistable-toggle-switch": [ + "test-models" + ], + "blood-coagulation-thrombin": [ + "immunology", + "test-models" + ], + "bmp-signaling": [ + "developmental", + "test-models" + ], + "brusselator-oscillator": [ + "physics", + "test-models" + ], + "calcineurin-nfat-pathway": [ + "neuroscience", + "test-models" + ], + "calcium-spike-signaling": [ + "neuroscience", + "test-models" + ], + "caspase-activation-loop": [ + "cell-cycle", + "test-models" + ], + "cd40-signaling": [ + "immunology", + "test-models" + ], + "cell-cycle-checkpoint": [ + "cell-cycle", + "test-models" + ], + "checkpoint-kinase-signaling": [ + "cancer", + "test-models" + ], + "chemotaxis-signal-transduction": [ + "test-models" + ], + "circadian-oscillator": [ + "test-models" + ], + "clock-bmal1-gene-circuit": [ + "cell-cycle", + "test-models" + ], + "competitive-enzyme-inhibition": [ + "metabolism", + "test-models" + ], + "complement-activation-cascade": [ + "immunology", + "test-models" + ], + "contact-inhibition-hippo-yap": [ + "test-models" + ], + "cooperative-binding": [ + "test-models" + ], + "dna-damage-repair": [ + "cancer", + "test-models" + ], + "dna-methylation-dynamics": [ + "test-models" + ], + "dr5-apoptosis-signaling": [ + "cell-cycle", + "test-models" + ], + "dual-site-phosphorylation": [ + "test-models" + ], + "e2f-rb-cell-cycle-switch": [ + "cell-cycle", + "test-models" + ], + "egfr-signaling-pathway": [ + "cancer", + "test-models" + ], + "eif2a-stress-response": [ + "test-models" + ], + "endosomal-sorting-rab": [ + "test-models" + ], + "erk-nuclear-translocation": [ + "test-models" + ], + "er-stress-response": [ + "test-models" + ], + "fgf-signaling-pathway": [ + "developmental", + "test-models" + ], + "gas6-axl-signaling": [ + "test-models" + ], + "gene-expression-toggle": [ + "test-models" + ], + "glioblastoma-egfrviii-signaling": [ + "cancer", + "test-models" + ], + "glycolysis-branch-point": [ + "metabolism", + "test-models" + ], + "gpcr-desensitization-arrestin": [ + "test-models" + ], + "hedgehog-signaling-pathway": [ + "developmental", + "test-models" + ], + "hematopoietic-growth-factor": [ + "test-models" + ], + "hif1a_degradation_loop": [ + "test-models" + ], + "hypoxia-response-signaling": [ + "cancer", + "test-models" + ], + "il1b-signaling": [ + "test-models" + ], + "il6-jak-stat-pathway": [ + "test-models" + ], + "immune-synapse-formation": [ + "immunology", + "test-models" + ], + "inflammasome-activation": [ + "immunology", + "test-models" + ], + "inositol-phosphate-metabolism": [ + "neuroscience", + "test-models" + ], + "insulin-glucose-homeostasis": [ + "metabolism", + "test-models" + ], + "interferon-signaling": [ + "immunology", + "test-models" + ], + "ire1a-xbp1-er-stress": [ + "test-models" + ], + "jak-stat-cytokine-signaling": [ + "immunology", + "test-models" + ], + "jnk-mapk-signaling": [ + "test-models" + ], + "kir-channel-regulation": [ + "test-models" + ], + "lac-operon-regulation": [ + "metabolism", + "test-models" + ], + "lipid-mediated-pip3-signaling": [ + "test-models" + ], + "l-type-calcium-channel-dynamics": [ + "neuroscience", + "test-models" + ], + "mapk-signaling-cascade": [ + "cancer", + "test-models" + ], + "michaelis-menten-kinetics": [ + "metabolism", + "test-models" + ], + "mtorc2-signaling": [ + "test-models" + ], + "mtor-signaling": [ + "neuroscience", + "test-models" + ], + "myogenic-differentiation": [ + "developmental", + "test-models" + ], + "negative-feedback-loop": [ + "test-models" + ], + "neurotransmitter-release": [ + "neuroscience", + "test-models" + ], + "nfkb-feedback": [ + "test-models" + ], + "no-cgmp-signaling": [ + "metabolism", + "test-models" + ], + "notch-delta-lateral-inhibition": [ + "developmental", + "test-models" + ], + "oxidative-stress-response": [ + "test-models" + ], + "p38-mapk-signaling": [ + "cancer", + "test-models" + ], + "p53-mdm2-oscillator": [ + "cell-cycle", + "test-models" + ], + "parp1-mediated-dna-repair": [ + "cell-cycle", + "test-models" + ], + "phosphorelay-chain": [ + "test-models" + ], + "platelet-activation": [ + "immunology", + "test-models" + ], + "predator-prey-dynamics": [ + "test-models" + ], + "quorum-sensing-circuit": [ + "test-models" + ], + "rab-gtpase-cycle": [ + "test-models" + ], + "rankl-rank-signaling": [ + "developmental", + "test-models" + ], + "ras-gef-gap-cycle": [ + "cancer", + "test-models" + ], + "repressilator-oscillator": [ + "test-models" + ], + "retinoic-acid-signaling": [ + "developmental", + "test-models" + ], + "rho-gtpase-actin-cytoskeleton": [ + "test-models" + ], + "shp2-phosphatase-regulation": [ + "test-models" + ], + "signal-amplification-cascade": [ + "test-models" + ], + "simple-dimerization": [ + "test-models" + ], + "sir-epidemic-model": [ + "ecology", + "tutorials", + "test-models" + ], + "smad-tgf-beta-signaling": [ + "developmental", + "test-models" + ], + "sonic-hedgehog-gradient": [ + "developmental", + "test-models" + ], + "stat3-mediated-transcription": [ + "test-models" + ], + "stress-response-adaptation": [ + "test-models" + ], + "synaptic-plasticity-ltp": [ + "neuroscience", + "test-models" + ], + "t-cell-activation": [ + "immunology", + "test-models" + ], + "tlr3-dsrna-sensing": [ + "immunology", + "test-models" + ], + "tnf-induced-apoptosis": [ + "cell-cycle", + "test-models" + ], + "two-component-system": [ + "test-models" + ], + "vegf-angiogenesis": [ + "cancer", + "test-models" + ], + "viral-sensing-innate-immunity": [ + "immunology", + "test-models" + ], + "wnt-beta-catenin-signaling": [ + "developmental", + "test-models" + ], + "wound-healing-pdgf-signaling": [ + "test-models" + ], + "compartment_endocytosis": [ + "test-models" + ], + "compartment_membrane_bound": [ + "test-models" + ], + "compartment_nested_transport": [ + "test-models" + ], + "compartment_nuclear_transport": [ + "test-models" + ], + "compartment_organelle_exchange": [ + "test-models" + ], + "cs_diffie_hellman": [ + "cs", + "test-models" + ], + "cs_hash_function": [ + "cs", + "test-models" + ], + "cs_huffman": [ + "cs", + "test-models" + ], + "cs_monte_carlo_pi": [ + "cs", + "test-models" + ], + "cs_pagerank": [ + "cs", + "test-models" + ], + "cs_pid_controller": [ + "cs", + "test-models" + ], + "cs_regex_nfa": [ + "cs", + "test-models" + ], + "eco_coevolution_host_parasite": [ + "ecology", + "test-models" + ], + "eco_food_web_chaos_3sp": [ + "ecology", + "test-models" + ], + "eco_lotka_volterra_grid": [ + "ecology", + "test-models" + ], + "eco_mutualism_obligate": [ + "ecology", + "test-models" + ], + "eco_rock_paper_scissors_spatial": [ + "ecology", + "test-models" + ], + "energy_allostery_mwc": [ + "test-models" + ], + "energy_catalysis_mm": [ + "test-models" + ], + "energy_cooperativity_adh": [ + "test-models" + ], + "energy_linear_chain": [ + "test-models" + ], + "energy_transport_pump": [ + "test-models" + ], + "feature_functional_rates_volume": [ + "test-models" + ], + "feature_global_functions_scan": [ + "test-models" + ], + "feature_local_functions_explicit": [ + "test-models" + ], + "feature_symmetry_factors_cyclic": [ + "test-models" + ], + "feature_synthesis_degradation_ss": [ + "test-models" + ], + "gm_game_of_life": [ + "test-models" + ], + "gm_ray_marcher": [ + "test-models" + ], + "genetic_bistability_energy": [ + "test-models" + ], + "genetic_dna_replication_stochastic": [ + "test-models" + ], + "genetic_goodwin_oscillator": [ + "test-models" + ], + "genetic_translation_kinetics": [ + "test-models" + ], + "genetic_turing_pattern_1d": [ + "test-models" + ], + "meta_formal_game_theory": [ + "test-models" + ], + "meta_formal_molecular_clock": [ + "test-models" + ], + "meta_formal_petri_net": [ + "test-models" + ], + "mt_arithmetic_compiler": [ + "cs", + "test-models" + ], + "mt_bngl_interpreter": [ + "cs", + "test-models" + ], + "mt_music_sequencer": [ + "cs", + "test-models" + ], + "mt_pascal_triangle": [ + "cs", + "test-models" + ], + "mt_quine": [ + "cs", + "test-models" + ], + "ml_gradient_descent": [ + "ml-signal", + "test-models" + ], + "ml_hopfield": [ + "ml-signal", + "test-models" + ], + "ml_kmeans": [ + "ml-signal", + "test-models" + ], + "ml_q_learning": [ + "ml-signal", + "test-models" + ], + "ml_svm": [ + "ml-signal", + "test-models" + ], + "nn_xor": [ + "ml-signal", + "test-models" + ], + "nfsim_aggregation_gelation": [ + "test-models" + ], + "nfsim_coarse_graining": [ + "test-models" + ], + "nfsim_dynamic_compartments": [ + "test-models" + ], + "nfsim_hybrid_particle_field": [ + "test-models" + ], + "nfsim_ring_closure_polymer": [ + "test-models" + ], + "ph_lorenz_attractor": [ + "physics", + "test-models" + ], + "ph_nbody_gravity": [ + "physics", + "test-models" + ], + "ph_schrodinger": [ + "physics", + "test-models" + ], + "ph_wave_equation": [ + "physics", + "test-models" + ], + "process_actin_treadmilling": [ + "test-models" + ], + "process_autophagy_flux": [ + "test-models" + ], + "process_cell_adhesion_strength": [ + "test-models" + ], + "process_kinetic_proofreading_tcr": [ + "test-models" + ], + "process_quorum_sensing_switch": [ + "test-models" + ], + "sp_fourier_synthesizer": [ + "ml-signal", + "test-models" + ], + "sp_image_convolution": [ + "ml-signal", + "test-models" + ], + "sp_kalman_filter": [ + "ml-signal", + "test-models" + ], + "synbio_band_pass_filter": [ + "synbio", + "test-models" + ], + "synbio_counter_molecular": [ + "synbio", + "test-models" + ], + "synbio_edge_detector": [ + "synbio", + "test-models" + ], + "synbio_logic_gates_enzymatic": [ + "synbio", + "test-models" + ], + "synbio_oscillator_synchronization": [ + "synbio", + "test-models" + ], + "wacky_alchemy_stone": [ + "synbio", + "test-models" + ], + "wacky_black_hole": [ + "test-models" + ], + "wacky_bouncing_ball": [ + "physics", + "test-models" + ], + "wacky_traffic_jam_asep": [ + "physics", + "test-models" + ], + "wacky_zombie_infection": [ + "ecology", + "test-models" + ], + "chemistry": [ + "tutorials", + "published-models" + ], + "polymer": [ + "tutorials", + "published-models" + ], + "polymer_draft": [ + "tutorials", + "published-models" + ], + "quasi_equilibrium": [ + "tutorials", + "native-tutorials", + "published-models" + ], + "simple": [ + "tutorials", + "published-models" + ], + "toy1": [ + "tutorials", + "published-models" + ], + "toy2": [ + "tutorials", + "published-models" + ], + "AB": [ + "native-tutorials" + ], + "ABC": [ + "metabolism", + "native-tutorials" + ], + "ABC_scan": [ + "native-tutorials" + ], + "ABC_ssa": [ + "native-tutorials" + ], + "ABp": [ + "metabolism", + "native-tutorials" + ], + "ABp_approx": [ + "native-tutorials" + ], + "BAB": [ + "native-tutorials" + ], + "BAB_coop": [ + "native-tutorials" + ], + "BAB_scan": [ + "native-tutorials" + ], + "birth-death": [ + "native-tutorials", + "published-models" + ], + "cBNGL_simple": [ + "native-tutorials" + ], + "Chylek_library": [ + "native-tutorials" + ], + "CircadianOscillator": [ + "cell-cycle", + "native-tutorials", + "published-models" + ], + "ComplexDegradation": [ + "native-tutorials", + "published-models" + ], + "Creamer_2012": [ + "native-tutorials" + ], + "egfr_simple": [ + "native-tutorials" + ], + "FceRI_ji": [ + "native-tutorials" + ], + "FceRI_viz": [ + "native-tutorials", + "published-models" + ], + "GK": [ + "metabolism", + "native-tutorials" + ], + "Lisman": [ + "neuroscience", + "native-tutorials" + ], + "Lisman_bifurcate": [ + "neuroscience", + "native-tutorials" + ], + "LR": [ + "native-tutorials" + ], + "LR_comp": [ + "native-tutorials" + ], + "LRR": [ + "native-tutorials" + ], + "LRR_comp": [ + "native-tutorials" + ], + "LV": [ + "native-tutorials" + ], + "LV_comp": [ + "native-tutorials" + ], + "organelle_transport": [ + "native-tutorials" + ], + "organelle_transport_struct": [ + "native-tutorials" + ], + "Repressilator": [ + "cell-cycle", + "synbio", + "native-tutorials", + "published-models" + ], + "SIR": [ + "native-tutorials" + ], + "Suderman_2013": [ + "native-tutorials" + ], + "toggle": [ + "synbio", + "native-tutorials", + "published-models" + ], + "visualize": [ + "native-tutorials", + "published-models" + ], + "Barua_2013": [ + "published-models" + ], + "Dreisigmeyer_2008": [ + "published-models" + ], + "Gardner_2000": [ + "published-models" + ], + "Hlavacek2018Egg_egg": [ + "published-models" + ], + "Hlavacek2018Elephant_elephant_EFA": [ + "published-models" + ], + "Hlavacek2018Restructuration_after_bunching": [ + "published-models" + ], + "Kocieniewski_2012": [ + "published-models" + ], + "Lin2019_ERK_model": [ + "published-models" + ], + "Mallela2021_States": [ + "published-models" + ], + "Mallela2021_Cities": [ + "published-models" + ], + "Alabama": [ + "published-models" + ], + "Mallela2022_MSAs": [ + "published-models" + ], + "Miller2022_NavajoNation": [ + "published-models" + ], + "Miller2025_MEK": [ + "published-models" + ], + "Mitra2019_02_egfr_bnf1_InputFiles_egfr": [ + "published-models" + ], + "02_egfr_egfr": [ + "published-models" + ], + "03_fcerig_fceri_gamma2": [ + "published-models" + ], + "04_egfrnf_egfr_nf": [ + "published-models" + ], + "05_threestep_m1": [ + "published-models" + ], + "06_degranulation_model_tofit": [ + "published-models" + ], + "07_egg_egg": [ + "published-models" + ], + "10_egfr_egfr_ode": [ + "published-models" + ], + "11_TLBR_tlbr": [ + "published-models" + ], + "12_TCR_tcr": [ + "published-models" + ], + "13_receptor_example5_starting_point": [ + "published-models" + ], + "14_receptor_nf_receptor_nf": [ + "published-models" + ], + "15_igf1r_IGF1R_fit_all": [ + "published-models" + ], + "17_egfr_ssa_egfr": [ + "published-models" + ], + "18_mapk_Scaff_22_ground": [ + "published-models" + ], + "19_raf_constraint_RAFi": [ + "published-models" + ], + "20_raf_constraint4_RAFi": [ + "published-models" + ], + "24_jnk_JNKmodel_180724_bnf": [ + "published-models" + ], + "26_tcr_sens_tcr_sens_tofit": [ + "published-models" + ], + "28_mapk_ensemble_tofit": [ + "published-models" + ], + "30_jobs_jobs_ground": [ + "published-models" + ], + "31_elephant_elephant": [ + "published-models" + ], + "model_ground": [ + "published-models" + ], + "problem16_model0_tofit": [ + "published-models" + ], + "problem16_3cat_model0_tofit": [ + "published-models" + ], + "problem32_model0_tofit": [ + "published-models" + ], + "problem32_3cat_model0_tofit": [ + "published-models" + ], + "problem4_model0_tofit": [ + "published-models" + ], + "problem4_3cat_model0_tofit": [ + "published-models" + ], + "problem64_model0_tofit": [ + "published-models" + ], + "problem64_3cat_model0_tofit": [ + "published-models" + ], + "problem8_model0_tofit": [ + "published-models" + ], + "problem8_3cat_model0_tofit": [ + "published-models" + ], + "problem_quant_model_tofit": [ + "published-models" + ], + "rab_mon1ccz1_ox": [ + "published-models" + ], + "pybnf_files_rab_mon1ccz1_ox": [ + "published-models" + ], + "notch": [ + "published-models" + ], + "CaMKII_holo": [ + "published-models" + ], + "extra_CaMKII_Holo": [ + "published-models" + ], + "mCaMKII_Ca_Spike": [ + "published-models" + ], + "Pekalski_2013": [ + "published-models" + ], + "egfr": [ + "published-models" + ], + "egfr_ground": [ + "published-models" + ], + "egfr_nf": [ + "published-models" + ], + "example1": [ + "published-models" + ], + "example2_starting_point": [ + "published-models" + ], + "fceri_gamma2": [ + "published-models" + ], + "fceri_gamma2_ground_truth": [ + "published-models" + ], + "IGF1R_Model_receptor_activation_bnf": [ + "published-models" + ], + "model": [ + "published-models" + ], + "model_tofit": [ + "published-models" + ], + "parabola": [ + "published-models" + ], + "parabola_ground": [ + "published-models" + ], + "polynomial": [ + "published-models" + ], + "polynomial_ground": [ + "published-models" + ], + "RAFi": [ + "published-models" + ], + "RAFi_ground": [ + "published-models" + ], + "receptor": [ + "published-models" + ], + "receptor_nf": [ + "published-models" + ], + "tcr": [ + "published-models" + ], + "pt303": [ + "published-models" + ], + "pt403": [ + "published-models" + ], + "pt409": [ + "published-models" + ], + "Rule_based_egfr_compart": [ + "published-models" + ], + "Rule_based_Ran_transport": [ + "published-models" + ], + "Rule_based_Ran_transport_draft": [ + "published-models" + ], + "Salazar_Cavazos2019_190127_CHO_EGFR_best_fit": [ + "published-models" + ], + "PyBNF_fitting_setup_190127_CHO_EGFR_forBNF": [ + "published-models" + ], + "example1_BNFfiles_example1": [ + "published-models" + ], + "example2_BNFfiles_example2": [ + "published-models" + ], + "example3_BNFfiles_example3": [ + "published-models" + ], + "example4_BNFfiles_example4": [ + "published-models" + ], + "example5_BNFfiles_example5": [ + "published-models" + ], + "example6_BNFfiles_example6": [ + "published-models" + ], + "Thomas2016_example1_fit": [ + "published-models" + ], + "Dallas": [ + "published-models" + ], + "Houston": [ + "published-models" + ], + "NYC": [ + "published-models" + ], + "Phoenix": [ + "published-models" + ], + "vilar_2002c": [ + "published-models" + ], + "wnt": [ + "published-models" + ] + }, + "sortOverrides": {} +} \ No newline at end of file diff --git a/gallery.json b/gallery.json new file mode 100644 index 0000000..6d77934 --- /dev/null +++ b/gallery.json @@ -0,0 +1,1387 @@ +{ + "version": 1, + "generated": "2026-05-03T22:49:19.469Z", + "categories": [ + { + "id": "cancer", + "name": "Cancer Biology", + "description": "Oncogenic signaling pathways and cancer models", + "sortOrder": 0 + }, + { + "id": "immunology", + "name": "Immunology", + "description": "Immune signaling models, TCR, BCR, Fc receptors", + "sortOrder": 1 + }, + { + "id": "neuroscience", + "name": "Neuroscience", + "description": "Neuronal signaling, neural networks, synaptic models", + "sortOrder": 2 + }, + { + "id": "cell-cycle", + "name": "Cell Cycle", + "description": "Cell division, cell cycle regulation models", + "sortOrder": 3 + }, + { + "id": "metabolism", + "name": "Metabolism", + "description": "Metabolic networks, biochemical pathways", + "sortOrder": 4 + }, + { + "id": "developmental", + "name": "Developmental Biology", + "description": "Developmental signaling, pattern formation", + "sortOrder": 5 + }, + { + "id": "ecology", + "name": "Ecology", + "description": "Population dynamics, ecological networks", + "sortOrder": 6 + }, + { + "id": "physics", + "name": "Physics", + "description": "Physical systems modeled with BNGL", + "sortOrder": 7 + }, + { + "id": "cs", + "name": "Computer Science", + "description": "CS models, computational systems", + "sortOrder": 8 + }, + { + "id": "ml-signal", + "name": "ML / Signal Processing", + "description": "Signal processing, machine learning models", + "sortOrder": 9 + }, + { + "id": "synbio", + "name": "Synthetic Biology", + "description": "Synthetic gene circuits, engineered systems", + "sortOrder": 10 + }, + { + "id": "published-models", + "name": "Published Models", + "description": "Peer-reviewed published models from literature", + "sortOrder": 11 + }, + { + "id": "multistage", + "name": "Multistage Models", + "description": "Models with multiple stages or compartments", + "sortOrder": 12 + }, + { + "id": "tutorials", + "name": "Tutorials", + "description": "Example models for learning BNGL", + "sortOrder": 13 + }, + { + "id": "native-tutorials", + "name": "Native Tutorials", + "description": "Built-in tutorial models with guided steps", + "sortOrder": 14 + }, + { + "id": "test-models", + "name": "Test Models", + "description": "Internal test and validation models", + "sortOrder": 15 + } + ], + "assignments": { + "02_egfr_egfr": [ + "published-models" + ], + "03_fcerig_fceri_gamma2": [ + "published-models" + ], + "04_egfrnf_egfr_nf": [ + "published-models" + ], + "05_threestep_m1": [ + "published-models" + ], + "06_degranulation_model_tofit": [ + "published-models" + ], + "07_egg_egg": [ + "published-models" + ], + "10_egfr_egfr_ode": [ + "published-models" + ], + "11_TLBR_tlbr": [ + "published-models" + ], + "12_TCR_tcr": [ + "published-models" + ], + "13_receptor_example5_starting_point": [ + "published-models" + ], + "14_receptor_nf_receptor_nf": [ + "published-models" + ], + "15_igf1r_IGF1R_fit_all": [ + "published-models" + ], + "17_egfr_ssa_egfr": [ + "published-models" + ], + "18_mapk_Scaff_22_ground": [ + "published-models" + ], + "19_raf_constraint_RAFi": [ + "published-models" + ], + "20_raf_constraint4_RAFi": [ + "published-models" + ], + "24_jnk_JNKmodel_180724_bnf": [ + "published-models" + ], + "26_tcr_sens_tcr_sens_tofit": [ + "published-models" + ], + "28_mapk_ensemble_tofit": [ + "published-models" + ], + "30_jobs_jobs_ground": [ + "published-models" + ], + "31_elephant_elephant": [ + "published-models" + ], + "AB": [ + "native-tutorials" + ], + "ABC": [ + "metabolism", + "native-tutorials" + ], + "ABC_scan": [ + "native-tutorials" + ], + "ABC_ssa": [ + "native-tutorials" + ], + "ABp": [ + "metabolism", + "native-tutorials" + ], + "ABp_approx": [ + "native-tutorials" + ], + "Alabama": [ + "published-models" + ], + "An_2009": [ + "immunology", + "published-models" + ], + "BAB": [ + "native-tutorials" + ], + "BAB_coop": [ + "native-tutorials" + ], + "BAB_scan": [ + "native-tutorials" + ], + "BaruaBCR_2012": [ + "immunology", + "published-models" + ], + "BaruaFceRI_2012": [ + "immunology", + "published-models" + ], + "Barua_2007": [ + "cancer", + "published-models" + ], + "Barua_2009": [ + "cancer", + "published-models" + ], + "Barua_2013": [ + "published-models" + ], + "Blinov_2006": [ + "cell-cycle", + "published-models" + ], + "Blinov_egfr": [ + "cancer", + "published-models" + ], + "Blinov_ran": [ + "cell-cycle", + "published-models" + ], + "CaMKII_holo": [ + "published-models" + ], + "Chattaraj_2021": [ + "neuroscience", + "published-models" + ], + "Cheemalavagu_JAK_STAT": [ + "immunology", + "published-models" + ], + "ChylekFceRI_2014": [ + "immunology", + "published-models" + ], + "ChylekTCR_2014": [ + "immunology", + "published-models" + ], + "Chylek_library": [ + "native-tutorials" + ], + "CircadianOscillator": [ + "cell-cycle", + "native-tutorials", + "published-models" + ], + "ComplexDegradation": [ + "native-tutorials", + "published-models" + ], + "Creamer_2012": [ + "native-tutorials" + ], + "Dallas": [ + "published-models" + ], + "Dembo_1978": [ + "physics", + "published-models" + ], + "Dolan_2015": [ + "metabolism", + "published-models" + ], + "Dreisigmeyer_2008": [ + "published-models" + ], + "Dushek_2011": [ + "immunology", + "published-models" + ], + "Dushek_2014": [ + "immunology", + "published-models" + ], + "Erdem_2021": [ + "metabolism", + "published-models" + ], + "Faeder_2003": [ + "immunology", + "published-models" + ], + "FceRI_ji": [ + "native-tutorials" + ], + "FceRI_viz": [ + "native-tutorials", + "published-models" + ], + "GK": [ + "metabolism", + "native-tutorials" + ], + "Gardner_2000": [ + "published-models" + ], + "Goldstein_1980": [ + "physics", + "published-models" + ], + "Harmon_2017": [ + "immunology", + "published-models" + ], + "Hat_2016": [ + "cell-cycle", + "multistage", + "published-models" + ], + "Hlavacek2018Egg_egg": [ + "published-models" + ], + "Hlavacek2018Elephant_elephant_EFA": [ + "published-models" + ], + "Hlavacek2018Restructuration_after_bunching": [ + "published-models" + ], + "Hlavacek_1999": [ + "physics", + "published-models" + ], + "Hlavacek_2001": [ + "physics", + "published-models" + ], + "Houston": [ + "published-models" + ], + "IGF1R_Model_receptor_activation_bnf": [ + "published-models" + ], + "Jaruszewicz-Blonska_2023": [ + "immunology", + "published-models" + ], + "Jung_2017": [ + "neuroscience", + "published-models" + ], + "Kesseler_2013": [ + "cell-cycle", + "published-models" + ], + "Kocieniewski_2012": [ + "published-models" + ], + "Kozer_2013": [ + "cancer", + "published-models" + ], + "Kozer_2014": [ + "cancer", + "published-models" + ], + "LR": [ + "native-tutorials" + ], + "LRR": [ + "native-tutorials" + ], + "LRR_comp": [ + "native-tutorials" + ], + "LR_comp": [ + "native-tutorials" + ], + "LV": [ + "native-tutorials" + ], + "LV_comp": [ + "native-tutorials" + ], + "Lang_2024": [ + "cell-cycle", + "published-models" + ], + "Ligon_2014": [ + "cancer", + "published-models" + ], + "Lin2019_ERK_model": [ + "published-models" + ], + "Lin_ERK_2019": [ + "developmental", + "published-models" + ], + "Lin_Prion_2019": [ + "neuroscience", + "published-models" + ], + "Lin_TCR_2019": [ + "immunology", + "published-models" + ], + "Lisman": [ + "native-tutorials", + "neuroscience" + ], + "Lisman_bifurcate": [ + "native-tutorials", + "neuroscience" + ], + "Macken_1982": [ + "physics", + "published-models" + ], + "Mallela2021_Cities": [ + "published-models" + ], + "Mallela2021_States": [ + "published-models" + ], + "Mallela2022_MSAs": [ + "published-models" + ], + "Massole_2023": [ + "developmental", + "published-models" + ], + "McMillan_2021": [ + "immunology", + "published-models" + ], + "Mertins_2023": [ + "cancer", + "published-models" + ], + "Miller2022_NavajoNation": [ + "published-models" + ], + "Miller2025_MEK": [ + "published-models" + ], + "Mitra2019_02_egfr_bnf1_InputFiles_egfr": [ + "published-models" + ], + "Model_ZAP": [ + "immunology", + "published-models" + ], + "Mukhopadhyay_2013": [ + "immunology", + "published-models" + ], + "NYC": [ + "published-models" + ], + "Nag_2009": [ + "cancer", + "published-models" + ], + "Nosbisch_2022": [ + "cancer", + "published-models" + ], + "Pekalski_2013": [ + "published-models" + ], + "Phoenix": [ + "published-models" + ], + "Posner_1995": [ + "physics", + "published-models" + ], + "Posner_2004": [ + "physics", + "published-models" + ], + "PyBNF_fitting_setup_190127_CHO_EGFR_forBNF": [ + "published-models" + ], + "RAFi": [ + "published-models" + ], + "RAFi_ground": [ + "published-models" + ], + "Repressilator": [ + "cell-cycle", + "native-tutorials", + "published-models", + "synbio" + ], + "Rule_based_Ran_transport": [ + "published-models" + ], + "Rule_based_Ran_transport_draft": [ + "published-models" + ], + "Rule_based_egfr_compart": [ + "published-models" + ], + "Rule_based_egfr_tutorial": [ + "cancer", + "published-models" + ], + "SIR": [ + "native-tutorials" + ], + "Salazar_Cavazos2019_190127_CHO_EGFR_best_fit": [ + "published-models" + ], + "Suderman_2013": [ + "native-tutorials" + ], + "Thomas2016_example1_fit": [ + "published-models" + ], + "Yang_2008": [ + "physics", + "published-models" + ], + "Zhang_2021": [ + "developmental", + "published-models" + ], + "Zhang_2023": [ + "developmental", + "published-models" + ], + "akt-signaling": [ + "test-models" + ], + "allosteric-activation": [ + "metabolism", + "test-models" + ], + "ampk-signaling": [ + "neuroscience", + "test-models" + ], + "apoptosis-cascade": [ + "cell-cycle", + "test-models" + ], + "auto-activation-loop": [ + "metabolism", + "test-models" + ], + "autophagy-regulation": [ + "metabolism", + "test-models" + ], + "bcr-signaling": [ + "immunology", + "test-models" + ], + "beta-adrenergic-response": [ + "neuroscience", + "test-models" + ], + "birth-death": [ + "native-tutorials", + "published-models" + ], + "bistable-toggle-switch": [ + "test-models" + ], + "blood-coagulation-thrombin": [ + "immunology", + "test-models" + ], + "bmp-signaling": [ + "developmental", + "test-models" + ], + "brusselator-oscillator": [ + "physics", + "test-models" + ], + "cBNGL_simple": [ + "native-tutorials" + ], + "calcineurin-nfat-pathway": [ + "neuroscience", + "test-models" + ], + "calcium-spike-signaling": [ + "neuroscience", + "test-models" + ], + "caspase-activation-loop": [ + "cell-cycle", + "test-models" + ], + "cd40-signaling": [ + "immunology", + "test-models" + ], + "cell-cycle-checkpoint": [ + "cell-cycle", + "test-models" + ], + "checkpoint-kinase-signaling": [ + "cancer", + "test-models" + ], + "chemistry": [ + "published-models", + "tutorials" + ], + "chemotaxis-signal-transduction": [ + "test-models" + ], + "circadian-oscillator": [ + "test-models" + ], + "clock-bmal1-gene-circuit": [ + "cell-cycle", + "test-models" + ], + "compartment_endocytosis": [ + "test-models" + ], + "compartment_membrane_bound": [ + "test-models" + ], + "compartment_nested_transport": [ + "test-models" + ], + "compartment_nuclear_transport": [ + "test-models" + ], + "compartment_organelle_exchange": [ + "test-models" + ], + "competitive-enzyme-inhibition": [ + "metabolism", + "test-models" + ], + "complement-activation-cascade": [ + "immunology", + "test-models" + ], + "contact-inhibition-hippo-yap": [ + "test-models" + ], + "cooperative-binding": [ + "test-models" + ], + "cs_diffie_hellman": [ + "cs", + "test-models" + ], + "cs_hash_function": [ + "cs", + "test-models" + ], + "cs_huffman": [ + "cs", + "test-models" + ], + "cs_monte_carlo_pi": [ + "cs", + "test-models" + ], + "cs_pagerank": [ + "cs", + "test-models" + ], + "cs_pid_controller": [ + "cs", + "test-models" + ], + "cs_regex_nfa": [ + "cs", + "test-models" + ], + "degranulation_model": [ + "immunology", + "published-models" + ], + "dna-damage-repair": [ + "cancer", + "test-models" + ], + "dna-methylation-dynamics": [ + "test-models" + ], + "dr5-apoptosis-signaling": [ + "cell-cycle", + "test-models" + ], + "dual-site-phosphorylation": [ + "test-models" + ], + "e2f-rb-cell-cycle-switch": [ + "cell-cycle", + "test-models" + ], + "eco_coevolution_host_parasite": [ + "ecology", + "test-models" + ], + "eco_food_web_chaos_3sp": [ + "ecology", + "test-models" + ], + "eco_lotka_volterra_grid": [ + "ecology", + "test-models" + ], + "eco_mutualism_obligate": [ + "ecology", + "test-models" + ], + "eco_rock_paper_scissors_spatial": [ + "ecology", + "test-models" + ], + "egfr": [ + "published-models" + ], + "egfr-signaling-pathway": [ + "cancer", + "test-models" + ], + "egfr_ground": [ + "published-models" + ], + "egfr_nf": [ + "published-models" + ], + "egfr_ode": [ + "cancer", + "published-models" + ], + "egfr_simple": [ + "native-tutorials" + ], + "eif2a-stress-response": [ + "test-models" + ], + "endosomal-sorting-rab": [ + "test-models" + ], + "energy_allostery_mwc": [ + "test-models" + ], + "energy_catalysis_mm": [ + "test-models" + ], + "energy_cooperativity_adh": [ + "test-models" + ], + "energy_linear_chain": [ + "test-models" + ], + "energy_transport_pump": [ + "test-models" + ], + "er-stress-response": [ + "test-models" + ], + "erk-nuclear-translocation": [ + "test-models" + ], + "example1": [ + "published-models" + ], + "example1_BNFfiles_example1": [ + "published-models" + ], + "example2_BNFfiles_example2": [ + "published-models" + ], + "example2_starting_point": [ + "published-models" + ], + "example3_BNFfiles_example3": [ + "published-models" + ], + "example4_BNFfiles_example4": [ + "published-models" + ], + "example5_BNFfiles_example5": [ + "published-models" + ], + "example6_BNFfiles_example6": [ + "published-models" + ], + "extra_CaMKII_Holo": [ + "published-models" + ], + "fceri_fyn": [ + "immunology", + "published-models" + ], + "fceri_gamma2": [ + "published-models" + ], + "fceri_gamma2_ground_truth": [ + "published-models" + ], + "feature_functional_rates_volume": [ + "test-models" + ], + "feature_global_functions_scan": [ + "test-models" + ], + "feature_local_functions_explicit": [ + "test-models" + ], + "feature_symmetry_factors_cyclic": [ + "test-models" + ], + "feature_synthesis_degradation_ss": [ + "test-models" + ], + "fgf-signaling-pathway": [ + "developmental", + "test-models" + ], + "gas6-axl-signaling": [ + "test-models" + ], + "gene-expression-toggle": [ + "test-models" + ], + "genetic_bistability_energy": [ + "test-models" + ], + "genetic_dna_replication_stochastic": [ + "test-models" + ], + "genetic_goodwin_oscillator": [ + "test-models" + ], + "genetic_translation_kinetics": [ + "test-models" + ], + "genetic_turing_pattern_1d": [ + "test-models" + ], + "glioblastoma-egfrviii-signaling": [ + "cancer", + "test-models" + ], + "glycolysis-branch-point": [ + "metabolism", + "test-models" + ], + "gm_game_of_life": [ + "test-models" + ], + "gm_ray_marcher": [ + "test-models" + ], + "gpcr-desensitization-arrestin": [ + "test-models" + ], + "hedgehog-signaling-pathway": [ + "developmental", + "test-models" + ], + "hematopoietic-growth-factor": [ + "test-models" + ], + "hif1a_degradation_loop": [ + "test-models" + ], + "hypoxia-response-signaling": [ + "cancer", + "test-models" + ], + "il1b-signaling": [ + "test-models" + ], + "il6-jak-stat-pathway": [ + "test-models" + ], + "immune-synapse-formation": [ + "immunology", + "test-models" + ], + "inflammasome-activation": [ + "immunology", + "test-models" + ], + "innate_immunity": [ + "immunology", + "published-models" + ], + "inositol-phosphate-metabolism": [ + "neuroscience", + "test-models" + ], + "insulin-glucose-homeostasis": [ + "metabolism", + "test-models" + ], + "interferon-signaling": [ + "immunology", + "test-models" + ], + "ire1a-xbp1-er-stress": [ + "test-models" + ], + "jak-stat-cytokine-signaling": [ + "immunology", + "test-models" + ], + "jnk-mapk-signaling": [ + "test-models" + ], + "kir-channel-regulation": [ + "test-models" + ], + "l-type-calcium-channel-dynamics": [ + "neuroscience", + "test-models" + ], + "lac-operon-regulation": [ + "metabolism", + "test-models" + ], + "lipid-mediated-pip3-signaling": [ + "test-models" + ], + "mCaMKII_Ca_Spike": [ + "published-models" + ], + "mapk-dimers": [ + "cancer", + "published-models" + ], + "mapk-monomers": [ + "cancer", + "published-models" + ], + "mapk-signaling-cascade": [ + "cancer", + "test-models" + ], + "meta_formal_game_theory": [ + "test-models" + ], + "meta_formal_molecular_clock": [ + "test-models" + ], + "meta_formal_petri_net": [ + "test-models" + ], + "michaelis-menten-kinetics": [ + "metabolism", + "test-models" + ], + "ml_gradient_descent": [ + "ml-signal", + "test-models" + ], + "ml_hopfield": [ + "ml-signal", + "test-models" + ], + "ml_kmeans": [ + "ml-signal", + "test-models" + ], + "ml_q_learning": [ + "ml-signal", + "test-models" + ], + "ml_svm": [ + "ml-signal", + "test-models" + ], + "model": [ + "published-models" + ], + "model_ground": [ + "published-models" + ], + "model_tofit": [ + "published-models" + ], + "mt_arithmetic_compiler": [ + "cs", + "test-models" + ], + "mt_bngl_interpreter": [ + "cs", + "test-models" + ], + "mt_music_sequencer": [ + "cs", + "test-models" + ], + "mt_pascal_triangle": [ + "cs", + "test-models" + ], + "mt_quine": [ + "cs", + "test-models" + ], + "mtor-signaling": [ + "neuroscience", + "test-models" + ], + "mtorc2-signaling": [ + "test-models" + ], + "myogenic-differentiation": [ + "developmental", + "test-models" + ], + "negative-feedback-loop": [ + "test-models" + ], + "neurotransmitter-release": [ + "neuroscience", + "test-models" + ], + "nfkb-feedback": [ + "test-models" + ], + "nfsim_aggregation_gelation": [ + "test-models" + ], + "nfsim_coarse_graining": [ + "test-models" + ], + "nfsim_dynamic_compartments": [ + "test-models" + ], + "nfsim_hybrid_particle_field": [ + "test-models" + ], + "nfsim_ring_closure_polymer": [ + "test-models" + ], + "nn_xor": [ + "ml-signal", + "test-models" + ], + "no-cgmp-signaling": [ + "metabolism", + "test-models" + ], + "notch": [ + "published-models" + ], + "notch-delta-lateral-inhibition": [ + "developmental", + "test-models" + ], + "organelle_transport": [ + "native-tutorials" + ], + "organelle_transport_struct": [ + "native-tutorials" + ], + "oxidative-stress-response": [ + "test-models" + ], + "p38-mapk-signaling": [ + "cancer", + "test-models" + ], + "p53-mdm2-oscillator": [ + "cell-cycle", + "test-models" + ], + "parabola": [ + "published-models" + ], + "parabola_ground": [ + "published-models" + ], + "parp1-mediated-dna-repair": [ + "cell-cycle", + "test-models" + ], + "ph_lorenz_attractor": [ + "physics", + "test-models" + ], + "ph_nbody_gravity": [ + "physics", + "test-models" + ], + "ph_schrodinger": [ + "physics", + "test-models" + ], + "ph_wave_equation": [ + "physics", + "test-models" + ], + "phosphorelay-chain": [ + "test-models" + ], + "platelet-activation": [ + "immunology", + "test-models" + ], + "polymer": [ + "published-models", + "tutorials" + ], + "polymer_draft": [ + "published-models", + "tutorials" + ], + "polynomial": [ + "published-models" + ], + "polynomial_ground": [ + "published-models" + ], + "predator-prey-dynamics": [ + "test-models" + ], + "problem16_3cat_model0_tofit": [ + "published-models" + ], + "problem16_model0_tofit": [ + "published-models" + ], + "problem32_3cat_model0_tofit": [ + "published-models" + ], + "problem32_model0_tofit": [ + "published-models" + ], + "problem4_3cat_model0_tofit": [ + "published-models" + ], + "problem4_model0_tofit": [ + "published-models" + ], + "problem64_3cat_model0_tofit": [ + "published-models" + ], + "problem64_model0_tofit": [ + "published-models" + ], + "problem8_3cat_model0_tofit": [ + "published-models" + ], + "problem8_model0_tofit": [ + "published-models" + ], + "problem_quant_model_tofit": [ + "published-models" + ], + "process_actin_treadmilling": [ + "test-models" + ], + "process_autophagy_flux": [ + "test-models" + ], + "process_cell_adhesion_strength": [ + "test-models" + ], + "process_kinetic_proofreading_tcr": [ + "test-models" + ], + "process_quorum_sensing_switch": [ + "test-models" + ], + "pt303": [ + "published-models" + ], + "pt403": [ + "published-models" + ], + "pt409": [ + "published-models" + ], + "pybnf_files_rab_mon1ccz1_ox": [ + "published-models" + ], + "quasi_equilibrium": [ + "native-tutorials", + "published-models", + "tutorials" + ], + "quorum-sensing-circuit": [ + "test-models" + ], + "rab-gtpase-cycle": [ + "test-models" + ], + "rab_mon1ccz1_ox": [ + "published-models" + ], + "rankl-rank-signaling": [ + "developmental", + "test-models" + ], + "ras-gef-gap-cycle": [ + "cancer", + "test-models" + ], + "receptor": [ + "published-models" + ], + "receptor_nf": [ + "published-models" + ], + "repressilator-oscillator": [ + "test-models" + ], + "retinoic-acid-signaling": [ + "developmental", + "test-models" + ], + "rho-gtpase-actin-cytoskeleton": [ + "test-models" + ], + "shp2-phosphatase-regulation": [ + "test-models" + ], + "signal-amplification-cascade": [ + "test-models" + ], + "simple": [ + "published-models", + "tutorials" + ], + "simple-dimerization": [ + "test-models" + ], + "sir-epidemic-model": [ + "ecology", + "test-models", + "tutorials" + ], + "smad-tgf-beta-signaling": [ + "developmental", + "test-models" + ], + "sonic-hedgehog-gradient": [ + "developmental", + "test-models" + ], + "sp_fourier_synthesizer": [ + "ml-signal", + "test-models" + ], + "sp_image_convolution": [ + "ml-signal", + "test-models" + ], + "sp_kalman_filter": [ + "ml-signal", + "test-models" + ], + "stat3-mediated-transcription": [ + "test-models" + ], + "stress-response-adaptation": [ + "test-models" + ], + "synaptic-plasticity-ltp": [ + "neuroscience", + "test-models" + ], + "synbio_band_pass_filter": [ + "synbio", + "test-models" + ], + "synbio_counter_molecular": [ + "synbio", + "test-models" + ], + "synbio_edge_detector": [ + "synbio", + "test-models" + ], + "synbio_logic_gates_enzymatic": [ + "synbio", + "test-models" + ], + "synbio_oscillator_synchronization": [ + "synbio", + "test-models" + ], + "t-cell-activation": [ + "immunology", + "test-models" + ], + "tcr": [ + "published-models" + ], + "tlbr": [ + "immunology", + "published-models" + ], + "tlr3-dsrna-sensing": [ + "immunology", + "test-models" + ], + "tnf-induced-apoptosis": [ + "cell-cycle", + "test-models" + ], + "toggle": [ + "native-tutorials", + "published-models", + "synbio" + ], + "toy1": [ + "published-models", + "tutorials" + ], + "toy2": [ + "published-models", + "tutorials" + ], + "two-component-system": [ + "test-models" + ], + "vegf-angiogenesis": [ + "cancer", + "test-models" + ], + "vilar_2002": [ + "cell-cycle", + "published-models" + ], + "vilar_2002b": [ + "cell-cycle", + "published-models" + ], + "vilar_2002c": [ + "published-models" + ], + "viral-sensing-innate-immunity": [ + "immunology", + "test-models" + ], + "visualize": [ + "native-tutorials", + "published-models" + ], + "wacky_alchemy_stone": [ + "synbio", + "test-models" + ], + "wacky_black_hole": [ + "test-models" + ], + "wacky_bouncing_ball": [ + "physics", + "test-models" + ], + "wacky_traffic_jam_asep": [ + "physics", + "test-models" + ], + "wacky_zombie_infection": [ + "ecology", + "test-models" + ], + "wnt": [ + "published-models" + ], + "wnt-beta-catenin-signaling": [ + "developmental", + "test-models" + ], + "wound-healing-pdgf-signaling": [ + "test-models" + ] + }, + "sortOverrides": {} +} \ No newline at end of file diff --git a/manifest-slim.generated.json b/manifest-slim.generated.json new file mode 100644 index 0000000..cc4a485 --- /dev/null +++ b/manifest-slim.generated.json @@ -0,0 +1,15294 @@ +[ + { + "id": "03_fcerig_fceri_gamma2", + "name": "03-fcerig", + "description": "Added molecule type definition block so that the", + "tags": [ + "immunology" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "04_egfrnf_egfr_nf", + "name": "example2_starting_point.bngl", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "f", + "lt_nm", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "molecules" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "06_degranulation_model_tofit", + "name": "of IgE receptor signaling", + "description": "A model of IgE receptor signaling", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "07_egg_egg", + "name": "07-egg", + "description": "BNGL model: egg", + "tags": [ + "a0", + "a1", + "a2", + "b1", + "b2", + "c0", + "c1", + "c2", + "d1", + "d2", + "period", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "10_egfr_egfr_ode", + "name": "example1.bngl", + "description": "Filename: example1.bngl", + "tags": [ + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "11_TLBR_tlbr", + "name": "11-TLBR", + "description": "BNGL model: tlbr", + "tags": [ + "alpha", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "12_TCR_tcr", + "name": "of T cell receptor signaling", + "description": "A model of T cell receptor signaling", + "tags": [ + "immunology" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "14_receptor_nf_receptor_nf", + "name": "of ligand/receptor binding and receptor phosphorylation.", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", + "tags": [ + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "15_igf1r_IGF1R_fit_all", + "name": "15-igf1r", + "description": "Author: William S. Hlavacek", + "tags": [ + "dilution", + "a1_permpers", + "a2_permpers", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "19_raf_constraint_RAFi", + "name": "19-raf-constraint", + "description": "BNGL model: RAFi", + "tags": [ + "k1", + "k2", + "k3", + "k5", + "kf1", + "kf2", + "kf3", + "kf4", + "kf5", + "kf6", + "rtot", + "ifree", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_CHO_EGFR_best-fit", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_CHO_EGFR_Epigen", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_CHO_EGFR_sensitivity", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_CHO_HA_EGFR_L858R", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_HeLa", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_HMEC", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_MCF10A", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "20_raf_constraint4_RAFi", + "name": "20-raf-constraint4", + "description": "BNGL model: RAFi", + "tags": [ + "k1", + "k2", + "k3", + "k5", + "kf1", + "kf2", + "kf3", + "kf4", + "kf5", + "kf6", + "rtot", + "ifree", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "24_jnk_JNKmodel_180724_bnf", + "name": "24-jnk", + "description": "BNGL model: JNKmodel_180724_bnf", + "tags": [ + "scale_t", + "ani", + "k3_zakbyu1", + "k1_u1tozak", + "d3_zak", + "d1_zak", + "k3_mkk4byzak", + "k1_zaktomkk4", + "d3_mkk4", + "d1_mkk4", + "k3_mkk7byzak", + "k1_zaktomkk7", + "f3_mkk7byzak", + "d3_mkk7", + "d1_mkk7", + "k3_jnkbymkk4", + "k1_mkk4tojnk", + "k3_jnkbymkk7", + "k1_mkk7tojnk", + "f3_jnkbymkk7", + "d3_jnk", + "d1_jnk", + "k3_mkk7byjnk", + "k1_jnktomkk7", + "inh_jnk", + "d3_mkk7byjnkpt", + "d1_jnkpttomkk7", + "f1_zaktomkk7p", + "k1_zaktojnk", + "k3_mkk4byakt", + "k1_akttomkk4", + "k3_mkk7byakt", + "k1_akttomkk7", + "d3_mkk4byaktpt", + "d1_aktpttomkk4", + "d3_mkk7byaktpt", + "d1_aktpttomkk7", + "scale_ppmkk4", + "scale_ppmkk7", + "scale_ppjnk", + "pakt", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "26_tcr_sens_tcr_sens_tofit", + "name": "for the Manz/Groves 2011 data", + "description": "Modification of Mukhopadhyay/Dushek 2013 model for the Manz/Groves 2011 data", + "tags": [ + "immunology" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "31_elephant_elephant", + "name": "31-elephant", + "description": "BNGL model: elephant", + "tags": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10", + "a11", + "a12", + "a13", + "a14", + "a15", + "a16", + "a17", + "a18", + "a19", + "a20", + "b1", + "b2", + "b3", + "b4", + "b5", + "b6", + "b7", + "b8", + "b9", + "b10", + "b11", + "b12", + "b13", + "b14", + "b15", + "b16", + "b17", + "b18", + "b19", + "b20", + "c0", + "c1", + "c2", + "c3", + "c4", + "c5", + "c6", + "c7", + "c8", + "c9", + "c10", + "c11", + "c12", + "c13", + "c14", + "c15", + "c16", + "c17", + "c18", + "c19", + "c20", + "d1", + "d2", + "d3", + "d4", + "d5", + "d6", + "d7", + "d8", + "d9", + "d10", + "d11", + "d12", + "d13", + "d14", + "d15", + "d16", + "d17", + "d18", + "d19", + "d20", + "tmax", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "AB", + "name": "AB", + "description": "BioNetGen model: AB", + "tags": [ + "ab", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "ABC", + "name": "ABC", + "description": "BioNetGen model: ABC", + "tags": [ + "abc", + "a", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "ABC_scan", + "name": "ABC scan", + "description": "BioNetGen model: ABC scan", + "tags": [ + "abc", + "scan", + "a", + "generate_network", + "parameter_scan" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "ABC_ssa", + "name": "ABC ssa", + "description": "BioNetGen model: ABC ssa", + "tags": [ + "abc", + "ssa", + "a", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "ABp", + "name": "ABp", + "description": "title: ABp.bngl", + "tags": [ + "abp", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "ABp_approx", + "name": "ABp approx", + "description": "title: ABp.bngl", + "tags": [ + "abp", + "approx", + "km", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "actions_syntax", + "name": "actions syntax", + "description": "Original values used to generate parabola.exp", + "tags": [ + "actions", + "syntax", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "after_bunching", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "after_decoupling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "after_scaling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "akt-signaling", + "name": "akt signaling", + "description": "Signaling rates", + "tags": [ + "akt", + "signaling", + "growthfactor", + "rtk", + "pi3k", + "mtorc2", + "mtorc1", + "s6k" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Alabama", + "name": "Alabama", + "description": "reporting period (1 d)", + "tags": [ + "alabama", + "fdcs", + "counter", + "s", + "e1", + "e2", + "e3", + "e4", + "e5" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": null + }, + { + "id": "allosteric-activation", + "name": "allosteric activation", + "description": "Binding constants", + "tags": [ + "allosteric", + "activation", + "enzyme", + "substrate", + "activator", + "product" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "ampk-signaling", + "name": "ampk signaling", + "description": "AMPK signaling: The cellular energy sensor.", + "tags": [ + "ampk", + "signaling", + "amp", + "lkb1", + "ca", + "sik", + "crtc" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "An_2009", + "name": "An 2009", + "description": "TLR4 signaling", + "tags": [ + "published", + "immunology", + "an", + "2009", + "cd14", + "md2", + "tlr4", + "tram", + "trif", + "sarm", + "traf4", + "irak1" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "apoptosis-cascade", + "name": "apoptosis cascade", + "description": "Apoptosis cascade: Integrated extrinsic and intrinsic death signaling.", + "tags": [ + "apoptosis", + "cascade", + "deathligand", + "caspase8", + "bid", + "mito", + "apaf1", + "caspase3", + "xiap", + "smac" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "auto-activation-loop", + "name": "auto activation loop", + "description": "Auto-activation loop: A positive feedback circuit.", + "tags": [ + "auto", + "activation", + "loop", + "gene", + "mrna", + "protein", + "rbp" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "autophagy-regulation", + "name": "autophagy regulation", + "description": "Autophagy regulation: mTOR and AMPK competition on the ULK1 switch.", + "tags": [ + "autophagy", + "regulation", + "mtor", + "ampk", + "ulk1", + "lc3", + "p62" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "BAB", + "name": "BAB", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "tags": [ + "bab", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "BAB_coop", + "name": "BAB coop", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "tags": [ + "bab", + "coop", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "BAB_scan", + "name": "BAB scan", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "tags": [ + "bab", + "scan", + "a", + "b", + "generate_network", + "parameter_scan" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "Barua_2007", + "name": "Barua 2007", + "description": "Model from Haugh (2006)", + "tags": [ + "published", + "barua", + "2007", + "version", + "r", + "s" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "Barua_2009", + "name": "Barua 2009", + "description": "JAK2-SH2B signaling", + "tags": [ + "published", + "barua", + "2009", + "s", + "j" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "Barua_2013", + "name": "Barua 2013", + "description": "Beta-catenin destruction", + "tags": [ + "published", + "barua", + "2013", + "axin", + "gsk3b", + "apc", + "bcat", + "ck1a" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "BaruaBCR_2012", + "name": "Barua 2012", + "description": "BCR signaling", + "tags": [ + "published", + "immunology", + "baruabcr", + "2012", + "bcr", + "lyn", + "fyn", + "csk", + "pag", + "syk" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "BaruaFceRI_2012", + "name": "BaruaFceRI 2012", + "description": "FcεRI signaling", + "tags": [ + "published", + "immunology", + "baruafceri", + "2012", + "r_o", + "rdimer_o", + "l_o", + "t_o", + "l", + "fcr", + "lyn", + "syk" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "bcr-signaling", + "name": "bcr signaling", + "description": "BCR signaling: The B-cell antigen receptor cascade.", + "tags": [ + "bcr", + "signaling", + "antigen", + "syk", + "plcg2", + "cd22", + "shp1", + "calcium" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "before_bunching", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "before_decoupling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "before_scaling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "beta-adrenergic-response", + "name": "beta adrenergic response", + "description": "Beta-adrenergic signaling: GPCR pathway and desensitization.", + "tags": [ + "beta", + "adrenergic", + "response", + "epi", + "betar", + "gs", + "ac", + "arr", + "camp" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "birth-death", + "name": "Birth-Death", + "description": "Stochastic process", + "tags": [ + "published", + "tutorial", + "native", + "birth", + "death", + "a", + "generate_network", + "saveconcentrations", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "bistable-toggle-switch", + "name": "bistable toggle switch", + "description": "Genetic Toggle Switch: Mutual repression circuit.", + "tags": [ + "bistable", + "toggle", + "switch", + "proml", + "promr", + "tf_l", + "tf_r", + "ind_l", + "ind_r" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "BLBR", + "name": "BLBR", + "description": "title: BLBR.bngl", + "tags": [ + "blbr", + "setoption", + "r", + "l", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode", + "nf" + ] + }, + "gallery": [ + "tutorial" + ], + "collectionId": null + }, + { + "id": "Blinov_2006", + "name": "Blinov 2006", + "description": "Phosphotyrosine signaling", + "tags": [ + "published", + "blinov", + "2006", + "egf", + "egfr", + "shc", + "grb2", + "sos" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "collectionId": null + }, + { + "id": "Blinov_egfr", + "name": "Blinov egfr", + "description": "EGFR signaling model", + "tags": [ + "published", + "nfsim", + "blinov", + "egfr", + "egf", + "grb2", + "shc", + "simulate_nf" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "Blinov_ran", + "name": "Blinov ran", + "description": "Ran GTPase cycle", + "tags": [ + "published", + "nfsim", + "blinov", + "ran", + "c", + "rcc1", + "simulate_nf" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "cell-cycle" + ], + "collectionId": null + }, + { + "id": "blood-coagulation-thrombin", + "name": "blood coagulation thrombin", + "description": "Blood coagulation: Thrombin burst and feedback propagation.", + "tags": [ + "blood", + "coagulation", + "thrombin", + "tf", + "factorx", + "factorv", + "prothrombin", + "fibrinogen", + "at" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "bmp-signaling", + "name": "bmp signaling", + "description": "BMP-Smad signaling: Developmental gradient relay.", + "tags": [ + "bmp", + "signaling", + "noggin", + "receptor1", + "receptor2", + "smad1", + "smad4", + "smad6" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "bng_error", + "name": "bng error", + "description": "Original values used to generate parabola.exp", + "tags": [ + "bng", + "error", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "brusselator-oscillator", + "name": "brusselator oscillator", + "description": "The Brusselator: Auto-catalytic chemical oscillator.", + "tags": [ + "brusselator", + "oscillator", + "a", + "b", + "x", + "y" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "calcineurin-nfat-pathway", + "name": "calcineurin nfat pathway", + "description": "NFAT Signaling: Calcium-dependent nuclear translocation.", + "tags": [ + "calcineurin", + "nfat", + "pathway", + "ca", + "cam", + "can", + "rcan1" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "calcium-spike-signaling", + "name": "calcium spike signaling", + "description": "Calcium spikes: Oscillations driven by IP3R and CICR feedback.", + "tags": [ + "calcium", + "spike", + "signaling", + "plc", + "ip3", + "ca", + "stim1" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "CaMKII_holo", + "name": "Ordyan 2020: CaMKII holo", + "description": "CaMKII holo", + "tags": [ + "published", + "neuroscience", + "camkii", + "holo", + "ca", + "cam", + "ng", + "pp1", + "time_counter" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "CaOscillate_Func", + "name": "CaOscillate_Func", + "description": "Calcium oscillations (func)", + "tags": [ + "validation", + "caoscillate", + "func", + "null", + "ga", + "plc", + "ca" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "CaOscillate_Sat", + "name": "CaOscillate_Sat", + "description": "Calcium oscillations (sat)", + "tags": [ + "validation", + "caoscillate", + "sat", + "null", + "ga", + "plc", + "ca" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "caspase-activation-loop", + "name": "caspase activation loop", + "description": "Caspase activation loop: The executioner feedback system.", + "tags": [ + "caspase", + "activation", + "loop", + "deathligand", + "caspase8", + "caspase3", + "iap", + "flip" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "catalysis", + "name": "catalysis", + "description": "Catalysis in energy BNG", + "tags": [ + "validation", + "catalysis", + "version", + "setoption", + "s", + "kinase", + "pptase", + "atp", + "adp" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "cBNGL_simple", + "name": "cBNGL simple", + "description": "A simplified signal transduction model including the following processes:", + "tags": [ + "cbngl", + "simple", + "l", + "r", + "tf", + "dna", + "mrna", + "p" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "cd40-signaling", + "name": "cd40 signaling", + "description": "CD40 Signaling: B-cell activation and TRAF-mediated relay.", + "tags": [ + "cd40", + "signaling", + "cd40l", + "traf", + "ikk", + "nik", + "nfkb", + "relb" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "cell-cycle-checkpoint", + "name": "cell cycle checkpoint", + "description": "Cell cycle checkpoint: Mitotic entry switch (CDK1).", + "tags": [ + "cell", + "cycle", + "checkpoint", + "cyclin", + "cdk", + "cdc25", + "wee1", + "apc", + "p21" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "Chattaraj_2021", + "name": "Chattaraj 2021", + "description": "NFkB oscillations", + "tags": [ + "published", + "chattaraj", + "2021", + "nephrin", + "nck", + "nwasp", + "writexml" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience" + ], + "collectionId": null + }, + { + "id": "check_scaling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "checkpoint-kinase-signaling", + "name": "checkpoint kinase signaling", + "description": "DNA Checkpoint: ATM/ATR mediated damage sensing.", + "tags": [ + "checkpoint", + "kinase", + "signaling", + "dna", + "atm", + "atr", + "chk1", + "chk2", + "p53", + "cdc25" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "Cheemalavagu_JAK_STAT", + "name": "Cheemalavagu 2024", + "description": "JAK-STAT signaling", + "tags": [ + "published", + "literature", + "signaling", + "cheemalavagu", + "jak", + "stat", + "l1", + "il6r", + "gp130", + "l2", + "il10r1", + "il10r2", + "jak1", + "jak2" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "chemistry", + "name": "chemistry", + "description": "Basic chemical reactions", + "tags": [ + "published", + "tutorials", + "chemistry", + "a", + "b", + "c", + "d", + "e" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "collectionId": null + }, + { + "id": "chemotaxis-signal-transduction", + "name": "chemotaxis signal transduction", + "description": "Bacterial Chemotaxis: Adaptation through methylation.", + "tags": [ + "chemotaxis", + "signal", + "transduction", + "attr", + "mcp", + "chea", + "chey", + "cheb", + "motor" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Chylek_library", + "name": "Chylek library", + "description": "Created by BioNetGen 2.2.6", + "tags": [ + "chylek", + "library", + "kflatplcg", + "kfgrb2gab2", + "kflcp2plcg1", + "kd1", + "kd2", + "sink", + "pre", + "pag1" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "ChylekFceRI_2014", + "name": "Chylek 2014 (FceRI)", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "chylekfceri", + "2014", + "lig", + "rec", + "lyn", + "fyn", + "syk", + "pag1", + "csk", + "lat" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "ChylekTCR_2014", + "name": "Chylek 2014 (TCR)", + "description": "TCR signaling", + "tags": [ + "published", + "immunology", + "chylektcr", + "2014", + "lig1", + "lig2", + "lig3", + "tcr", + "cd28", + "lck", + "itk", + "zap70" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "circadian-oscillator", + "name": "circadian oscillator", + "description": "title: Vilar Circadian Oscillator Model", + "tags": [ + "circadian", + "oscillator", + "a", + "r", + "pa", + "pr", + "mrna_a", + "mrna_r" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "CircadianOscillator", + "name": "CircadianOscillator", + "description": "Circadian rhythm", + "tags": [ + "published", + "tutorial", + "native", + "circadianoscillator", + "a", + "r", + "pa", + "pr", + "mrna_a", + "mrna_r" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "cell-cycle", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "clock-bmal1-gene-circuit", + "name": "clock bmal1 gene circuit", + "description": "BMAL1-CLOCK: The master activator of the circadian circuit.", + "tags": [ + "clock", + "bmal1", + "gene", + "circuit", + "ror", + "reverb", + "dna" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "compartment_endocytosis", + "name": "compartment endocytosis", + "description": "Model: compartment_endocytosis.bngl", + "tags": [ + "compartment", + "endocytosis", + "l", + "r", + "t" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "compartment_membrane_bound", + "name": "compartment membrane bound", + "description": "Model: compartment_membrane_bound.bngl", + "tags": [ + "compartment", + "membrane", + "bound", + "p", + "lipid", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "compartment_nested_transport", + "name": "compartment nested transport", + "description": "Model: compartment_nested_transport.bngl", + "tags": [ + "compartment", + "nested", + "transport", + "s", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "compartment_nuclear_transport", + "name": "compartment nuclear transport", + "description": "Model: compartment_nuclear_transport.bngl", + "tags": [ + "compartment", + "nuclear", + "transport", + "tf", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "compartment_organelle_exchange", + "name": "compartment organelle exchange", + "description": "Model: compartment_organelle_exchange.bngl", + "tags": [ + "compartment", + "organelle", + "exchange", + "cargo", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "competitive-enzyme-inhibition", + "name": "competitive enzyme inhibition", + "description": "Competitive inhibition: Inhibitor (I) and Substrate (S) compete for the same", + "tags": [ + "competitive", + "enzyme", + "inhibition", + "substrate1", + "substrate2", + "inhibitor", + "product" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "complement-activation-cascade", + "name": "complement activation cascade", + "description": "Complement System: Pathogen opsonization and the Alternative Pathway.", + "tags": [ + "complement", + "activation", + "cascade", + "c3", + "fb", + "c5", + "mac", + "surf" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "ComplexDegradation", + "name": "ComplexDegradation", + "description": "Degradation model", + "tags": [ + "published", + "tutorial", + "native", + "complexdegradation", + "a", + "b", + "c", + "generate_network" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "contact-inhibition-hippo-yap", + "name": "contact inhibition hippo yap", + "description": "Hippo Pathway: Contact inhibition and YAP regulation.", + "tags": [ + "contact", + "inhibition", + "hippo", + "yap", + "mst", + "lats", + "tead" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "continue", + "name": "continue", + "description": "Test trajectory continuation", + "tags": [ + "validation", + "continue", + "a", + "b", + "c", + "trash" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "cooperative-binding", + "name": "cooperative binding", + "description": "Cooperative binding: The binding of the first ligand molecule increases", + "tags": [ + "cooperative", + "binding", + "receptor", + "ligand", + "competitor" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Creamer_2012", + "name": "Creamer 2012", + "description": "Initial values", + "tags": [ + "creamer", + "2012", + "egf", + "hrg", + "egfr", + "erbb2", + "erbb3", + "erbb4", + "p52shc1", + "grb2" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "cs_diffie_hellman", + "name": "cs diffie hellman", + "description": "Model: cs_diffie_hellman.bngl", + "tags": [ + "cs", + "diffie", + "hellman", + "agent", + "target", + "dshareda_dt", + "dsharedb_dt" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "cs_hash_function", + "name": "cs hash function", + "description": "Cryptographic Hash Function in BNGL", + "tags": [ + "cs", + "hash", + "function", + "b0", + "b1", + "b2", + "b3", + "h0", + "h1", + "h2", + "h3" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "cs_huffman", + "name": "cs huffman", + "description": "Model: cs_huffman.bngl", + "tags": [ + "cs", + "huffman", + "char", + "hnode", + "generate_network", + "simulate" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "cs_monte_carlo_pi", + "name": "cs monte carlo pi", + "description": "Model: cs_monte_carlo_pi.bngl", + "tags": [ + "cs", + "monte", + "carlo", + "pi", + "trial", + "pi_estimate", + "generate_network", + "simulate" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "cs_pagerank", + "name": "cs pagerank", + "description": "Model: cs_pagerank.bngl", + "tags": [ + "cs", + "pagerank", + "teleport", + "page" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "cs_pid_controller", + "name": "cs pid controller", + "description": "PID Controller in BNGL", + "tags": [ + "cs", + "pid", + "controller", + "sensor", + "accumulator", + "leakyerror", + "actuator", + "disturbance" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "cs_regex_nfa", + "name": "cs regex nfa", + "description": "Model: cs_regex_nfa.bngl", + "tags": [ + "cs", + "regex", + "nfa", + "state", + "char", + "generate_network", + "simulate", + "setparameter" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "Dallas", + "name": "Dallas", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "dallas", + "counter", + "fdcs", + "s", + "sv", + "e", + "a", + "i", + "v" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": null + }, + { + "id": "degranulation_model", + "name": "PyBNG: Degranulation model", + "description": "Degranulation model", + "tags": [ + "published", + "pybng", + "degranulation", + "model", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "Dembo_1978", + "name": "Dembo 1978", + "description": "BLBR dembo 1978", + "tags": [ + "published", + "physics", + "dembo", + "1978" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "dna-damage-repair", + "name": "dna damage repair", + "description": "DNA damage sensing and repair pathway (ATM-CHK2-p53 axis)", + "tags": [ + "dna", + "damage", + "repair", + "mrn", + "atm", + "chk2", + "repaircomplex" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "dna-methylation-dynamics", + "name": "dna methylation dynamics", + "description": "DNA Methylation: Maintenance and de novo dynamics.", + "tags": [ + "dna", + "methylation", + "dynamics", + "cpg", + "dnmt1", + "tet", + "v_maint", + "v_erase" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Dolan_2015", + "name": "Dolan 2015", + "description": "Insulin signaling", + "tags": [ + "published", + "literature", + "signaling", + "dolan", + "2015", + "time", + "t", + "p", + "e", + "ir", + "d", + "p53_mrna", + "p53" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism" + ], + "collectionId": null + }, + { + "id": "Dolan2015", + "name": "Dolan 2015", + "description": "Insulin signaling", + "tags": [ + "published", + "literature", + "signaling", + "dolan", + "2015", + "time", + "t", + "p", + "e", + "ir", + "d", + "p53_mrna", + "p53" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism" + ], + "collectionId": null + }, + { + "id": "dr5-apoptosis-signaling", + "name": "dr5 apoptosis signaling", + "description": "DR5 (TRAIL) Signaling: Extrinsic apoptosis and DISC formation.", + "tags": [ + "dr5", + "apoptosis", + "signaling", + "trail", + "fadd", + "caspase8", + "flip", + "death_signal" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "Dreisigmeyer_2008", + "name": "Dreisigmeyer 2008", + "description": "Lac operon", + "tags": [ + "published", + "gene-expression", + "dreisigmeyer", + "2008" + ], + "category": "gene-expression", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "gene-expression" + ], + "collectionId": null + }, + { + "id": "dual-site-phosphorylation", + "name": "dual site phosphorylation", + "description": "Dual-site phosphorylation: Requires two sequential modifications for activity.", + "tags": [ + "dual", + "site", + "phosphorylation", + "kinase", + "phosphatase", + "substrate" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Dushek_2011", + "name": "Dushek 2011", + "description": "TCR signaling", + "tags": [ + "published", + "dushek", + "2011", + "s" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "Dushek_2014", + "name": "Dushek 2014", + "description": "TCR signaling dynamics", + "tags": [ + "published", + "dushek", + "2014", + "e", + "f", + "b" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "e2f-rb-cell-cycle-switch", + "name": "e2f rb cell cycle switch", + "description": "E2F/Rb Switch: The G1/S transition gate.", + "tags": [ + "e2f", + "rb", + "cell", + "cycle", + "switch", + "mitogen", + "cycd", + "cyce", + "p27" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "eco_coevolution_host_parasite", + "name": "eco coevolution host parasite", + "description": "Model: eco_coevolution_host_parasite.bngl", + "tags": [ + "eco", + "coevolution", + "host", + "parasite" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "collectionId": null + }, + { + "id": "eco_food_web_chaos_3sp", + "name": "eco food web chaos 3sp", + "description": "Model: eco_food_web_chaos_3sp.bngl", + "tags": [ + "eco", + "food", + "web", + "chaos", + "3sp", + "r", + "c", + "p", + "k_eat_r", + "k_eat_c" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "collectionId": null + }, + { + "id": "eco_lotka_volterra_grid", + "name": "eco lotka volterra grid", + "description": "Model: eco_lotka_volterra_grid.bngl", + "tags": [ + "eco", + "lotka", + "volterra", + "grid", + "prey", + "pred" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "collectionId": null + }, + { + "id": "eco_mutualism_obligate", + "name": "eco mutualism obligate", + "description": "Model: eco_mutualism_obligate.bngl", + "tags": [ + "eco", + "mutualism", + "obligate", + "a", + "b" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "collectionId": null + }, + { + "id": "eco_rock_paper_scissors_spatial", + "name": "eco rock paper scissors spatial", + "description": "Model: eco_rock_paper_scissors_spatial.bngl", + "tags": [ + "eco", + "rock", + "paper", + "scissors", + "spatial", + "s", + "generate_network" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "collectionId": null + }, + { + "id": "egfr", + "name": "02-egfr", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "egfr", + "name": "17-egfr-ssa", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "egfr", + "name": "egfr", + "description": "Blinov et al. 2006. Biosystems, 83:136", + "tags": [ + "egfr", + "egf", + "grb2", + "shc", + "sos" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "egfr_ground", + "name": "02-egfr", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "egfr_ground", + "name": "17-egfr-ssa", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "egfr_ground", + "name": "egfr ground", + "description": "Blinov et al. 2006. Biosystems, 83:136", + "tags": [ + "egfr", + "ground", + "egf", + "grb2", + "shc", + "sos" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "egfr_net", + "name": "egfr_net", + "description": "check detailed balanced", + "tags": [ + "validation", + "egfr", + "net", + "egf", + "shc", + "grb2", + "sos" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "egfr_net_red", + "name": "egfr_net_red", + "description": "Reduced state-space version of EGFR_NET.BNGL with equivalent ODE dynamics", + "tags": [ + "validation", + "egfr", + "net", + "red", + "egf", + "egfr_1", + "egfr_2", + "egfr_3", + "grb2", + "shc", + "sos" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "egfr_nf", + "name": "egfr nf", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "egfr", + "nf", + "egf", + "clusters", + "pre1_dose", + "pre2_time" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "egfr_ode", + "name": "egfr ode", + "description": "Filename: example1.bngl", + "tags": [ + "egfr", + "ode", + "egf", + "pre1_dose", + "pre2_time", + "pre3_dose" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "egfr_ode", + "name": "PyBNG: EGFR ODE", + "description": "EGFR ODE", + "tags": [ + "published", + "pybng", + "egfr", + "ode", + "egf", + "pre1_dose", + "pre2_time", + "pre3_dose" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "egfr_path", + "name": "egfr_path", + "description": "The primary focus of the model developed by Kholodenko", + "tags": [ + "validation", + "egfr", + "path", + "generate_network", + "setconcentration", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "egfr_simple", + "name": "egfr simple", + "description": "This is a demo model of EGFR signaling.", + "tags": [ + "egfr", + "simple", + "egf", + "grb2", + "sos1" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "egfr-signaling-pathway", + "name": "egfr signaling pathway", + "description": "Enhanced EGFR Signaling: Combinatorial complexity with multiple phosphorylation sites.", + "tags": [ + "egfr", + "signaling", + "pathway", + "egf", + "grb2", + "shc" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "egg", + "name": "egg", + "description": "BioNetGen model: egg", + "tags": [ + "egg", + "x", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "eif2a-stress-response", + "name": "eif2a stress response", + "description": "Integrated Stress Response: eIF2alpha and the translational gate.", + "tags": [ + "eif2a", + "stress", + "response", + "eif2b", + "perk", + "gadd34" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "elephant_EFA", + "name": "Hlavacek2018Elephant", + "description": "BNGL model: elephant_EFA", + "tags": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10", + "a11", + "a12", + "a13", + "a14", + "a15", + "a16", + "a17", + "a18", + "a19", + "a20", + "b0", + "b1", + "b2", + "b3", + "b4", + "b5", + "b6", + "b7", + "b8", + "b9", + "b10", + "b11", + "b12", + "b13", + "b14", + "b15", + "b16", + "b17", + "b18", + "b19", + "b20", + "c0", + "c1", + "c2", + "c3", + "c4", + "c5", + "c6", + "c7", + "c8", + "c9", + "c10", + "c11", + "c12", + "c13", + "c14", + "c15", + "c16", + "c17", + "c18", + "c19", + "c20", + "d0", + "d1", + "d2", + "d3", + "d4", + "d5", + "d6", + "d7", + "d8", + "d9", + "d10", + "d11", + "d12", + "d13", + "d14", + "d15", + "d16", + "d17", + "d18", + "d19", + "d20", + "period", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "elephant_fit", + "name": "Hlavacek2018Elephant", + "description": "BNGL model: elephant_EFA", + "tags": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10", + "a11", + "a12", + "a13", + "a14", + "a15", + "a16", + "a17", + "a18", + "a19", + "a20", + "b0", + "b1", + "b2", + "b3", + "b4", + "b5", + "b6", + "b7", + "b8", + "b9", + "b10", + "b11", + "b12", + "b13", + "b14", + "b15", + "b16", + "b17", + "b18", + "b19", + "b20", + "c0", + "c1", + "c2", + "c3", + "c4", + "c5", + "c6", + "c7", + "c8", + "c9", + "c10", + "c11", + "c12", + "c13", + "c14", + "c15", + "c16", + "c17", + "c18", + "c19", + "c20", + "d0", + "d1", + "d2", + "d3", + "d4", + "d5", + "d6", + "d7", + "d8", + "d9", + "d10", + "d11", + "d12", + "d13", + "d14", + "d15", + "d16", + "d17", + "d18", + "d19", + "d20", + "period", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "endosomal-sorting-rab", + "name": "endosomal sorting rab", + "description": "Endosomal Sorting: Rab GTPase conversion and effector recruitment.", + "tags": [ + "endosomal", + "sorting", + "rab", + "rab5", + "rab7", + "effector", + "v_gef", + "v_gap_drive" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "energy_allostery_mwc", + "name": "energy allostery mwc", + "description": "Model: energy_allostery_mwc.bngl", + "tags": [ + "energy", + "allostery", + "mwc", + "p", + "l" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "energy_catalysis_mm", + "name": "energy catalysis mm", + "description": "Model: energy_catalysis_mm.bngl", + "tags": [ + "energy", + "catalysis", + "mm", + "e", + "s", + "p" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "energy_cooperativity_adh", + "name": "energy cooperativity adh", + "description": "Model: energy_cooperativity_adh.bngl", + "tags": [ + "energy", + "cooperativity", + "adh", + "r", + "l" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "energy_example1", + "name": "energy_example1", + "description": "Illustration of energy modeling approach w/ a simple protein scaffold model", + "tags": [ + "validation", + "energy", + "example1", + "version", + "setoption", + "s", + "a", + "b", + "c" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "energy_linear_chain", + "name": "energy linear chain", + "description": "Model: energy_linear_chain.bngl", + "tags": [ + "energy", + "linear", + "chain", + "m", + "generate_network" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "energy_transport_pump", + "name": "energy transport pump", + "description": "Model: energy_transport_pump.bngl", + "tags": [ + "energy", + "transport", + "pump", + "a", + "atp", + "adp", + "pi", + "t" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "ensemble_tofit", + "name": "translated into BNGL", + "description": "Ensemble model translated into BNGL", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "er-stress-response", + "name": "er stress response", + "description": "Rate Constants", + "tags": [ + "er", + "stress", + "response", + "unfoldedprotein", + "perk", + "eif2a", + "chaperone" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Erdem_2021", + "name": "Erdem 2021", + "description": "InsR/IGF1R signaling", + "tags": [ + "published", + "erdem", + "2021", + "igf1", + "ins", + "igf1r", + "insr", + "irs", + "sos", + "ras", + "raf" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism" + ], + "collectionId": null + }, + { + "id": "ERK_model", + "name": "ERK_model.bngl", + "description": "filename: ERK_model.bngl", + "tags": [ + "egf", + "erkpp_sos1_fb", + "erkpp_mek_fb", + "erkpp_raf1_fb", + "lambda", + "egfr_tot", + "ras_tot", + "sos_tot", + "rasgap_tot", + "raf_tot", + "mek_tot", + "erk_tot", + "ekar3_tot", + "erktr_tot", + "a1", + "d1", + "b1", + "u1a", + "u1b", + "b2a", + "u2a", + "b2b", + "u2b", + "k2a", + "k2b", + "b3", + "u3", + "k3", + "a2", + "d2", + "p1", + "q1", + "p2", + "q2", + "p3", + "q3", + "p4", + "q4", + "q5", + "p6", + "q6", + "a0_ekar3", + "d0_ekar3", + "a0_erktr", + "d0_erktr", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "erk-nuclear-translocation", + "name": "erk nuclear translocation", + "description": "ERK Translocation: Spatial signaling and transcriptional assembly.", + "tags": [ + "erk", + "nuclear", + "translocation", + "mek", + "elk1", + "dusp", + "transcription_signal" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "ErrNoFrees", + "name": "ErrNoFrees", + "description": "An example from a real application", + "tags": [ + "errnofrees", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "example1", + "name": "example1", + "description": "Filename: example1.bngl", + "tags": [ + "example1", + "egf", + "egfr", + "pre1_dose", + "pre2_time", + "pre3_dose" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "example1", + "name": "example1", + "description": "Example file for BNG2 tutorial.", + "tags": [ + "validation", + "example1", + "version", + "generate_network", + "simulate_ode" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "example1_BNFfiles_example1", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example1_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example2_BNFfiles_example2", + "name": "example2_starting_point.bngl", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "f", + "lt_nm", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example2_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example2_starting_point", + "name": "example2 starting point", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "example2", + "starting", + "point", + "egf", + "egfr", + "clusters", + "pre1_dose", + "pre2_time" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "example3_BNFfiles_example3", + "name": "example3 BNFfiles", + "description": "BNGL model: example3", + "tags": [ + "alpha", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example3_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example4_BNFfiles_example4", + "name": "in BNGL. For a description of BNGL, see:", + "description": "Supplementary File A in File S1", + "tags": [ + "other" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example4_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example5_BNFfiles_example5", + "name": "example5 BNFfiles", + "description": "A simple model", + "tags": [ + "ligand_ispresent", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example5_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example5_ground_truth", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example5_starting_point", + "name": "13-receptor", + "description": "A simple model", + "tags": [ + "ligand_ispresent", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example6_BNFfiles_example6", + "name": "example6 BNFfiles", + "description": "A simple model", + "tags": [ + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example6_ground_truth", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "extra_CaMKII_Holo", + "name": "Ordyan 2020: extra CaMKII holo", + "description": "Extra CaMKII holo (supplement)", + "tags": [ + "published", + "neuroscience", + "extra", + "camkii", + "holo", + "t1", + "t2", + "t3", + "t4", + "t5", + "t6", + "t7", + "t8" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "collectionId": null + }, + { + "id": "Faeder_2003", + "name": "Faeder 2003", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "faeder", + "2003", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "fceri_fyn", + "name": "FceRI Fyn", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "fceri", + "fyn", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "fceri_gamma2", + "name": "fceri gamma2", + "description": "BioNetGen model: fceri gamma2", + "tags": [ + "fceri", + "gamma2", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "fceri_gamma2_ground_truth", + "name": "fceri gamma2 ground truth", + "description": "BioNetGen model: fceri gamma2 ground truth", + "tags": [ + "fceri", + "gamma2", + "ground", + "truth", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "fceri_ji", + "name": "Faeder 2003", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "faeder", + "2003", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "FceRI_ji", + "name": "FceRI ji", + "description": "title: FceRI_ji.bngl", + "tags": [ + "fceri", + "ji", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "fceri_ji_comp", + "name": "fceri_ji_comp", + "description": "Ligand-receptor binding", + "tags": [ + "validation", + "fceri", + "ji", + "comp", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "FceRI_viz", + "name": "FceRI Viz", + "description": "FcεRI (viz)", + "tags": [ + "published", + "tutorial", + "native", + "fceri", + "viz", + "fcr", + "ige", + "lat", + "lyn", + "syk", + "pb", + "pg", + "sykp" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "feature_functional_rates_volume", + "name": "feature functional rates volume", + "description": "Model: feature_functional_rates_volume.bngl", + "tags": [ + "feature", + "functional", + "rates", + "volume", + "a", + "b", + "c" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "feature_global_functions_scan", + "name": "feature global functions scan", + "description": "Model: feature_global_functions_scan.bngl", + "tags": [ + "feature", + "global", + "functions", + "scan", + "signal", + "response", + "stimulus" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "feature_local_functions_explicit", + "name": "feature local functions explicit", + "description": "Model: feature_local_functions_explicit.bngl", + "tags": [ + "feature", + "local", + "functions", + "explicit", + "s", + "p", + "e", + "mm_rate", + "ratelaw" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "feature_symmetry_factors_cyclic", + "name": "feature symmetry factors cyclic", + "description": "Model: feature_symmetry_factors_cyclic.bngl", + "tags": [ + "feature", + "symmetry", + "factors", + "cyclic", + "x", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "feature_synthesis_degradation_ss", + "name": "feature synthesis degradation ss", + "description": "Model: feature_synthesis_degradation_ss.bngl", + "tags": [ + "feature", + "synthesis", + "degradation", + "ss", + "m", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "fgf-signaling-pathway", + "name": "fgf signaling pathway", + "description": "FGF Signaling: FGFR dimerization and FRS2-Ras/PI3K relay.", + "tags": [ + "fgf", + "signaling", + "pathway", + "fgfr", + "frs2", + "spry", + "rasgef", + "internalized_rec" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "free_missing", + "name": "free missing", + "description": "Original values used to generate parabola.exp", + "tags": [ + "free", + "missing", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Gardner_2000", + "name": "Gardner 2000", + "description": "Genetic toggle switch", + "tags": [ + "published", + "synthetic-biology", + "gardner", + "2000" + ], + "category": "synthetic-biology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synthetic-biology" + ], + "collectionId": null + }, + { + "id": "gas6-axl-signaling", + "name": "gas6 axl signaling", + "description": "GAS6/AXL Signaling: AKT activation and SOCS feedback.", + "tags": [ + "gas6", + "axl", + "signaling", + "pi3k", + "akt", + "socs", + "survival_burst" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "gene-expression-toggle", + "name": "gene expression toggle", + "description": "Kinetic Parameters", + "tags": [ + "gene", + "expression", + "toggle", + "mrna", + "protein" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "genetic_bistability_energy", + "name": "genetic bistability energy", + "description": "Model: genetic_bistability_energy.bngl", + "tags": [ + "genetic", + "bistability", + "energy", + "genea", + "geneb", + "prota", + "protb" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "genetic_dna_replication_stochastic", + "name": "genetic dna replication stochastic", + "description": "Model: genetic_dna_replication_stochastic.bngl", + "tags": [ + "genetic", + "dna", + "replication", + "stochastic", + "pol", + "n", + "generate_network" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "genetic_goodwin_oscillator", + "name": "genetic goodwin oscillator", + "description": "Model: genetic_goodwin_oscillator.bngl", + "tags": [ + "genetic", + "goodwin", + "oscillator", + "gene", + "mrna", + "protein", + "repressor" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "genetic_translation_kinetics", + "name": "genetic translation kinetics", + "description": "Model: genetic_translation_kinetics.bngl", + "tags": [ + "genetic", + "translation", + "kinetics", + "mrna", + "rib", + "protein" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "genetic_turing_pattern_1d", + "name": "genetic turing pattern 1d", + "description": "Model: genetic_turing_pattern_1d.bngl", + "tags": [ + "genetic", + "turing", + "pattern", + "1d", + "a", + "b" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "GK", + "name": "GK", + "description": "title: GK.bngl", + "tags": [ + "gk", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "glioblastoma-egfrviii-signaling", + "name": "glioblastoma egfrviii signaling", + "description": "EGFRvIII in Glioblastoma: Constitutive AKT drive and escape from decay.", + "tags": [ + "glioblastoma", + "egfrviii", + "signaling", + "pi3k", + "akt", + "oncogenic_output", + "v_viii_act" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "glycolysis-branch-point", + "name": "glycolysis branch point", + "description": "BioNetGen model: glycolysis branch point", + "tags": [ + "glycolysis", + "branch", + "point", + "glucose", + "atp", + "biomass" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "gm_game_of_life", + "name": "gm game of life", + "description": "Model: gm_game_of_life.bngl", + "tags": [ + "gm", + "game", + "of", + "life", + "cell" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "gm_ray_marcher", + "name": "gm ray marcher", + "description": "Ray Marching Renderer in BNGL", + "tags": [ + "gm", + "ray", + "marcher", + "ray0", + "hit0", + "bright0", + "sdf0", + "sdf1", + "sdf2", + "sdf3", + "speed0" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Goldstein_1980", + "name": "Goldstein 1980", + "description": "BLBR heterogeneity", + "tags": [ + "published", + "physics", + "goldstein", + "1980" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "gpcr-desensitization-arrestin", + "name": "gpcr desensitization arrestin", + "description": "GPCR Desensitization: Arrestin-mediated spatial sequestration.", + "tags": [ + "gpcr", + "desensitization", + "arrestin", + "ligand", + "gprotein" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Harmon_2017", + "name": "Harmon 2017", + "description": "Antigen pulses", + "tags": [ + "published", + "immunology", + "harmon", + "2017" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "Hat_2016", + "name": "Hat 2016", + "description": "Nuclear transport", + "tags": [ + "published", + "hat", + "2016", + "dna_dsb", + "atm", + "siah1", + "hipk2", + "wip1", + "gene_wip1", + "mrna_wip1", + "p53" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "cell-cycle", + "multistage" + ], + "collectionId": null + }, + { + "id": "Haugh2b", + "name": "Haugh2b", + "description": "R(KD,Y1~U,Y2~U) 1.00", + "tags": [ + "validation", + "haugh2b", + "r", + "s1", + "s2", + "exclude_reactants", + "include_reactants" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "hedgehog-signaling-pathway", + "name": "hedgehog signaling pathway", + "description": "Hedgehog (Hh) Signaling: Ciliary translocation and Gli processing.", + "tags": [ + "hedgehog", + "signaling", + "pathway", + "hh", + "ptch", + "smo", + "gli", + "sufu" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "heise", + "name": "heise", + "description": "Validate state inheritance in a symmetric context", + "tags": [ + "validation", + "heise", + "a", + "b", + "generate_network", + "simulate_ode", + "setparameter" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "hematopoietic-growth-factor", + "name": "hematopoietic growth factor", + "description": "Kinetic Parameters", + "tags": [ + "hematopoietic", + "growth", + "factor", + "epo", + "epor", + "jak2", + "stat5" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "hif1a_degradation_loop", + "name": "hif1a degradation loop", + "description": "HIF-1alpha Oxygen Sensing: Hydroxylation and VHL-mediated decay.", + "tags": [ + "hif1a", + "degradation", + "loop", + "vhl", + "arnt", + "v_hydrox" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Hlavacek_1999", + "name": "Hlavacek 1999", + "description": "Steric effects", + "tags": [ + "published", + "physics", + "hlavacek", + "1999" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "Hlavacek_2001", + "name": "Hlavacek 2001", + "description": "Kinetic proofreading", + "tags": [ + "published", + "physics", + "hlavacek", + "2001" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "Hlavacek2018Egg_egg", + "name": "Hlavacek2018Egg", + "description": "End of permute change log", + "tags": [ + "a0__free", + "a1__free", + "a2__free", + "b1__free", + "b2__free", + "c0__free", + "c1__free", + "c2__free", + "d1__free", + "d2__free", + "a0", + "a1", + "a2", + "b1", + "b2", + "c0", + "c1", + "c2", + "d1", + "d2", + "period", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "Houston", + "name": "Houston", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "houston", + "counter", + "fdcs", + "s", + "sv", + "e", + "a", + "i", + "v" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": null + }, + { + "id": "hypoxia-response-signaling", + "name": "hypoxia response signaling", + "description": "Rate Constants", + "tags": [ + "hypoxia", + "response", + "signaling", + "oxygensensor", + "hif1", + "vegf" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "IGF1R_Model_receptor_activation_bnf", + "name": "IGF1R Model receptor activation bnf", + "description": "Author: William S. Hlavacek", + "tags": [ + "igf1r", + "model", + "receptor", + "activation", + "bnf", + "igf1" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "il1b-signaling", + "name": "il1b signaling", + "description": "IL-1beta Signaling: MyD88/IRAK assembly and NF-kB translocation.", + "tags": [ + "il1b", + "signaling", + "il1ri", + "myd88", + "irak", + "nfkb" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "il6-jak-stat-pathway", + "name": "il6 jak stat pathway", + "description": "IL-6 Signaling: gp130 hexamerization and pSTAT3 import.", + "tags": [ + "il6", + "jak", + "stat", + "pathway", + "gp130", + "stat3", + "socs" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "immune-synapse-formation", + "name": "immune synapse formation", + "description": "Kinetic Parameters", + "tags": [ + "immune", + "synapse", + "formation", + "tcr", + "pmhc", + "lck", + "zap70" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "inflammasome-activation", + "name": "inflammasome activation", + "description": "Rate Constants", + "tags": [ + "inflammasome", + "activation", + "sensor", + "asc", + "caspase1", + "il1b" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "innate_immunity", + "name": "Korwek 2023", + "description": "Immune response", + "tags": [ + "published", + "immunology", + "innate", + "immunity", + "polyic", + "rigi", + "mavs", + "pkr", + "oas3", + "rnasel", + "eif2a", + "rigi_mrna" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "inositol-phosphate-metabolism", + "name": "inositol phosphate metabolism", + "description": "Inositol Phosphate (IP) Metabolism: PLC signaling and branch points.", + "tags": [ + "inositol", + "phosphate", + "metabolism", + "pip2", + "ip3", + "ip4", + "calcium", + "agonist" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "insulin-glucose-homeostasis", + "name": "insulin glucose homeostasis", + "description": "Insulin-Glucose: Compartmentalized transport.", + "tags": [ + "insulin", + "glucose", + "homeostasis", + "ir", + "glut4", + "pancreas" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "interferon-signaling", + "name": "interferon signaling", + "description": "Rate Constants", + "tags": [ + "interferon", + "signaling", + "ifn", + "ifnar", + "tyk2", + "stat1" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "ire1a-xbp1-er-stress", + "name": "ire1a xbp1 er stress", + "description": "IRE1a/XBP1 ER Stress: Chaperone buffering and mRNA decay (RIDD).", + "tags": [ + "ire1a", + "xbp1", + "er", + "stress", + "ire1", + "bip", + "unfolded", + "ridd_target" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "issue_198_short", + "name": "issue_198_short", + "description": "No description available", + "tags": [ + "validation", + "issue", + "198", + "short", + "a", + "b", + "c", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "jak-stat-cytokine-signaling", + "name": "jak stat cytokine signaling", + "description": "Rate Constants", + "tags": [ + "jak", + "stat", + "cytokine", + "signaling", + "receptor" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "Jaruszewicz-Blonska_2023", + "name": "Jaruszewicz 2023", + "description": "T-cell discrimination", + "tags": [ + "published", + "immunology", + "jaruszewicz", + "blonska", + "2023", + "ikk", + "ikba", + "ikba_mrna", + "a20", + "nfkb" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "jnk-mapk-signaling", + "name": "jnk mapk signaling", + "description": "JNK MAPK Signaling: Scaffold-mediated activation and feedback.", + "tags": [ + "jnk", + "mapk", + "signaling", + "mkk7", + "jip1", + "v_dephos" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "jobs_ground", + "name": "30-jobs", + "description": "NFsim simulation of the job market", + "tags": [ + "other" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "jobs_tofit", + "name": "30-jobs", + "description": "NFsim simulation of the job market", + "tags": [ + "other" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "Jung_2017", + "name": "Jung 2017", + "description": "M1 receptor signaling", + "tags": [ + "published", + "jung", + "2017", + "m1r", + "oxo", + "arrestin", + "mek", + "erk", + "perk", + "oxo_ec", + "pp2a" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience" + ], + "collectionId": null + }, + { + "id": "Kesseler_2013", + "name": "Kesseler 2013", + "description": "G2/Mitosis transition", + "tags": [ + "published", + "kesseler", + "2013", + "mpf", + "cdc25", + "wee1", + "myt1", + "pin1", + "pp2a", + "prox", + "e33" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "collectionId": null + }, + { + "id": "Kiefhaber_emodel", + "name": "Kiefhaber_emodel", + "description": "Allow molar units to be used for bimolecular rate constants", + "tags": [ + "validation", + "kiefhaber", + "emodel", + "setoption", + "l", + "p", + "s", + "a" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "kir-channel-regulation", + "name": "kir channel regulation", + "description": "Kir Channel Regulation: PIP2 modulation and G-protein potentiation.", + "tags": [ + "kir", + "channel", + "regulation", + "pip2", + "gbg", + "v_opening", + "v_gbg_factor" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Kocieniewski_2012", + "name": "Kocieniewski 2012", + "description": "Actin dynamics", + "tags": [ + "published", + "kocieniewski", + "2012", + "map3k", + "map2k", + "mapk", + "scaff" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "Korwek_2023", + "name": "Korwek_2023", + "description": "This BioNetGen file features the article:", + "tags": [ + "validation", + "korwek", + "2023", + "polyic", + "rigi", + "mavs", + "pkr", + "oas3", + "rnasel", + "eif2a", + "rigi_mrna" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Kozer_2013", + "name": "Kozer 2013", + "description": "EGFR oligomerization", + "tags": [ + "published", + "kozer", + "2013", + "egf", + "egfr" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "Kozer_2014", + "name": "Kozer 2014", + "description": "Grb2-EGFR recruitment", + "tags": [ + "published", + "kozer", + "2014", + "egf", + "egfr", + "grb2" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "l-type-calcium-channel-dynamics", + "name": "l type calcium channel dynamics", + "description": "L-type Calcium Channel: Voltage gating and CDI (Calcium-dependent inactivation).", + "tags": [ + "l", + "type", + "calcium", + "channel", + "dynamics", + "ltcc", + "voltage", + "v_open", + "v_inact" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "lac-operon-regulation", + "name": "lac operon regulation", + "description": "Kinetic Parameters", + "tags": [ + "lac", + "operon", + "regulation", + "laci", + "promoter", + "mrna", + "betagal", + "lactose", + "allolactose" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "Lang_2024", + "name": "Lang 2024", + "description": "Cell cycle regulation", + "tags": [ + "published", + "lang", + "2024", + "e2f", + "rb1", + "ppp2r2b", + "ccnb_promoter", + "ccna", + "ccna_promoter", + "foxm1_promoter", + "ensa_arpp19" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "collectionId": null + }, + { + "id": "Ligon_2014", + "name": "Ligon 2014", + "description": "Lipoplex delivery", + "tags": [ + "published", + "nfsim", + "ligon", + "2014", + "lext", + "pit", + "lint" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "LilyIgE", + "name": "LilyIgE", + "description": "An example from a real application", + "tags": [ + "lilyige", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Lin_ERK_2019", + "name": "Lin 2019", + "description": "ERK signaling", + "tags": [ + "published", + "literature", + "signaling", + "lin", + "erk", + "2019", + "egfr", + "sos", + "ras", + "rasgap", + "raf", + "mek", + "ekar3" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "developmental" + ], + "collectionId": null + }, + { + "id": "Lin_Prion_2019", + "name": "Lin 2019", + "description": "Prion replication", + "tags": [ + "published", + "literature", + "prion", + "lin", + "2019", + "prp", + "scaledupspecies1", + "scaledupspecies2", + "scaledupspecies15", + "scaledupspecies30" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "neuroscience" + ], + "collectionId": null + }, + { + "id": "Lin_TCR_2019", + "name": "Lin 2019", + "description": "TCR signaling", + "tags": [ + "published", + "literature", + "immune", + "lin", + "tcr", + "2019", + "pmhc", + "lck", + "shp", + "zap", + "mek", + "erk" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "lipid-mediated-pip3-signaling", + "name": "lipid mediated pip3 signaling", + "description": "Kinetic Parameters", + "tags": [ + "lipid", + "mediated", + "pip3", + "signaling", + "pi3k", + "pip2", + "pten", + "pdk1" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Lisman", + "name": "Lisman", + "description": "title: auto.bngl", + "tags": [ + "lisman", + "k1", + "p", + "input", + "visualize", + "setparameter", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "Lisman_bifurcate", + "name": "Lisman bifurcate", + "description": "title: Lisman_bifurcate.bngl", + "tags": [ + "lisman", + "bifurcate", + "k1", + "p" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "localfunc", + "name": "localfunc", + "description": "Test local function expansion", + "tags": [ + "validation", + "localfunc", + "a", + "b", + "c", + "trash", + "f_synth" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "LR", + "name": "LR", + "description": "title: LR.bngl", + "tags": [ + "lr", + "l", + "r", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "LR_comp", + "name": "LR comp", + "description": "title: LR_comp.bngl", + "tags": [ + "lr", + "comp", + "l", + "r", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "LRR", + "name": "LRR", + "description": "title: LRR.bngl", + "tags": [ + "lrr", + "l", + "r" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "LRR_comp", + "name": "LRR comp", + "description": "title: LRR_comp.bngl", + "tags": [ + "lrr", + "comp", + "l", + "r", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "LV", + "name": "LV", + "description": "title: LV.bgl", + "tags": [ + "lv", + "s", + "w", + "generate_network", + "writesbml", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "LV_comp", + "name": "LV comp", + "description": "title: LV_comp.bgl", + "tags": [ + "lv", + "comp", + "k2", + "s", + "w" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "m1", + "name": "of a 3-step signaling cascade", + "description": "Toy model of a 3-step signaling cascade", + "tags": [ + "k1", + "k2", + "k3", + "ainit", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "m1_ground", + "name": "of a 3-step signaling cascade", + "description": "Toy model of a 3-step signaling cascade", + "tags": [ + "k1", + "k2", + "k3", + "ainit", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "machine_tofit", + "name": "translated into BNGL", + "description": "Ensemble model translated into BNGL", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "Macken_1982", + "name": "Macken 1982", + "description": "TLBR solution macken 1982", + "tags": [ + "published", + "physics", + "macken", + "1982" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "Mallela2021_Cities", + "name": "Mallela 2021 - COVID-19 City Models", + "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", + "tags": [ + "covid-19", + "epidemiology", + "parameter-estimation", + "pybionetgen" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": "Mallela2021_Cities" + }, + { + "id": "Mallela2021_States", + "name": "Mallela 2021 - COVID-19 State-Level Models", + "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", + "tags": [ + "covid-19", + "epidemiology", + "parameter-estimation", + "pybionetgen" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": "Mallela2021_States" + }, + { + "id": "Mallela2022_MSAs", + "name": "Mallela 2022 - COVID-19 MSA Models", + "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", + "tags": [ + "covid-19", + "epidemiology", + "parameter-estimation", + "pybionetgen" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": "Mallela2022_MSAs" + }, + { + "id": "mapk-dimers", + "name": "MAPK Dimers", + "description": "MAPK dimerization", + "tags": [ + "published", + "mapk", + "dimers", + "ste5", + "ste11", + "ste7", + "fus3" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "mapk-monomers", + "name": "MAPK Monomers", + "description": "MAPK cascade", + "tags": [ + "published", + "mapk", + "monomers", + "ste5", + "ste11", + "ste7", + "fus3" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "mapk-signaling-cascade", + "name": "mapk signaling cascade", + "description": "Rate Constants", + "tags": [ + "mapk", + "signaling", + "cascade", + "ligand", + "receptor", + "mapkkk", + "mapkk" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "Massole_2023", + "name": "Massole 2023", + "description": "Epo receptor signaling", + "tags": [ + "published", + "massole", + "2023" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental" + ], + "collectionId": null + }, + { + "id": "mCaMKII_Ca_Spike", + "name": "Ordyan 2020: mCaMKII Ca Spike", + "description": "mCaMKII Ca Spike model", + "tags": [ + "published", + "neuroscience", + "mcamkii", + "ca", + "spike", + "cam", + "ng", + "camkii", + "pp1", + "time_counter" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "collectionId": null + }, + { + "id": "McMillan_2021", + "name": "McMillan 2021", + "description": "TNF signaling", + "tags": [ + "published", + "nfsim", + "mcmillan", + "2021", + "r0_tot", + "t0_tot", + "r", + "t", + "generate_network", + "simulate_ode" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "Mertins_2023", + "name": "Mertins 2023", + "description": "DNA damage response", + "tags": [ + "published", + "mertins", + "2023", + "dnadsb", + "p53", + "mrna_bax", + "bax", + "bclxl", + "bad", + "fourteen_3_3", + "caspase" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "meta_formal_game_theory", + "name": "meta formal game theory", + "description": "Model: meta_formal_game_theory.bngl", + "tags": [ + "meta", + "formal", + "game", + "theory", + "hawk", + "dove", + "pop", + "payoffh", + "payoffd" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "meta_formal_molecular_clock", + "name": "meta formal molecular clock", + "description": "Model: meta_formal_molecular_clock.bngl", + "tags": [ + "meta", + "formal", + "molecular", + "clock", + "fasta", + "fastb", + "slowc", + "slowd" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "meta_formal_petri_net", + "name": "meta formal petri net", + "description": "Model: meta_formal_petri_net.bngl", + "tags": [ + "meta", + "formal", + "petri", + "net", + "p1", + "p2", + "p3", + "p4" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "michaelis-menten-kinetics", + "name": "michaelis menten kinetics", + "description": "Kinetic Constants", + "tags": [ + "michaelis", + "menten", + "kinetics", + "e", + "s", + "p", + "generate_network", + "simulate", + "writesbml" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "michment", + "name": "michment", + "description": "Michaelis Menten", + "tags": [ + "validation", + "michment", + "e", + "s", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "michment_cont", + "name": "michment_cont", + "description": "Michaelis Menten Continue", + "tags": [ + "validation", + "michment", + "cont", + "readfile", + "setconcentration", + "simulate_ode", + "addconcentration" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Miller2022_NavajoNation", + "name": "Miller 2022 - Navajo Nation Models", + "description": "COVID-19 epidemiological models fit to Navajo Nation regional data.", + "tags": [ + "covid-19", + "epidemiology", + "pybionetgen" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": "Miller2022_NavajoNation" + }, + { + "id": "Miller2025_MEK", + "name": "Miller 2025 - MEK Isoform Models", + "description": "MEK isoform variant models curated for PyBioNetGen.", + "tags": [ + "mek", + "isoforms", + "signaling", + "pybionetgen" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "collectionId": "Miller2025_MEK" + }, + { + "id": "Mitra2019_02_egfr_bnf1_InputFiles_egfr", + "name": "InputFiles", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "ml_gradient_descent", + "name": "ml gradient descent", + "description": "Gradient Descent Optimizer in BNGL", + "tags": [ + "ml", + "gradient", + "descent", + "posx", + "posy", + "velx", + "vely", + "loss" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "ml_hopfield", + "name": "ml hopfield", + "description": "Model: ml_hopfield.bngl", + "tags": [ + "ml", + "hopfield", + "neuron", + "net1", + "net2", + "net3", + "target1" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "ml_kmeans", + "name": "ml kmeans", + "description": "Model: ml_kmeans.bngl", + "tags": [ + "ml", + "kmeans", + "ax", + "ay", + "bx", + "by" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "ml_q_learning", + "name": "ml q learning", + "description": "Q-Learning Agent in BNGL", + "tags": [ + "ml", + "q", + "learning", + "pos", + "ql", + "qr", + "reward", + "action" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "ml_svm", + "name": "ml svm", + "description": "Model: ml_svm.bngl", + "tags": [ + "ml", + "svm", + "w1", + "w2", + "b", + "db_dt", + "dw1_dt" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "model", + "name": "model", + "description": "filename: model.bngl", + "tags": [ + "model", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "model", + "name": "model", + "description": "A model of IgE receptor signaling", + "tags": [ + "model", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "model_ground", + "name": "model_ground.bngl", + "description": "filename: model_ground.bngl", + "tags": [ + "x_tot__free", + "k_xoff__free", + "k_xon__free", + "kase__free", + "kdegx__free", + "kdegran__free", + "km_ship1__free", + "km_syk__free", + "km_x__free", + "koff__free", + "kp_ship1__free", + "kp_syk__free", + "kp_x__free", + "kpten__free", + "ksynth1__free", + "pase__free", + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "model_tofit", + "name": "model tofit", + "description": "A model of IgE receptor signaling", + "tags": [ + "model", + "tofit", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "Model_ZAP", + "name": "Model ZAP", + "description": "ZAP-70 recruitment", + "tags": [ + "published", + "immunology", + "nfsim", + "model", + "zap", + "kon", + "a", + "cbl", + "cd16", + "lck", + "ligand", + "zeta", + "dead" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "Motivating_example", + "name": "Motivating_example", + "description": "Signal Transduction with receptor internalization", + "tags": [ + "validation", + "motivating", + "example", + "l", + "r", + "tf", + "dna", + "mrna1", + "mrna2", + "p1", + "p2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Motivating_example_cBNGL", + "name": "Motivating_example_cBNGL", + "description": "Signal transduction with receptor internalization", + "tags": [ + "validation", + "motivating", + "example", + "cbngl", + "l", + "r", + "tf", + "dna", + "mrna1", + "mrna2", + "p1", + "p2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "motor", + "name": "motor", + "description": "Motor protein", + "tags": [ + "validation", + "motor", + "chey", + "kplus", + "kminus" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "mt_arithmetic_compiler", + "name": "mt arithmetic compiler", + "description": "Model: mt_arithmetic_compiler.bngl", + "tags": [ + "mt", + "arithmetic", + "compiler", + "node", + "target_add", + "target_mult" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "mt_bngl_interpreter", + "name": "mt bngl interpreter", + "description": "Model: mt_bngl_interpreter.bngl", + "tags": [ + "mt", + "bngl", + "interpreter", + "rule", + "species", + "exec_s1_s2", + "generate_network", + "simulate" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "mt_music_sequencer", + "name": "mt music sequencer", + "description": "Music Sequencer / Chord Synthesizer in BNGL", + "tags": [ + "mt", + "music", + "sequencer", + "v1s", + "v1c", + "v2s", + "v2c", + "v3s", + "v3c", + "mix", + "chordphase" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "mt_pascal_triangle", + "name": "mt pascal triangle", + "description": "Model: mt_pascal_triangle.bngl", + "tags": [ + "mt", + "pascal", + "triangle", + "node" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "mt_quine", + "name": "mt quine", + "description": "Model: mt_quine.bngl", + "tags": [ + "mt", + "quine", + "gene", + "protein" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "mtor-signaling", + "name": "mtor signaling", + "description": "mTOR Signaling Pathway", + "tags": [ + "mtor", + "signaling", + "rheb", + "mtorc1", + "s6k", + "ampk" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "mtorc2-signaling", + "name": "mtorc2 signaling", + "description": "mTORC2 signaling regulates cell survival and growth via AKT and SGK1.", + "tags": [ + "mtorc2", + "signaling", + "mtor", + "sin1", + "rictor", + "akt", + "sgk1", + "pip3" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Mukhopadhyay_2013", + "name": "Mukhopadhyay 2013", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "mukhopadhyay", + "2013", + "s", + "e", + "f", + "z" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "mwc", + "name": "mwc", + "description": "Monod-Wyman-Changeux model", + "tags": [ + "validation", + "mwc", + "setoption", + "h", + "ox", + "b" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "myogenic-differentiation", + "name": "myogenic differentiation", + "description": "Myogenic Differentiation", + "tags": [ + "myogenic", + "differentiation", + "myod", + "myog", + "mef2" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", + "name": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", + "description": "Runtime-only BNGL model migrated from public/models: Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", + "tags": [ + "myrtle", + "beach", + "conway", + "north", + "sc", + "nc" + ], + "category": "other", + "origin": "contributed", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "Nag_2009", + "name": "Nag 2009", + "description": "LAT-Grb2-SOS1 signaling", + "tags": [ + "published", + "nag", + "2009", + "lig", + "lyn", + "syk", + "rec", + "lat", + "grb", + "sos" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "negative-feedback-loop", + "name": "negative feedback loop", + "description": "Negative Feedback Loop", + "tags": [ + "negative", + "feedback", + "loop", + "gene", + "mrna", + "protein" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "neurotransmitter-release", + "name": "neurotransmitter release", + "description": "Neurotransmitter Release", + "tags": [ + "neurotransmitter", + "release", + "calcium", + "snare", + "vesicle", + "postsynaptic" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "nfkb", + "name": "nfkb", + "description": "NF-kB signaling pathway", + "tags": [ + "validation", + "nfkb", + "tnfr", + "ikkk", + "tnf", + "ikk", + "ikba", + "a20", + "competitor" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "nfkb_illustrating_protocols", + "name": "nfkb_illustrating_protocols", + "description": "NF-kB signaling pathway", + "tags": [ + "validation", + "nfkb", + "illustrating", + "protocols", + "tnfr", + "ikkk", + "tnf", + "ikk", + "ikba", + "a20", + "competitor" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "nfkb-feedback", + "name": "nfkb feedback", + "description": "TNFalpha-induced NF-kB signaling with IkappaB-alpha feedback.", + "tags": [ + "nfkb", + "feedback", + "ikb", + "ikk", + "a20" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "NFmodel", + "name": "NFmodel", + "description": "BioNetGen model: NFmodel", + "tags": [ + "nfmodel", + "ag", + "ab", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "nfsim_aggregation_gelation", + "name": "nfsim aggregation gelation", + "description": "Model: nfsim_aggregation_gelation.bngl", + "tags": [ + "nfsim", + "aggregation", + "gelation", + "m" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "nfsim_coarse_graining", + "name": "nfsim coarse graining", + "description": "Model: nfsim_coarse_graining.bngl", + "tags": [ + "nfsim", + "coarse", + "graining", + "droplet" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "nfsim_dynamic_compartments", + "name": "nfsim dynamic compartments", + "description": "Model: nfsim_dynamic_compartments.bngl", + "tags": [ + "nfsim", + "dynamic", + "compartments", + "cell", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "nfsim_hybrid_particle_field", + "name": "nfsim hybrid particle field", + "description": "Model: nfsim_hybrid_particle_field.bngl", + "tags": [ + "nfsim", + "hybrid", + "particle", + "field" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "nfsim_ring_closure_polymer", + "name": "nfsim ring closure polymer", + "description": "Model: nfsim_ring_closure_polymer.bngl", + "tags": [ + "nfsim", + "ring", + "closure", + "polymer", + "a", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "nn_xor", + "name": "nn xor", + "description": "Model: nn_xor.bngl", + "tags": [ + "nn", + "xor", + "input", + "hidden", + "output", + "target", + "weightih", + "weightho", + "dopamine" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "no_frees", + "name": "no frees", + "description": "Original values used to generate parabola.exp", + "tags": [ + "no", + "frees", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "no_generate_network", + "name": "no generate network", + "description": "Original values used to generate parabola.exp", + "tags": [ + "no", + "generate", + "network", + "counter", + "y", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "no_suffix", + "name": "no suffix", + "description": "Original values used to generate parabola.exp", + "tags": [ + "no", + "suffix", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "no-cgmp-signaling", + "name": "no cgmp signaling", + "description": "Nitric Oxide (NO) / cGMP signaling pathway.", + "tags": [ + "no", + "cgmp", + "signaling", + "sgc", + "pkg" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "Nosbisch_2022", + "name": "Nosbisch 2022", + "description": "RTK-PLCgamma1 signaling", + "tags": [ + "published", + "nosbisch", + "2022", + "rtk", + "plcgamma1", + "generate_network" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "notch", + "name": "Notch", + "description": "Notch signaling", + "tags": [ + "published", + "notch", + "icn", + "ofut1", + "fringe", + "furin", + "dsl", + "csl", + "maml" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "notch-delta-lateral-inhibition", + "name": "notch delta lateral inhibition", + "description": "Notch-Delta Lateral Inhibition", + "tags": [ + "notch", + "delta", + "lateral", + "inhibition", + "cellnotch", + "celldelta" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "NYC", + "name": "NYC", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "nyc", + "counter", + "fdcs", + "s", + "sv", + "e", + "a", + "i", + "v" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": null + }, + { + "id": "organelle_transport", + "name": "organelle transport", + "description": "title: organelle_transport.bngl", + "tags": [ + "organelle", + "transport", + "a", + "b", + "c", + "d", + "t1", + "at1", + "ct1", + "t2" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "organelle_transport_struct", + "name": "organelle transport struct", + "description": "title: organelle_transport_abcd.bngl", + "tags": [ + "organelle", + "transport", + "struct", + "a", + "b", + "t1", + "t2" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "oxidative-stress-response", + "name": "oxidative stress response", + "description": "Oxidative Stress Response (Keap1-Nrf2 Pathway)", + "tags": [ + "oxidative", + "stress", + "response", + "ros", + "keap1", + "nrf2", + "antioxidant" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "p38-mapk-signaling", + "name": "p38 mapk signaling", + "description": "p38 MAPK stress signaling cascade.", + "tags": [ + "p38", + "mapk", + "signaling", + "mkk3", + "mapkap2", + "v_thermal" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "p53-mdm2-oscillator", + "name": "p53 mdm2 oscillator", + "description": "BioNetGen model: p53 mdm2 oscillator", + "tags": [ + "p53", + "mdm2", + "oscillator", + "generate_network" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "parabola", + "name": "parabola", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "parabola", + "counter", + "par", + "line", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "parabola", + "name": "parabola", + "description": "Original values used to generate parabola.exp", + "tags": [ + "parabola", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "parabola", + "name": "parabola", + "description": "Original values used to generate parabola.exp", + "tags": [ + "parabola", + "counter", + "y", + "generate_network", + "simulate", + "resetconcentrations" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "parabola", + "name": "parabola", + "description": "Original values used to generate parabola.exp", + "tags": [ + "parabola", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "parabola", + "name": "parabola", + "description": "Original values used to generate parabola.exp", + "tags": [ + "parabola", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "parabola_ground", + "name": "parabola ground", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "parabola", + "ground", + "counter", + "par", + "line", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "parabola2", + "name": "parabola2", + "description": "A file for testing behavior with duplicate file names", + "tags": [ + "parabola2", + "counter", + "y", + "generate_network", + "simulate", + "resetconcentrations" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "ParamsEverywhere", + "name": "ParamsEverywhere", + "description": "An example from a real application", + "tags": [ + "paramseverywhere", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "parp1-mediated-dna-repair", + "name": "parp1 mediated dna repair", + "description": "PARP1-mediated DNA damage sensing and repair.", + "tags": [ + "parp1", + "mediated", + "dna", + "repair", + "par", + "nad", + "v_parylate" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "Pekalski_2013", + "name": "Pekalski 2013", + "description": "Spontaneous signaling", + "tags": [ + "published", + "pekalski", + "2013", + "tnfr", + "ikk", + "ikkk", + "ikba", + "ikba_mrna", + "a20", + "a20_mrna", + "nfkb" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "ph_lorenz_attractor", + "name": "ph lorenz attractor", + "description": "Lorenz Attractor in BNGL", + "tags": [ + "ph", + "lorenz", + "attractor", + "lx", + "ly", + "lz", + "x", + "y" + ], + "category": "physics", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "ph_nbody_gravity", + "name": "ph nbody gravity", + "description": "Model: ph_nbody_gravity.bngl", + "tags": [ + "ph", + "nbody", + "gravity", + "body", + "r2" + ], + "category": "physics", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "ph_schrodinger", + "name": "ph schrodinger", + "description": "Model: ph_schrodinger.bngl", + "tags": [ + "ph", + "schrodinger", + "psi" + ], + "category": "physics", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "ph_wave_equation", + "name": "ph wave equation", + "description": "Model: ph_wave_equation.bngl", + "tags": [ + "ph", + "wave", + "equation", + "node" + ], + "category": "physics", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "Phoenix", + "name": "Phoenix", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "phoenix", + "counter", + "fdcs", + "s", + "sv", + "e", + "a", + "i", + "v" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": null + }, + { + "id": "phosphorelay-chain", + "name": "phosphorelay chain", + "description": "BioNetGen model: phosphorelay chain", + "tags": [ + "phosphorelay", + "chain", + "sensor", + "relay", + "output" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "platelet-activation", + "name": "platelet activation", + "description": "BioNetGen model: platelet activation", + "tags": [ + "platelet", + "activation", + "adp", + "p2y12", + "integrin", + "thromboxane" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "polymer", + "name": "polymer", + "description": "Polymerization model", + "tags": [ + "published", + "tutorials", + "nfsim", + "polymer", + "a", + "b", + "c", + "simulate_nf" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "tutorials" + ], + "collectionId": null + }, + { + "id": "polymer_draft", + "name": "polymer draft", + "description": "Polymerization (draft)", + "tags": [ + "published", + "tutorials", + "nfsim", + "polymer", + "draft", + "a", + "b", + "c", + "simulate_nf" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "tutorials" + ], + "collectionId": null + }, + { + "id": "polymer_fixed", + "name": "polymer_fixed", + "description": "Runtime-only BNGL model migrated from public/models: polymer_fixed", + "tags": [ + "polymer", + "fixed" + ], + "category": "other", + "origin": "contributed", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "polynomial", + "name": "polynomial", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "polynomial", + "counter", + "y1", + "y2", + "generate_network", + "simulate", + "setparameter", + "resetconcentrations" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "polynomial", + "name": "polynomial", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "polynomial", + "counter", + "y1", + "y2", + "generate_network", + "simulate", + "setparameter", + "resetconcentrations" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "polynomial", + "name": "polynomial", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "polynomial", + "counter", + "y1", + "y2", + "generate_network", + "simulate", + "setparameter", + "resetconcentrations" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "polynomial_ground", + "name": "polynomial ground", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "polynomial", + "ground", + "counter", + "y1", + "y2", + "generate_network", + "simulate", + "setparameter", + "resetconcentrations" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "Posner_1995", + "name": "Posner 1995", + "description": "BLBR rings", + "tags": [ + "published", + "physics", + "posner", + "1995" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "Posner_2004", + "name": "Posner 2004", + "description": "BLBR cooperativity", + "tags": [ + "published", + "physics", + "posner", + "2004" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "predator-prey-dynamics", + "name": "predator prey dynamics", + "description": "BioNetGen model: predator prey dynamics", + "tags": [ + "predator", + "prey", + "dynamics" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "prion_model", + "name": "ERK_model.bngl", + "description": "filename: ERK_model.bngl", + "tags": [ + "egf", + "erkpp_sos1_fb", + "erkpp_mek_fb", + "erkpp_raf1_fb", + "lambda", + "egfr_tot", + "ras_tot", + "sos_tot", + "rasgap_tot", + "raf_tot", + "mek_tot", + "erk_tot", + "ekar3_tot", + "erktr_tot", + "a1", + "d1", + "b1", + "u1a", + "u1b", + "b2a", + "u2a", + "b2b", + "u2b", + "k2a", + "k2b", + "b3", + "u3", + "k3", + "a2", + "d2", + "p1", + "q1", + "p2", + "q2", + "p3", + "q3", + "p4", + "q4", + "q5", + "p6", + "q6", + "a0_ekar3", + "d0_ekar3", + "a0_erktr", + "d0_erktr", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem_quant_model_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem16_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem16_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem32_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem32_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem4_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem4_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem64_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem64_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem8_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem8_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "process_actin_treadmilling", + "name": "process actin treadmilling", + "description": "Model: process_actin_treadmilling.bngl", + "tags": [ + "process", + "actin", + "treadmilling", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "process_autophagy_flux", + "name": "process autophagy flux", + "description": "Model: process_autophagy_flux.bngl", + "tags": [ + "process", + "autophagy", + "flux", + "phagophore", + "autophagosome", + "lysosome", + "autolysosome", + "cargo" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "process_cell_adhesion_strength", + "name": "process cell adhesion strength", + "description": "Model: process_cell_adhesion_strength.bngl", + "tags": [ + "process", + "cell", + "adhesion", + "strength", + "c1", + "c2", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "process_kinetic_proofreading_tcr", + "name": "process kinetic proofreading tcr", + "description": "Model: process_kinetic_proofreading_tcr.bngl", + "tags": [ + "process", + "kinetic", + "proofreading", + "tcr", + "l" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "process_quorum_sensing_switch", + "name": "process quorum sensing switch", + "description": "Model: process_quorum_sensing_switch.bngl", + "tags": [ + "process", + "quorum", + "sensing", + "switch", + "gene_ai", + "ai", + "r", + "gene_light" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "pt303", + "name": "pt303", + "description": "c = 0.20 /d t_1/2 = 3.5 d (inferred)", + "tags": [ + "pt303", + "counter", + "v", + "lnv", + "s", + "c", + "half_life", + "lnv_tangent" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "pt403", + "name": "pt403", + "description": "c = 0.23 /d t_1/2 = 3.0 d (inferred)", + "tags": [ + "pt403", + "counter", + "v", + "lnv", + "s", + "c", + "half_life", + "lnv_tangent" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "pt409", + "name": "pt409", + "description": "c = 0.39 /d t_1/2 = 1.8 d (inferred)", + "tags": [ + "pt409", + "counter", + "v", + "lnv", + "s", + "c", + "half_life", + "lnv_tangent" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "PyBNF_fitting_setup_190127_CHO_EGFR_forBNF", + "name": "PyBNF-fitting-setup", + "description": "BNGL model: 190127_CHO_EGFR_forBNF", + "tags": [ + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "quasi_equilibrium", + "name": "quasi equilibrium", + "description": "Quasi-equilibrium approximation", + "tags": [ + "published", + "toy models", + "quasi", + "equilibrium", + "a", + "b", + "c" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "quorum-sensing-circuit", + "name": "quorum sensing circuit", + "description": "BioNetGen model: quorum sensing circuit", + "tags": [ + "quorum", + "sensing", + "circuit", + "autoinducer", + "autoinducer_env", + "gene", + "protein" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "rab_mon1ccz1_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_mon1ccz1_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_rab5_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_rab5_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_rab7_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_rab7_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_wt", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_wt", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab-gtpase-cycle", + "name": "rab gtpase cycle", + "description": "BioNetGen model: rab gtpase cycle", + "tags": [ + "rab", + "gtpase", + "cycle", + "gef", + "gap", + "effector" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "RAFi", + "name": "RAFi", + "description": "BioNetGen model: RAFi", + "tags": [ + "rafi", + "r", + "i", + "ybar", + "activity" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "RAFi_ground", + "name": "RAFi ground", + "description": "BioNetGen model: RAFi ground", + "tags": [ + "rafi", + "ground", + "r", + "i", + "ybar", + "activity" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "rankl-rank-signaling", + "name": "rankl rank signaling", + "description": "RANKL-RANK-OPG signaling in bone remodeling.", + "tags": [ + "rankl", + "rank", + "signaling", + "opg", + "nfat", + "traf6" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "ras-gef-gap-cycle", + "name": "ras gef gap cycle", + "description": "Ras-GEF-GAP cycle with explicit nucleotide exchange.", + "tags": [ + "ras", + "gef", + "gap", + "cycle", + "sos", + "rasgap", + "v_gef", + "v_gap" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "rec_dim", + "name": "rec_dim", + "description": "Ligand-receptor binding", + "tags": [ + "validation", + "rec", + "dim", + "lig", + "writemdl", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "rec_dim_comp", + "name": "rec_dim_comp", + "description": "name dimension volume contained_by", + "tags": [ + "validation", + "rec", + "dim", + "comp", + "kp1", + "kp2", + "lig", + "writemdl", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "receptor", + "name": "13-receptor", + "description": "A simple model", + "tags": [ + "ligand_ispresent", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "receptor", + "name": "receptor", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", + "tags": [ + "receptor", + "l", + "r", + "func" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "receptor_nf", + "name": "receptor nf", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", + "tags": [ + "receptor", + "nf", + "l", + "r" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "receptor_nf", + "name": "receptor nf", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", + "tags": [ + "receptor", + "nf", + "l", + "r" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Repressilator", + "name": "Repressilator", + "description": "Repressilator circuit", + "tags": [ + "published", + "tutorial", + "native", + "repressilator", + "gtetr", + "gci", + "glaci", + "mtetr", + "mci", + "mlaci", + "ptetr", + "pci" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "synbio", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "repressilator-oscillator", + "name": "repressilator oscillator", + "description": "BioNetGen model: repressilator oscillator", + "tags": [ + "repressilator", + "oscillator", + "genea", + "geneb", + "genec", + "mrna_a", + "mrna_b", + "mrna_c", + "proteina", + "proteinb" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "retinoic-acid-signaling", + "name": "retinoic acid signaling", + "description": "BioNetGen model: retinoic acid signaling", + "tags": [ + "retinoic", + "acid", + "signaling", + "ra", + "rarrxr", + "corepressor", + "targetgene" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "rho-gtpase-actin-cytoskeleton", + "name": "rho gtpase actin cytoskeleton", + "description": "RhoA-GTPase regulation of the actin cytoskeleton.", + "tags": [ + "rho", + "gtpase", + "actin", + "cytoskeleton", + "rhoa", + "rock", + "limk", + "cofilin" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Rule_based_egfr_compart", + "name": "Rule based egfr compart", + "description": "Compartmental EGFR model", + "tags": [ + "published", + "rule", + "based", + "egfr", + "compart", + "egf", + "grb2", + "shc", + "generate_network" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "collectionId": null + }, + { + "id": "Rule_based_egfr_tutorial", + "name": "Faeder 2009", + "description": "EGFR signaling", + "tags": [ + "published", + "rule", + "based", + "egfr", + "tutorial", + "egf", + "grb2", + "shc", + "generate_network" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "Rule_based_Ran_transport", + "name": "Rule based Ran transport", + "description": "Nuclear Ran transport", + "tags": [ + "published", + "rule", + "based", + "ran", + "transport", + "c", + "rcc1", + "generate_network" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "Rule_based_Ran_transport_draft", + "name": "Rule based Ran transport draft", + "description": "Ran transport (draft)", + "tags": [ + "published", + "rule", + "based", + "ran", + "transport", + "draft", + "c", + "rcc1", + "generate_network" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "Scaff-22_ground", + "name": "18-mapk", + "description": "For \"ground truth\" model, use median values such that hierarchy H1 occurs, as shown in Table 3.", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "Scaff-22_tofit", + "name": "18-mapk", + "description": "For \"ground truth\" model, use median values such that hierarchy H1 occurs, as shown in Table 3.", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "SHP2_base_model", + "name": "SHP2_base_model", + "description": "Base model of Shp2 regulation", + "tags": [ + "validation", + "shp2", + "base", + "model", + "r", + "s", + "exclude_reactants" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "shp2-phosphatase-regulation", + "name": "shp2 phosphatase regulation", + "description": "SHP2 phosphatase regulation via autoinhibition and SH2 binding.", + "tags": [ + "shp2", + "phosphatase", + "regulation", + "rtk", + "substrate", + "v_dephos" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "signal-amplification-cascade", + "name": "signal amplification cascade", + "description": "BioNetGen model: signal amplification cascade", + "tags": [ + "signal", + "amplification", + "cascade", + "ligand", + "receptor", + "effector", + "messenger" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "simple", + "name": "simple", + "description": "Simple binding model", + "tags": [ + "published", + "tutorials", + "simple", + "s", + "t", + "dnat", + "trash" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "collectionId": null + }, + { + "id": "Simple", + "name": "Simple", + "description": "An example from a real application", + "tags": [ + "simple", + "setoption", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Simple_AddActions", + "name": "Simple AddActions", + "description": "An example from a real application", + "tags": [ + "simple", + "addactions", + "setoption", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Simple_Answer", + "name": "Simple Answer", + "description": "An example from a real application", + "tags": [ + "simple", + "answer", + "setoption", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Simple_GenOnly", + "name": "Simple GenOnly", + "description": "An example from a real application", + "tags": [ + "simple", + "genonly", + "setoption", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "simple_nf_seed", + "name": "simple nf seed", + "description": "BioNetGen model: simple nf seed", + "tags": [ + "simple", + "nf", + "seed", + "a", + "b", + "function1", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "simple_nfsim_test", + "name": "simple_nfsim_test", + "description": "Runtime-only BNGL model migrated from public/models: simple_nfsim_test", + "tags": [ + "simple", + "nfsim", + "test" + ], + "category": "other", + "origin": "contributed", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "Simple_nogen", + "name": "Simple nogen", + "description": "An example from a real application", + "tags": [ + "simple", + "nogen", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "simple_sbml_import", + "name": "simple_sbml_import", + "description": "SBML import test", + "tags": [ + "validation", + "simple", + "sbml", + "import", + "readfile", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "simple_system", + "name": "simple_system", + "description": "Simple binding system", + "tags": [ + "validation", + "simple", + "system", + "x", + "y" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "simple-dimerization", + "name": "simple dimerization", + "description": "BioNetGen model: simple dimerization", + "tags": [ + "simple", + "dimerization", + "a", + "b", + "generate_network", + "simulate" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "SIR", + "name": "SIR", + "description": "BioNetGen model: SIR", + "tags": [ + "sir", + "saveconcentrations", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "sir-epidemic-model", + "name": "sir epidemic model", + "description": "BioNetGen model: sir epidemic model", + "tags": [ + "sir", + "epidemic", + "model", + "human", + "generate_network", + "simulate" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "tutorials", + "test-models" + ], + "collectionId": null + }, + { + "id": "smad-tgf-beta-signaling", + "name": "smad tgf beta signaling", + "description": "BioNetGen model: smad tgf beta signaling", + "tags": [ + "smad", + "tgf", + "beta", + "signaling", + "tgfb", + "tgfbr", + "smad2", + "smad4" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "sonic-hedgehog-gradient", + "name": "sonic hedgehog gradient", + "description": "Sonic Hedgehog (Shh) morphogen gradient formation.", + "tags": [ + "sonic", + "hedgehog", + "gradient", + "shh", + "ptc1", + "v_prod" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "sp_fourier_synthesizer", + "name": "sp fourier synthesizer", + "description": "Fourier Series Synthesizer in BNGL", + "tags": [ + "sp", + "fourier", + "synthesizer", + "s1", + "s3", + "s5", + "s7", + "s9", + "wave", + "c1" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "sp_image_convolution", + "name": "sp image convolution", + "description": "Image Convolution Filter in BNGL", + "tags": [ + "sp", + "image", + "convolution", + "px", + "ex", + "sink" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "sp_kalman_filter", + "name": "sp kalman filter", + "description": "Kalman Filter in BNGL", + "tags": [ + "sp", + "kalman", + "filter", + "truex", + "obs", + "estx", + "estv", + "variance", + "innovation" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "stat3-mediated-transcription", + "name": "stat3 mediated transcription", + "description": "STAT3-mediated transcription and feedback.", + "tags": [ + "stat3", + "mediated", + "transcription", + "dna", + "pias3", + "mrna" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "stress-response-adaptation", + "name": "stress response adaptation", + "description": "BioNetGen model: stress response adaptation", + "tags": [ + "stress", + "response", + "adaptation", + "sensor", + "adapter", + "enzyme" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Suderman_2013", + "name": "Suderman 2013", + "description": "Ensemble model translated into BNGL", + "tags": [ + "suderman", + "2013", + "i", + "trash", + "pheromone", + "ste2", + "gpa1", + "ste4", + "sst2", + "ste20" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "synaptic-plasticity-ltp", + "name": "synaptic plasticity ltp", + "description": "Initial Concentrations", + "tags": [ + "synaptic", + "plasticity", + "ltp", + "glutamate", + "nmda", + "calcium", + "camkii", + "ampar", + "glusource" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "synbio_band_pass_filter", + "name": "synbio band pass filter", + "description": "Model: synbio_band_pass_filter.bngl", + "tags": [ + "synbio", + "band", + "pass", + "filter", + "i", + "a", + "r", + "out" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "collectionId": null + }, + { + "id": "synbio_counter_molecular", + "name": "synbio counter molecular", + "description": "Model: synbio_counter_molecular.bngl", + "tags": [ + "synbio", + "counter", + "molecular", + "state", + "input" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "collectionId": null + }, + { + "id": "synbio_edge_detector", + "name": "synbio edge detector", + "description": "Model: synbio_edge_detector.bngl", + "tags": [ + "synbio", + "edge", + "detector", + "x", + "y", + "z" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "collectionId": null + }, + { + "id": "synbio_logic_gates_enzymatic", + "name": "synbio logic gates enzymatic", + "description": "Model: synbio_logic_gates_enzymatic.bngl", + "tags": [ + "synbio", + "logic", + "gates", + "enzymatic", + "i1", + "i2", + "gateand", + "gateor", + "outand", + "outor" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "collectionId": null + }, + { + "id": "synbio_oscillator_synchronization", + "name": "synbio oscillator synchronization", + "description": "Model: synbio_oscillator_synchronization.bngl", + "tags": [ + "synbio", + "oscillator", + "synchronization", + "osc1", + "osc2", + "signal" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "collectionId": null + }, + { + "id": "t-cell-activation", + "name": "t cell activation", + "description": "BioNetGen model: t cell activation", + "tags": [ + "t", + "cell", + "activation", + "tcr", + "antigen", + "cytokine" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "tcr", + "name": "tcr", + "description": "A model of T cell receptor signaling", + "tags": [ + "tcr", + "lig1", + "lig2", + "lig3", + "cd28", + "lck", + "itk", + "zap70" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "TCR_model", + "name": "ERK_model.bngl", + "description": "filename: ERK_model.bngl", + "tags": [ + "egf", + "erkpp_sos1_fb", + "erkpp_mek_fb", + "erkpp_raf1_fb", + "lambda", + "egfr_tot", + "ras_tot", + "sos_tot", + "rasgap_tot", + "raf_tot", + "mek_tot", + "erk_tot", + "ekar3_tot", + "erktr_tot", + "a1", + "d1", + "b1", + "u1a", + "u1b", + "b2a", + "u2a", + "b2b", + "u2b", + "k2a", + "k2b", + "b3", + "u3", + "k3", + "a2", + "d2", + "p1", + "q1", + "p2", + "q2", + "p3", + "q3", + "p4", + "q4", + "q5", + "p6", + "q6", + "a0_ekar3", + "d0_ekar3", + "a0_erktr", + "d0_erktr", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "test_ANG_synthesis_simple", + "name": "test_ANG_synthesis_simple", + "description": "Synthesis network test", + "tags": [ + "validation", + "test", + "ang", + "synthesis", + "simple", + "a", + "b", + "c", + "source", + "source2", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_fixed", + "name": "test_fixed", + "description": "# actions ##", + "tags": [ + "validation", + "test", + "fixed", + "a", + "b", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_MM", + "name": "test_MM", + "description": "Kinetic constants", + "tags": [ + "validation", + "test", + "mm", + "e", + "s", + "p", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_mratio", + "name": "test_mratio", + "description": "Reaction ratio test", + "tags": [ + "validation", + "test", + "mratio", + "a", + "b", + "c_theory", + "c_upper", + "c_lower" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_network_gen", + "name": "test_network_gen", + "description": "fceri model with network generation", + "tags": [ + "validation", + "test", + "network", + "gen", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_sat", + "name": "test_sat", + "description": "Kinetic constants", + "tags": [ + "validation", + "test", + "sat", + "e", + "s", + "p", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_synthesis_cBNGL_simple", + "name": "test_synthesis_cBNGL_simple", + "description": "Compartmental synthesis", + "tags": [ + "validation", + "test", + "synthesis", + "cbngl", + "simple", + "a", + "a2", + "b", + "c", + "source", + "source2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_synthesis_complex", + "name": "test_synthesis_complex", + "description": "Complex synthesis test", + "tags": [ + "validation", + "test", + "synthesis", + "complex", + "a", + "b", + "c", + "receptor", + "source", + "source2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_synthesis_complex_0_cBNGL", + "name": "test_synthesis_complex_0_cBNGL", + "description": "volume-surface", + "tags": [ + "validation", + "test", + "synthesis", + "complex", + "0", + "cbngl", + "volume_molecule1", + "volume_molecule2", + "surface_molecule1", + "surface_molecule2", + "volume_molecule3", + "volume_molecule4", + "volume_receptor", + "surface_receptor" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_synthesis_complex_source_cBNGL", + "name": "test_synthesis_complex_source_cBNGL", + "description": "volume-surface", + "tags": [ + "validation", + "test", + "synthesis", + "complex", + "source", + "cbngl", + "volume_molecule1", + "volume_molecule2", + "surface_molecule1", + "surface_molecule2", + "volume_molecule3", + "volume_molecule4", + "volume_receptor", + "surface_receptor" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_synthesis_simple", + "name": "test_synthesis_simple", + "description": "Simple synthesis test", + "tags": [ + "validation", + "test", + "synthesis", + "simple", + "a", + "b", + "c", + "source", + "source2", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "tlbr", + "name": "tlbr", + "description": "A model of trivalent ligand, bivalent receptor", + "tags": [ + "tlbr", + "l", + "r", + "lambda", + "fl" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "tlbr", + "name": "TLBR Tutorial", + "description": "Ligand binding", + "tags": [ + "published", + "immunology", + "tlbr", + "l", + "r", + "simulate_rm" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "tlmr", + "name": "tlmr", + "description": "Trivalent ligand monovalent receptor", + "tags": [ + "validation", + "tlmr", + "l", + "r", + "generate_network", + "simulate_ode" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "tlr3-dsrna-sensing", + "name": "tlr3 dsrna sensing", + "description": "TLR3-mediated dsRNA sensing and TRIF pathway activation.", + "tags": [ + "tlr3", + "dsrna", + "sensing", + "trif", + "irf3", + "sarm" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "tnf-induced-apoptosis", + "name": "tnf induced apoptosis", + "description": "BioNetGen model: tnf induced apoptosis", + "tags": [ + "tnf", + "induced", + "apoptosis", + "tnfr", + "caspase8", + "bid", + "caspase3" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "toggle", + "name": "Toggle", + "description": "Toggle switch", + "tags": [ + "published", + "tutorial", + "native", + "toggle", + "x", + "y", + "generate_network", + "writemfile", + "setconcentration" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "synbio", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "toy-jim", + "name": "toy-jim", + "description": "The model consists of a monovalent extracellular ligand,", + "tags": [ + "validation", + "toy", + "jim", + "l", + "r", + "a", + "k", + "null" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "toy1", + "name": "toy1", + "description": "Basic signaling toy", + "tags": [ + "published", + "tutorials", + "toy1", + "l", + "r", + "a", + "generate_network", + "writesbml", + "simulate_ode" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "collectionId": null + }, + { + "id": "toy2", + "name": "toy2", + "description": "Enzymatic reaction toy", + "tags": [ + "published", + "tutorials", + "toy2", + "l", + "r", + "a", + "k" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "collectionId": null + }, + { + "id": "translateSBML", + "name": "translateSBML", + "description": "title: translateSBML.bngl", + "tags": [ + "translatesbml", + "generate_network", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorial" + ], + "collectionId": null + }, + { + "id": "Tricky", + "name": "Tricky", + "description": "An example from a real application", + "tags": [ + "tricky", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "TrickyUS", + "name": "TrickyUS", + "description": "An example from a real application", + "tags": [ + "trickyus", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "trivial", + "name": "trivial", + "description": "A trivial model file for testing MCMC distributions.", + "tags": [ + "trivial", + "q", + "r", + "output", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "two-component-system", + "name": "two component system", + "description": "BioNetGen model: two component system", + "tags": [ + "two", + "component", + "system", + "kinase", + "regulator", + "target" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "univ_synth", + "name": "univ_synth", + "description": "example of universal synthesis", + "tags": [ + "validation", + "univ", + "synth", + "a", + "b", + "c", + "generate_network", + "simulate_ode" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "vegf-angiogenesis", + "name": "vegf angiogenesis", + "description": "VEGF-mediated signaling in angiogenesis.", + "tags": [ + "vegf", + "angiogenesis", + "vegfr2", + "vegfr1", + "erk", + "endothelial" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "vilar_2002", + "name": "Vilar 2002", + "description": "Genetic oscillator", + "tags": [ + "published", + "vilar", + "2002", + "dna", + "a", + "r" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "collectionId": null + }, + { + "id": "vilar_2002b", + "name": "Vilar 2002b", + "description": "Gene oscillator", + "tags": [ + "published", + "vilar", + "2002b", + "dna", + "a", + "r" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "collectionId": null + }, + { + "id": "vilar_2002c", + "name": "Vilar 2002c", + "description": "Gene oscillator", + "tags": [ + "published", + "vilar", + "2002c", + "dna", + "a", + "r" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "viral-sensing-innate-immunity", + "name": "viral sensing innate immunity", + "description": "BioNetGen model: viral sensing innate immunity", + "tags": [ + "viral", + "sensing", + "innate", + "immunity", + "viralrna", + "rigi", + "mavs", + "irf3", + "ifnb" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "visualize", + "name": "Visualize", + "description": "Visualization toy", + "tags": [ + "published", + "tutorial", + "native", + "visualize", + "x", + "a1", + "a2", + "b" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "wacky_alchemy_stone", + "name": "wacky alchemy stone", + "description": "Model: wacky_alchemy_stone.bngl", + "tags": [ + "wacky", + "alchemy", + "stone", + "lead", + "gold" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "collectionId": null + }, + { + "id": "wacky_black_hole", + "name": "wacky black hole", + "description": "Model: wacky_black_hole.bngl", + "tags": [ + "wacky", + "black", + "hole", + "m", + "bh", + "k_accrete", + "k_evap" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "wacky_bouncing_ball", + "name": "wacky bouncing ball", + "description": "Model: wacky_bouncing_ball.bngl", + "tags": [ + "wacky", + "bouncing", + "ball", + "height", + "velocity" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "wacky_traffic_jam_asep", + "name": "wacky traffic jam asep", + "description": "Model: wacky_traffic_jam_asep.bngl", + "tags": [ + "wacky", + "traffic", + "jam", + "asep", + "site", + "car", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "wacky_zombie_infection", + "name": "wacky zombie infection", + "description": "Model: wacky_zombie_infection.bngl", + "tags": [ + "wacky", + "zombie", + "infection", + "human" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "collectionId": null + }, + { + "id": "wnt", + "name": "Wnt Signaling", + "description": "Wnt signaling", + "tags": [ + "published", + "wnt", + "dsh", + "axc", + "frz", + "lrp5", + "bcat" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "wnt-beta-catenin-signaling", + "name": "wnt beta catenin signaling", + "description": "Wnt/Beta-Catenin signaling (Canonical pathway).", + "tags": [ + "wnt", + "beta", + "catenin", + "signaling", + "frizzled", + "dvl", + "dest_complex", + "betacatenin", + "tcf" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "wound-healing-pdgf-signaling", + "name": "wound healing pdgf signaling", + "description": "BioNetGen model: wound healing pdgf signaling", + "tags": [ + "wound", + "healing", + "pdgf", + "signaling", + "pdgfr", + "stat3", + "fibroblast" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Yang_2008", + "name": "Yang 2008", + "description": "TLBR yang 2008", + "tags": [ + "published", + "physics", + "yang", + "2008" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "Zhang_2021", + "name": "Zhang 2021", + "description": "CAR-T signaling", + "tags": [ + "published", + "zhang", + "2021", + "tie2", + "tie1", + "ang1_4", + "ang2_2", + "ang2_3", + "ang2_4", + "veptp", + "pten" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental" + ], + "collectionId": null + }, + { + "id": "Zhang_2023", + "name": "Zhang 2023", + "description": "VEGF signaling", + "tags": [ + "published", + "zhang", + "2023", + "vegf", + "vegfr2", + "vegfr1", + "nrp1", + "pi", + "plcgamma", + "dag", + "ip3_cyto" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental" + ], + "collectionId": null + } +] \ No newline at end of file diff --git a/manifest-slim.json b/manifest-slim.json new file mode 100644 index 0000000..cc4a485 --- /dev/null +++ b/manifest-slim.json @@ -0,0 +1,15294 @@ +[ + { + "id": "03_fcerig_fceri_gamma2", + "name": "03-fcerig", + "description": "Added molecule type definition block so that the", + "tags": [ + "immunology" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "04_egfrnf_egfr_nf", + "name": "example2_starting_point.bngl", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "f", + "lt_nm", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "molecules" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "06_degranulation_model_tofit", + "name": "of IgE receptor signaling", + "description": "A model of IgE receptor signaling", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "07_egg_egg", + "name": "07-egg", + "description": "BNGL model: egg", + "tags": [ + "a0", + "a1", + "a2", + "b1", + "b2", + "c0", + "c1", + "c2", + "d1", + "d2", + "period", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "10_egfr_egfr_ode", + "name": "example1.bngl", + "description": "Filename: example1.bngl", + "tags": [ + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "11_TLBR_tlbr", + "name": "11-TLBR", + "description": "BNGL model: tlbr", + "tags": [ + "alpha", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "12_TCR_tcr", + "name": "of T cell receptor signaling", + "description": "A model of T cell receptor signaling", + "tags": [ + "immunology" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "14_receptor_nf_receptor_nf", + "name": "of ligand/receptor binding and receptor phosphorylation.", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", + "tags": [ + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "15_igf1r_IGF1R_fit_all", + "name": "15-igf1r", + "description": "Author: William S. Hlavacek", + "tags": [ + "dilution", + "a1_permpers", + "a2_permpers", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "19_raf_constraint_RAFi", + "name": "19-raf-constraint", + "description": "BNGL model: RAFi", + "tags": [ + "k1", + "k2", + "k3", + "k5", + "kf1", + "kf2", + "kf3", + "kf4", + "kf5", + "kf6", + "rtot", + "ifree", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_CHO_EGFR_best-fit", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_CHO_EGFR_Epigen", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_CHO_EGFR_sensitivity", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_CHO_HA_EGFR_L858R", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_HeLa", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_HMEC", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "190127_MCF10A", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "20_raf_constraint4_RAFi", + "name": "20-raf-constraint4", + "description": "BNGL model: RAFi", + "tags": [ + "k1", + "k2", + "k3", + "k5", + "kf1", + "kf2", + "kf3", + "kf4", + "kf5", + "kf6", + "rtot", + "ifree", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "24_jnk_JNKmodel_180724_bnf", + "name": "24-jnk", + "description": "BNGL model: JNKmodel_180724_bnf", + "tags": [ + "scale_t", + "ani", + "k3_zakbyu1", + "k1_u1tozak", + "d3_zak", + "d1_zak", + "k3_mkk4byzak", + "k1_zaktomkk4", + "d3_mkk4", + "d1_mkk4", + "k3_mkk7byzak", + "k1_zaktomkk7", + "f3_mkk7byzak", + "d3_mkk7", + "d1_mkk7", + "k3_jnkbymkk4", + "k1_mkk4tojnk", + "k3_jnkbymkk7", + "k1_mkk7tojnk", + "f3_jnkbymkk7", + "d3_jnk", + "d1_jnk", + "k3_mkk7byjnk", + "k1_jnktomkk7", + "inh_jnk", + "d3_mkk7byjnkpt", + "d1_jnkpttomkk7", + "f1_zaktomkk7p", + "k1_zaktojnk", + "k3_mkk4byakt", + "k1_akttomkk4", + "k3_mkk7byakt", + "k1_akttomkk7", + "d3_mkk4byaktpt", + "d1_aktpttomkk4", + "d3_mkk7byaktpt", + "d1_aktpttomkk7", + "scale_ppmkk4", + "scale_ppmkk7", + "scale_ppjnk", + "pakt", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "26_tcr_sens_tcr_sens_tofit", + "name": "for the Manz/Groves 2011 data", + "description": "Modification of Mukhopadhyay/Dushek 2013 model for the Manz/Groves 2011 data", + "tags": [ + "immunology" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "31_elephant_elephant", + "name": "31-elephant", + "description": "BNGL model: elephant", + "tags": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10", + "a11", + "a12", + "a13", + "a14", + "a15", + "a16", + "a17", + "a18", + "a19", + "a20", + "b1", + "b2", + "b3", + "b4", + "b5", + "b6", + "b7", + "b8", + "b9", + "b10", + "b11", + "b12", + "b13", + "b14", + "b15", + "b16", + "b17", + "b18", + "b19", + "b20", + "c0", + "c1", + "c2", + "c3", + "c4", + "c5", + "c6", + "c7", + "c8", + "c9", + "c10", + "c11", + "c12", + "c13", + "c14", + "c15", + "c16", + "c17", + "c18", + "c19", + "c20", + "d1", + "d2", + "d3", + "d4", + "d5", + "d6", + "d7", + "d8", + "d9", + "d10", + "d11", + "d12", + "d13", + "d14", + "d15", + "d16", + "d17", + "d18", + "d19", + "d20", + "tmax", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "AB", + "name": "AB", + "description": "BioNetGen model: AB", + "tags": [ + "ab", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "ABC", + "name": "ABC", + "description": "BioNetGen model: ABC", + "tags": [ + "abc", + "a", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "ABC_scan", + "name": "ABC scan", + "description": "BioNetGen model: ABC scan", + "tags": [ + "abc", + "scan", + "a", + "generate_network", + "parameter_scan" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "ABC_ssa", + "name": "ABC ssa", + "description": "BioNetGen model: ABC ssa", + "tags": [ + "abc", + "ssa", + "a", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "ABp", + "name": "ABp", + "description": "title: ABp.bngl", + "tags": [ + "abp", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "ABp_approx", + "name": "ABp approx", + "description": "title: ABp.bngl", + "tags": [ + "abp", + "approx", + "km", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "actions_syntax", + "name": "actions syntax", + "description": "Original values used to generate parabola.exp", + "tags": [ + "actions", + "syntax", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "after_bunching", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "after_decoupling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "after_scaling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "akt-signaling", + "name": "akt signaling", + "description": "Signaling rates", + "tags": [ + "akt", + "signaling", + "growthfactor", + "rtk", + "pi3k", + "mtorc2", + "mtorc1", + "s6k" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Alabama", + "name": "Alabama", + "description": "reporting period (1 d)", + "tags": [ + "alabama", + "fdcs", + "counter", + "s", + "e1", + "e2", + "e3", + "e4", + "e5" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": null + }, + { + "id": "allosteric-activation", + "name": "allosteric activation", + "description": "Binding constants", + "tags": [ + "allosteric", + "activation", + "enzyme", + "substrate", + "activator", + "product" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "ampk-signaling", + "name": "ampk signaling", + "description": "AMPK signaling: The cellular energy sensor.", + "tags": [ + "ampk", + "signaling", + "amp", + "lkb1", + "ca", + "sik", + "crtc" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "An_2009", + "name": "An 2009", + "description": "TLR4 signaling", + "tags": [ + "published", + "immunology", + "an", + "2009", + "cd14", + "md2", + "tlr4", + "tram", + "trif", + "sarm", + "traf4", + "irak1" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "apoptosis-cascade", + "name": "apoptosis cascade", + "description": "Apoptosis cascade: Integrated extrinsic and intrinsic death signaling.", + "tags": [ + "apoptosis", + "cascade", + "deathligand", + "caspase8", + "bid", + "mito", + "apaf1", + "caspase3", + "xiap", + "smac" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "auto-activation-loop", + "name": "auto activation loop", + "description": "Auto-activation loop: A positive feedback circuit.", + "tags": [ + "auto", + "activation", + "loop", + "gene", + "mrna", + "protein", + "rbp" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "autophagy-regulation", + "name": "autophagy regulation", + "description": "Autophagy regulation: mTOR and AMPK competition on the ULK1 switch.", + "tags": [ + "autophagy", + "regulation", + "mtor", + "ampk", + "ulk1", + "lc3", + "p62" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "BAB", + "name": "BAB", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "tags": [ + "bab", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "BAB_coop", + "name": "BAB coop", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "tags": [ + "bab", + "coop", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "BAB_scan", + "name": "BAB scan", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "tags": [ + "bab", + "scan", + "a", + "b", + "generate_network", + "parameter_scan" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "Barua_2007", + "name": "Barua 2007", + "description": "Model from Haugh (2006)", + "tags": [ + "published", + "barua", + "2007", + "version", + "r", + "s" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "Barua_2009", + "name": "Barua 2009", + "description": "JAK2-SH2B signaling", + "tags": [ + "published", + "barua", + "2009", + "s", + "j" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "Barua_2013", + "name": "Barua 2013", + "description": "Beta-catenin destruction", + "tags": [ + "published", + "barua", + "2013", + "axin", + "gsk3b", + "apc", + "bcat", + "ck1a" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "BaruaBCR_2012", + "name": "Barua 2012", + "description": "BCR signaling", + "tags": [ + "published", + "immunology", + "baruabcr", + "2012", + "bcr", + "lyn", + "fyn", + "csk", + "pag", + "syk" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "BaruaFceRI_2012", + "name": "BaruaFceRI 2012", + "description": "FcεRI signaling", + "tags": [ + "published", + "immunology", + "baruafceri", + "2012", + "r_o", + "rdimer_o", + "l_o", + "t_o", + "l", + "fcr", + "lyn", + "syk" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "bcr-signaling", + "name": "bcr signaling", + "description": "BCR signaling: The B-cell antigen receptor cascade.", + "tags": [ + "bcr", + "signaling", + "antigen", + "syk", + "plcg2", + "cd22", + "shp1", + "calcium" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "before_bunching", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "before_decoupling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "before_scaling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "beta-adrenergic-response", + "name": "beta adrenergic response", + "description": "Beta-adrenergic signaling: GPCR pathway and desensitization.", + "tags": [ + "beta", + "adrenergic", + "response", + "epi", + "betar", + "gs", + "ac", + "arr", + "camp" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "birth-death", + "name": "Birth-Death", + "description": "Stochastic process", + "tags": [ + "published", + "tutorial", + "native", + "birth", + "death", + "a", + "generate_network", + "saveconcentrations", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "bistable-toggle-switch", + "name": "bistable toggle switch", + "description": "Genetic Toggle Switch: Mutual repression circuit.", + "tags": [ + "bistable", + "toggle", + "switch", + "proml", + "promr", + "tf_l", + "tf_r", + "ind_l", + "ind_r" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "BLBR", + "name": "BLBR", + "description": "title: BLBR.bngl", + "tags": [ + "blbr", + "setoption", + "r", + "l", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode", + "nf" + ] + }, + "gallery": [ + "tutorial" + ], + "collectionId": null + }, + { + "id": "Blinov_2006", + "name": "Blinov 2006", + "description": "Phosphotyrosine signaling", + "tags": [ + "published", + "blinov", + "2006", + "egf", + "egfr", + "shc", + "grb2", + "sos" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "collectionId": null + }, + { + "id": "Blinov_egfr", + "name": "Blinov egfr", + "description": "EGFR signaling model", + "tags": [ + "published", + "nfsim", + "blinov", + "egfr", + "egf", + "grb2", + "shc", + "simulate_nf" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "Blinov_ran", + "name": "Blinov ran", + "description": "Ran GTPase cycle", + "tags": [ + "published", + "nfsim", + "blinov", + "ran", + "c", + "rcc1", + "simulate_nf" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "cell-cycle" + ], + "collectionId": null + }, + { + "id": "blood-coagulation-thrombin", + "name": "blood coagulation thrombin", + "description": "Blood coagulation: Thrombin burst and feedback propagation.", + "tags": [ + "blood", + "coagulation", + "thrombin", + "tf", + "factorx", + "factorv", + "prothrombin", + "fibrinogen", + "at" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "bmp-signaling", + "name": "bmp signaling", + "description": "BMP-Smad signaling: Developmental gradient relay.", + "tags": [ + "bmp", + "signaling", + "noggin", + "receptor1", + "receptor2", + "smad1", + "smad4", + "smad6" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "bng_error", + "name": "bng error", + "description": "Original values used to generate parabola.exp", + "tags": [ + "bng", + "error", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "brusselator-oscillator", + "name": "brusselator oscillator", + "description": "The Brusselator: Auto-catalytic chemical oscillator.", + "tags": [ + "brusselator", + "oscillator", + "a", + "b", + "x", + "y" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "calcineurin-nfat-pathway", + "name": "calcineurin nfat pathway", + "description": "NFAT Signaling: Calcium-dependent nuclear translocation.", + "tags": [ + "calcineurin", + "nfat", + "pathway", + "ca", + "cam", + "can", + "rcan1" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "calcium-spike-signaling", + "name": "calcium spike signaling", + "description": "Calcium spikes: Oscillations driven by IP3R and CICR feedback.", + "tags": [ + "calcium", + "spike", + "signaling", + "plc", + "ip3", + "ca", + "stim1" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "CaMKII_holo", + "name": "Ordyan 2020: CaMKII holo", + "description": "CaMKII holo", + "tags": [ + "published", + "neuroscience", + "camkii", + "holo", + "ca", + "cam", + "ng", + "pp1", + "time_counter" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "CaOscillate_Func", + "name": "CaOscillate_Func", + "description": "Calcium oscillations (func)", + "tags": [ + "validation", + "caoscillate", + "func", + "null", + "ga", + "plc", + "ca" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "CaOscillate_Sat", + "name": "CaOscillate_Sat", + "description": "Calcium oscillations (sat)", + "tags": [ + "validation", + "caoscillate", + "sat", + "null", + "ga", + "plc", + "ca" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "caspase-activation-loop", + "name": "caspase activation loop", + "description": "Caspase activation loop: The executioner feedback system.", + "tags": [ + "caspase", + "activation", + "loop", + "deathligand", + "caspase8", + "caspase3", + "iap", + "flip" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "catalysis", + "name": "catalysis", + "description": "Catalysis in energy BNG", + "tags": [ + "validation", + "catalysis", + "version", + "setoption", + "s", + "kinase", + "pptase", + "atp", + "adp" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "cBNGL_simple", + "name": "cBNGL simple", + "description": "A simplified signal transduction model including the following processes:", + "tags": [ + "cbngl", + "simple", + "l", + "r", + "tf", + "dna", + "mrna", + "p" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "cd40-signaling", + "name": "cd40 signaling", + "description": "CD40 Signaling: B-cell activation and TRAF-mediated relay.", + "tags": [ + "cd40", + "signaling", + "cd40l", + "traf", + "ikk", + "nik", + "nfkb", + "relb" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "cell-cycle-checkpoint", + "name": "cell cycle checkpoint", + "description": "Cell cycle checkpoint: Mitotic entry switch (CDK1).", + "tags": [ + "cell", + "cycle", + "checkpoint", + "cyclin", + "cdk", + "cdc25", + "wee1", + "apc", + "p21" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "Chattaraj_2021", + "name": "Chattaraj 2021", + "description": "NFkB oscillations", + "tags": [ + "published", + "chattaraj", + "2021", + "nephrin", + "nck", + "nwasp", + "writexml" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience" + ], + "collectionId": null + }, + { + "id": "check_scaling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "checkpoint-kinase-signaling", + "name": "checkpoint kinase signaling", + "description": "DNA Checkpoint: ATM/ATR mediated damage sensing.", + "tags": [ + "checkpoint", + "kinase", + "signaling", + "dna", + "atm", + "atr", + "chk1", + "chk2", + "p53", + "cdc25" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "Cheemalavagu_JAK_STAT", + "name": "Cheemalavagu 2024", + "description": "JAK-STAT signaling", + "tags": [ + "published", + "literature", + "signaling", + "cheemalavagu", + "jak", + "stat", + "l1", + "il6r", + "gp130", + "l2", + "il10r1", + "il10r2", + "jak1", + "jak2" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "chemistry", + "name": "chemistry", + "description": "Basic chemical reactions", + "tags": [ + "published", + "tutorials", + "chemistry", + "a", + "b", + "c", + "d", + "e" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "collectionId": null + }, + { + "id": "chemotaxis-signal-transduction", + "name": "chemotaxis signal transduction", + "description": "Bacterial Chemotaxis: Adaptation through methylation.", + "tags": [ + "chemotaxis", + "signal", + "transduction", + "attr", + "mcp", + "chea", + "chey", + "cheb", + "motor" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Chylek_library", + "name": "Chylek library", + "description": "Created by BioNetGen 2.2.6", + "tags": [ + "chylek", + "library", + "kflatplcg", + "kfgrb2gab2", + "kflcp2plcg1", + "kd1", + "kd2", + "sink", + "pre", + "pag1" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "ChylekFceRI_2014", + "name": "Chylek 2014 (FceRI)", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "chylekfceri", + "2014", + "lig", + "rec", + "lyn", + "fyn", + "syk", + "pag1", + "csk", + "lat" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "ChylekTCR_2014", + "name": "Chylek 2014 (TCR)", + "description": "TCR signaling", + "tags": [ + "published", + "immunology", + "chylektcr", + "2014", + "lig1", + "lig2", + "lig3", + "tcr", + "cd28", + "lck", + "itk", + "zap70" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "circadian-oscillator", + "name": "circadian oscillator", + "description": "title: Vilar Circadian Oscillator Model", + "tags": [ + "circadian", + "oscillator", + "a", + "r", + "pa", + "pr", + "mrna_a", + "mrna_r" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "CircadianOscillator", + "name": "CircadianOscillator", + "description": "Circadian rhythm", + "tags": [ + "published", + "tutorial", + "native", + "circadianoscillator", + "a", + "r", + "pa", + "pr", + "mrna_a", + "mrna_r" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "cell-cycle", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "clock-bmal1-gene-circuit", + "name": "clock bmal1 gene circuit", + "description": "BMAL1-CLOCK: The master activator of the circadian circuit.", + "tags": [ + "clock", + "bmal1", + "gene", + "circuit", + "ror", + "reverb", + "dna" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "compartment_endocytosis", + "name": "compartment endocytosis", + "description": "Model: compartment_endocytosis.bngl", + "tags": [ + "compartment", + "endocytosis", + "l", + "r", + "t" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "compartment_membrane_bound", + "name": "compartment membrane bound", + "description": "Model: compartment_membrane_bound.bngl", + "tags": [ + "compartment", + "membrane", + "bound", + "p", + "lipid", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "compartment_nested_transport", + "name": "compartment nested transport", + "description": "Model: compartment_nested_transport.bngl", + "tags": [ + "compartment", + "nested", + "transport", + "s", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "compartment_nuclear_transport", + "name": "compartment nuclear transport", + "description": "Model: compartment_nuclear_transport.bngl", + "tags": [ + "compartment", + "nuclear", + "transport", + "tf", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "compartment_organelle_exchange", + "name": "compartment organelle exchange", + "description": "Model: compartment_organelle_exchange.bngl", + "tags": [ + "compartment", + "organelle", + "exchange", + "cargo", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "competitive-enzyme-inhibition", + "name": "competitive enzyme inhibition", + "description": "Competitive inhibition: Inhibitor (I) and Substrate (S) compete for the same", + "tags": [ + "competitive", + "enzyme", + "inhibition", + "substrate1", + "substrate2", + "inhibitor", + "product" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "complement-activation-cascade", + "name": "complement activation cascade", + "description": "Complement System: Pathogen opsonization and the Alternative Pathway.", + "tags": [ + "complement", + "activation", + "cascade", + "c3", + "fb", + "c5", + "mac", + "surf" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "ComplexDegradation", + "name": "ComplexDegradation", + "description": "Degradation model", + "tags": [ + "published", + "tutorial", + "native", + "complexdegradation", + "a", + "b", + "c", + "generate_network" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "contact-inhibition-hippo-yap", + "name": "contact inhibition hippo yap", + "description": "Hippo Pathway: Contact inhibition and YAP regulation.", + "tags": [ + "contact", + "inhibition", + "hippo", + "yap", + "mst", + "lats", + "tead" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "continue", + "name": "continue", + "description": "Test trajectory continuation", + "tags": [ + "validation", + "continue", + "a", + "b", + "c", + "trash" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "cooperative-binding", + "name": "cooperative binding", + "description": "Cooperative binding: The binding of the first ligand molecule increases", + "tags": [ + "cooperative", + "binding", + "receptor", + "ligand", + "competitor" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Creamer_2012", + "name": "Creamer 2012", + "description": "Initial values", + "tags": [ + "creamer", + "2012", + "egf", + "hrg", + "egfr", + "erbb2", + "erbb3", + "erbb4", + "p52shc1", + "grb2" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "cs_diffie_hellman", + "name": "cs diffie hellman", + "description": "Model: cs_diffie_hellman.bngl", + "tags": [ + "cs", + "diffie", + "hellman", + "agent", + "target", + "dshareda_dt", + "dsharedb_dt" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "cs_hash_function", + "name": "cs hash function", + "description": "Cryptographic Hash Function in BNGL", + "tags": [ + "cs", + "hash", + "function", + "b0", + "b1", + "b2", + "b3", + "h0", + "h1", + "h2", + "h3" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "cs_huffman", + "name": "cs huffman", + "description": "Model: cs_huffman.bngl", + "tags": [ + "cs", + "huffman", + "char", + "hnode", + "generate_network", + "simulate" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "cs_monte_carlo_pi", + "name": "cs monte carlo pi", + "description": "Model: cs_monte_carlo_pi.bngl", + "tags": [ + "cs", + "monte", + "carlo", + "pi", + "trial", + "pi_estimate", + "generate_network", + "simulate" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "cs_pagerank", + "name": "cs pagerank", + "description": "Model: cs_pagerank.bngl", + "tags": [ + "cs", + "pagerank", + "teleport", + "page" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "cs_pid_controller", + "name": "cs pid controller", + "description": "PID Controller in BNGL", + "tags": [ + "cs", + "pid", + "controller", + "sensor", + "accumulator", + "leakyerror", + "actuator", + "disturbance" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "cs_regex_nfa", + "name": "cs regex nfa", + "description": "Model: cs_regex_nfa.bngl", + "tags": [ + "cs", + "regex", + "nfa", + "state", + "char", + "generate_network", + "simulate", + "setparameter" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "Dallas", + "name": "Dallas", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "dallas", + "counter", + "fdcs", + "s", + "sv", + "e", + "a", + "i", + "v" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": null + }, + { + "id": "degranulation_model", + "name": "PyBNG: Degranulation model", + "description": "Degranulation model", + "tags": [ + "published", + "pybng", + "degranulation", + "model", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "Dembo_1978", + "name": "Dembo 1978", + "description": "BLBR dembo 1978", + "tags": [ + "published", + "physics", + "dembo", + "1978" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "dna-damage-repair", + "name": "dna damage repair", + "description": "DNA damage sensing and repair pathway (ATM-CHK2-p53 axis)", + "tags": [ + "dna", + "damage", + "repair", + "mrn", + "atm", + "chk2", + "repaircomplex" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "dna-methylation-dynamics", + "name": "dna methylation dynamics", + "description": "DNA Methylation: Maintenance and de novo dynamics.", + "tags": [ + "dna", + "methylation", + "dynamics", + "cpg", + "dnmt1", + "tet", + "v_maint", + "v_erase" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Dolan_2015", + "name": "Dolan 2015", + "description": "Insulin signaling", + "tags": [ + "published", + "literature", + "signaling", + "dolan", + "2015", + "time", + "t", + "p", + "e", + "ir", + "d", + "p53_mrna", + "p53" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism" + ], + "collectionId": null + }, + { + "id": "Dolan2015", + "name": "Dolan 2015", + "description": "Insulin signaling", + "tags": [ + "published", + "literature", + "signaling", + "dolan", + "2015", + "time", + "t", + "p", + "e", + "ir", + "d", + "p53_mrna", + "p53" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism" + ], + "collectionId": null + }, + { + "id": "dr5-apoptosis-signaling", + "name": "dr5 apoptosis signaling", + "description": "DR5 (TRAIL) Signaling: Extrinsic apoptosis and DISC formation.", + "tags": [ + "dr5", + "apoptosis", + "signaling", + "trail", + "fadd", + "caspase8", + "flip", + "death_signal" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "Dreisigmeyer_2008", + "name": "Dreisigmeyer 2008", + "description": "Lac operon", + "tags": [ + "published", + "gene-expression", + "dreisigmeyer", + "2008" + ], + "category": "gene-expression", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "gene-expression" + ], + "collectionId": null + }, + { + "id": "dual-site-phosphorylation", + "name": "dual site phosphorylation", + "description": "Dual-site phosphorylation: Requires two sequential modifications for activity.", + "tags": [ + "dual", + "site", + "phosphorylation", + "kinase", + "phosphatase", + "substrate" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Dushek_2011", + "name": "Dushek 2011", + "description": "TCR signaling", + "tags": [ + "published", + "dushek", + "2011", + "s" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "Dushek_2014", + "name": "Dushek 2014", + "description": "TCR signaling dynamics", + "tags": [ + "published", + "dushek", + "2014", + "e", + "f", + "b" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "e2f-rb-cell-cycle-switch", + "name": "e2f rb cell cycle switch", + "description": "E2F/Rb Switch: The G1/S transition gate.", + "tags": [ + "e2f", + "rb", + "cell", + "cycle", + "switch", + "mitogen", + "cycd", + "cyce", + "p27" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "eco_coevolution_host_parasite", + "name": "eco coevolution host parasite", + "description": "Model: eco_coevolution_host_parasite.bngl", + "tags": [ + "eco", + "coevolution", + "host", + "parasite" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "collectionId": null + }, + { + "id": "eco_food_web_chaos_3sp", + "name": "eco food web chaos 3sp", + "description": "Model: eco_food_web_chaos_3sp.bngl", + "tags": [ + "eco", + "food", + "web", + "chaos", + "3sp", + "r", + "c", + "p", + "k_eat_r", + "k_eat_c" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "collectionId": null + }, + { + "id": "eco_lotka_volterra_grid", + "name": "eco lotka volterra grid", + "description": "Model: eco_lotka_volterra_grid.bngl", + "tags": [ + "eco", + "lotka", + "volterra", + "grid", + "prey", + "pred" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "collectionId": null + }, + { + "id": "eco_mutualism_obligate", + "name": "eco mutualism obligate", + "description": "Model: eco_mutualism_obligate.bngl", + "tags": [ + "eco", + "mutualism", + "obligate", + "a", + "b" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "collectionId": null + }, + { + "id": "eco_rock_paper_scissors_spatial", + "name": "eco rock paper scissors spatial", + "description": "Model: eco_rock_paper_scissors_spatial.bngl", + "tags": [ + "eco", + "rock", + "paper", + "scissors", + "spatial", + "s", + "generate_network" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "collectionId": null + }, + { + "id": "egfr", + "name": "02-egfr", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "egfr", + "name": "17-egfr-ssa", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "egfr", + "name": "egfr", + "description": "Blinov et al. 2006. Biosystems, 83:136", + "tags": [ + "egfr", + "egf", + "grb2", + "shc", + "sos" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "egfr_ground", + "name": "02-egfr", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "egfr_ground", + "name": "17-egfr-ssa", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "egfr_ground", + "name": "egfr ground", + "description": "Blinov et al. 2006. Biosystems, 83:136", + "tags": [ + "egfr", + "ground", + "egf", + "grb2", + "shc", + "sos" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "egfr_net", + "name": "egfr_net", + "description": "check detailed balanced", + "tags": [ + "validation", + "egfr", + "net", + "egf", + "shc", + "grb2", + "sos" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "egfr_net_red", + "name": "egfr_net_red", + "description": "Reduced state-space version of EGFR_NET.BNGL with equivalent ODE dynamics", + "tags": [ + "validation", + "egfr", + "net", + "red", + "egf", + "egfr_1", + "egfr_2", + "egfr_3", + "grb2", + "shc", + "sos" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "egfr_nf", + "name": "egfr nf", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "egfr", + "nf", + "egf", + "clusters", + "pre1_dose", + "pre2_time" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "egfr_ode", + "name": "egfr ode", + "description": "Filename: example1.bngl", + "tags": [ + "egfr", + "ode", + "egf", + "pre1_dose", + "pre2_time", + "pre3_dose" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "egfr_ode", + "name": "PyBNG: EGFR ODE", + "description": "EGFR ODE", + "tags": [ + "published", + "pybng", + "egfr", + "ode", + "egf", + "pre1_dose", + "pre2_time", + "pre3_dose" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "egfr_path", + "name": "egfr_path", + "description": "The primary focus of the model developed by Kholodenko", + "tags": [ + "validation", + "egfr", + "path", + "generate_network", + "setconcentration", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "egfr_simple", + "name": "egfr simple", + "description": "This is a demo model of EGFR signaling.", + "tags": [ + "egfr", + "simple", + "egf", + "grb2", + "sos1" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "egfr-signaling-pathway", + "name": "egfr signaling pathway", + "description": "Enhanced EGFR Signaling: Combinatorial complexity with multiple phosphorylation sites.", + "tags": [ + "egfr", + "signaling", + "pathway", + "egf", + "grb2", + "shc" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "egg", + "name": "egg", + "description": "BioNetGen model: egg", + "tags": [ + "egg", + "x", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "eif2a-stress-response", + "name": "eif2a stress response", + "description": "Integrated Stress Response: eIF2alpha and the translational gate.", + "tags": [ + "eif2a", + "stress", + "response", + "eif2b", + "perk", + "gadd34" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "elephant_EFA", + "name": "Hlavacek2018Elephant", + "description": "BNGL model: elephant_EFA", + "tags": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10", + "a11", + "a12", + "a13", + "a14", + "a15", + "a16", + "a17", + "a18", + "a19", + "a20", + "b0", + "b1", + "b2", + "b3", + "b4", + "b5", + "b6", + "b7", + "b8", + "b9", + "b10", + "b11", + "b12", + "b13", + "b14", + "b15", + "b16", + "b17", + "b18", + "b19", + "b20", + "c0", + "c1", + "c2", + "c3", + "c4", + "c5", + "c6", + "c7", + "c8", + "c9", + "c10", + "c11", + "c12", + "c13", + "c14", + "c15", + "c16", + "c17", + "c18", + "c19", + "c20", + "d0", + "d1", + "d2", + "d3", + "d4", + "d5", + "d6", + "d7", + "d8", + "d9", + "d10", + "d11", + "d12", + "d13", + "d14", + "d15", + "d16", + "d17", + "d18", + "d19", + "d20", + "period", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "elephant_fit", + "name": "Hlavacek2018Elephant", + "description": "BNGL model: elephant_EFA", + "tags": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10", + "a11", + "a12", + "a13", + "a14", + "a15", + "a16", + "a17", + "a18", + "a19", + "a20", + "b0", + "b1", + "b2", + "b3", + "b4", + "b5", + "b6", + "b7", + "b8", + "b9", + "b10", + "b11", + "b12", + "b13", + "b14", + "b15", + "b16", + "b17", + "b18", + "b19", + "b20", + "c0", + "c1", + "c2", + "c3", + "c4", + "c5", + "c6", + "c7", + "c8", + "c9", + "c10", + "c11", + "c12", + "c13", + "c14", + "c15", + "c16", + "c17", + "c18", + "c19", + "c20", + "d0", + "d1", + "d2", + "d3", + "d4", + "d5", + "d6", + "d7", + "d8", + "d9", + "d10", + "d11", + "d12", + "d13", + "d14", + "d15", + "d16", + "d17", + "d18", + "d19", + "d20", + "period", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "endosomal-sorting-rab", + "name": "endosomal sorting rab", + "description": "Endosomal Sorting: Rab GTPase conversion and effector recruitment.", + "tags": [ + "endosomal", + "sorting", + "rab", + "rab5", + "rab7", + "effector", + "v_gef", + "v_gap_drive" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "energy_allostery_mwc", + "name": "energy allostery mwc", + "description": "Model: energy_allostery_mwc.bngl", + "tags": [ + "energy", + "allostery", + "mwc", + "p", + "l" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "energy_catalysis_mm", + "name": "energy catalysis mm", + "description": "Model: energy_catalysis_mm.bngl", + "tags": [ + "energy", + "catalysis", + "mm", + "e", + "s", + "p" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "energy_cooperativity_adh", + "name": "energy cooperativity adh", + "description": "Model: energy_cooperativity_adh.bngl", + "tags": [ + "energy", + "cooperativity", + "adh", + "r", + "l" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "energy_example1", + "name": "energy_example1", + "description": "Illustration of energy modeling approach w/ a simple protein scaffold model", + "tags": [ + "validation", + "energy", + "example1", + "version", + "setoption", + "s", + "a", + "b", + "c" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "energy_linear_chain", + "name": "energy linear chain", + "description": "Model: energy_linear_chain.bngl", + "tags": [ + "energy", + "linear", + "chain", + "m", + "generate_network" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "energy_transport_pump", + "name": "energy transport pump", + "description": "Model: energy_transport_pump.bngl", + "tags": [ + "energy", + "transport", + "pump", + "a", + "atp", + "adp", + "pi", + "t" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "ensemble_tofit", + "name": "translated into BNGL", + "description": "Ensemble model translated into BNGL", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "er-stress-response", + "name": "er stress response", + "description": "Rate Constants", + "tags": [ + "er", + "stress", + "response", + "unfoldedprotein", + "perk", + "eif2a", + "chaperone" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Erdem_2021", + "name": "Erdem 2021", + "description": "InsR/IGF1R signaling", + "tags": [ + "published", + "erdem", + "2021", + "igf1", + "ins", + "igf1r", + "insr", + "irs", + "sos", + "ras", + "raf" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism" + ], + "collectionId": null + }, + { + "id": "ERK_model", + "name": "ERK_model.bngl", + "description": "filename: ERK_model.bngl", + "tags": [ + "egf", + "erkpp_sos1_fb", + "erkpp_mek_fb", + "erkpp_raf1_fb", + "lambda", + "egfr_tot", + "ras_tot", + "sos_tot", + "rasgap_tot", + "raf_tot", + "mek_tot", + "erk_tot", + "ekar3_tot", + "erktr_tot", + "a1", + "d1", + "b1", + "u1a", + "u1b", + "b2a", + "u2a", + "b2b", + "u2b", + "k2a", + "k2b", + "b3", + "u3", + "k3", + "a2", + "d2", + "p1", + "q1", + "p2", + "q2", + "p3", + "q3", + "p4", + "q4", + "q5", + "p6", + "q6", + "a0_ekar3", + "d0_ekar3", + "a0_erktr", + "d0_erktr", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "erk-nuclear-translocation", + "name": "erk nuclear translocation", + "description": "ERK Translocation: Spatial signaling and transcriptional assembly.", + "tags": [ + "erk", + "nuclear", + "translocation", + "mek", + "elk1", + "dusp", + "transcription_signal" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "ErrNoFrees", + "name": "ErrNoFrees", + "description": "An example from a real application", + "tags": [ + "errnofrees", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "example1", + "name": "example1", + "description": "Filename: example1.bngl", + "tags": [ + "example1", + "egf", + "egfr", + "pre1_dose", + "pre2_time", + "pre3_dose" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "example1", + "name": "example1", + "description": "Example file for BNG2 tutorial.", + "tags": [ + "validation", + "example1", + "version", + "generate_network", + "simulate_ode" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "example1_BNFfiles_example1", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example1_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example2_BNFfiles_example2", + "name": "example2_starting_point.bngl", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "f", + "lt_nm", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example2_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example2_starting_point", + "name": "example2 starting point", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "example2", + "starting", + "point", + "egf", + "egfr", + "clusters", + "pre1_dose", + "pre2_time" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "example3_BNFfiles_example3", + "name": "example3 BNFfiles", + "description": "BNGL model: example3", + "tags": [ + "alpha", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example3_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example4_BNFfiles_example4", + "name": "in BNGL. For a description of BNGL, see:", + "description": "Supplementary File A in File S1", + "tags": [ + "other" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example4_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example5_BNFfiles_example5", + "name": "example5 BNFfiles", + "description": "A simple model", + "tags": [ + "ligand_ispresent", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example5_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example5_ground_truth", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example5_starting_point", + "name": "13-receptor", + "description": "A simple model", + "tags": [ + "ligand_ispresent", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example6_BNFfiles_example6", + "name": "example6 BNFfiles", + "description": "A simple model", + "tags": [ + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "example6_ground_truth", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "extra_CaMKII_Holo", + "name": "Ordyan 2020: extra CaMKII holo", + "description": "Extra CaMKII holo (supplement)", + "tags": [ + "published", + "neuroscience", + "extra", + "camkii", + "holo", + "t1", + "t2", + "t3", + "t4", + "t5", + "t6", + "t7", + "t8" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "collectionId": null + }, + { + "id": "Faeder_2003", + "name": "Faeder 2003", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "faeder", + "2003", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "fceri_fyn", + "name": "FceRI Fyn", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "fceri", + "fyn", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "fceri_gamma2", + "name": "fceri gamma2", + "description": "BioNetGen model: fceri gamma2", + "tags": [ + "fceri", + "gamma2", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "fceri_gamma2_ground_truth", + "name": "fceri gamma2 ground truth", + "description": "BioNetGen model: fceri gamma2 ground truth", + "tags": [ + "fceri", + "gamma2", + "ground", + "truth", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "fceri_ji", + "name": "Faeder 2003", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "faeder", + "2003", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "FceRI_ji", + "name": "FceRI ji", + "description": "title: FceRI_ji.bngl", + "tags": [ + "fceri", + "ji", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "fceri_ji_comp", + "name": "fceri_ji_comp", + "description": "Ligand-receptor binding", + "tags": [ + "validation", + "fceri", + "ji", + "comp", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "FceRI_viz", + "name": "FceRI Viz", + "description": "FcεRI (viz)", + "tags": [ + "published", + "tutorial", + "native", + "fceri", + "viz", + "fcr", + "ige", + "lat", + "lyn", + "syk", + "pb", + "pg", + "sykp" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "feature_functional_rates_volume", + "name": "feature functional rates volume", + "description": "Model: feature_functional_rates_volume.bngl", + "tags": [ + "feature", + "functional", + "rates", + "volume", + "a", + "b", + "c" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "feature_global_functions_scan", + "name": "feature global functions scan", + "description": "Model: feature_global_functions_scan.bngl", + "tags": [ + "feature", + "global", + "functions", + "scan", + "signal", + "response", + "stimulus" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "feature_local_functions_explicit", + "name": "feature local functions explicit", + "description": "Model: feature_local_functions_explicit.bngl", + "tags": [ + "feature", + "local", + "functions", + "explicit", + "s", + "p", + "e", + "mm_rate", + "ratelaw" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "feature_symmetry_factors_cyclic", + "name": "feature symmetry factors cyclic", + "description": "Model: feature_symmetry_factors_cyclic.bngl", + "tags": [ + "feature", + "symmetry", + "factors", + "cyclic", + "x", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "feature_synthesis_degradation_ss", + "name": "feature synthesis degradation ss", + "description": "Model: feature_synthesis_degradation_ss.bngl", + "tags": [ + "feature", + "synthesis", + "degradation", + "ss", + "m", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "fgf-signaling-pathway", + "name": "fgf signaling pathway", + "description": "FGF Signaling: FGFR dimerization and FRS2-Ras/PI3K relay.", + "tags": [ + "fgf", + "signaling", + "pathway", + "fgfr", + "frs2", + "spry", + "rasgef", + "internalized_rec" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "free_missing", + "name": "free missing", + "description": "Original values used to generate parabola.exp", + "tags": [ + "free", + "missing", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Gardner_2000", + "name": "Gardner 2000", + "description": "Genetic toggle switch", + "tags": [ + "published", + "synthetic-biology", + "gardner", + "2000" + ], + "category": "synthetic-biology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synthetic-biology" + ], + "collectionId": null + }, + { + "id": "gas6-axl-signaling", + "name": "gas6 axl signaling", + "description": "GAS6/AXL Signaling: AKT activation and SOCS feedback.", + "tags": [ + "gas6", + "axl", + "signaling", + "pi3k", + "akt", + "socs", + "survival_burst" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "gene-expression-toggle", + "name": "gene expression toggle", + "description": "Kinetic Parameters", + "tags": [ + "gene", + "expression", + "toggle", + "mrna", + "protein" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "genetic_bistability_energy", + "name": "genetic bistability energy", + "description": "Model: genetic_bistability_energy.bngl", + "tags": [ + "genetic", + "bistability", + "energy", + "genea", + "geneb", + "prota", + "protb" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "genetic_dna_replication_stochastic", + "name": "genetic dna replication stochastic", + "description": "Model: genetic_dna_replication_stochastic.bngl", + "tags": [ + "genetic", + "dna", + "replication", + "stochastic", + "pol", + "n", + "generate_network" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "genetic_goodwin_oscillator", + "name": "genetic goodwin oscillator", + "description": "Model: genetic_goodwin_oscillator.bngl", + "tags": [ + "genetic", + "goodwin", + "oscillator", + "gene", + "mrna", + "protein", + "repressor" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "genetic_translation_kinetics", + "name": "genetic translation kinetics", + "description": "Model: genetic_translation_kinetics.bngl", + "tags": [ + "genetic", + "translation", + "kinetics", + "mrna", + "rib", + "protein" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "genetic_turing_pattern_1d", + "name": "genetic turing pattern 1d", + "description": "Model: genetic_turing_pattern_1d.bngl", + "tags": [ + "genetic", + "turing", + "pattern", + "1d", + "a", + "b" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "GK", + "name": "GK", + "description": "title: GK.bngl", + "tags": [ + "gk", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "glioblastoma-egfrviii-signaling", + "name": "glioblastoma egfrviii signaling", + "description": "EGFRvIII in Glioblastoma: Constitutive AKT drive and escape from decay.", + "tags": [ + "glioblastoma", + "egfrviii", + "signaling", + "pi3k", + "akt", + "oncogenic_output", + "v_viii_act" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "glycolysis-branch-point", + "name": "glycolysis branch point", + "description": "BioNetGen model: glycolysis branch point", + "tags": [ + "glycolysis", + "branch", + "point", + "glucose", + "atp", + "biomass" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "gm_game_of_life", + "name": "gm game of life", + "description": "Model: gm_game_of_life.bngl", + "tags": [ + "gm", + "game", + "of", + "life", + "cell" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "gm_ray_marcher", + "name": "gm ray marcher", + "description": "Ray Marching Renderer in BNGL", + "tags": [ + "gm", + "ray", + "marcher", + "ray0", + "hit0", + "bright0", + "sdf0", + "sdf1", + "sdf2", + "sdf3", + "speed0" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Goldstein_1980", + "name": "Goldstein 1980", + "description": "BLBR heterogeneity", + "tags": [ + "published", + "physics", + "goldstein", + "1980" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "gpcr-desensitization-arrestin", + "name": "gpcr desensitization arrestin", + "description": "GPCR Desensitization: Arrestin-mediated spatial sequestration.", + "tags": [ + "gpcr", + "desensitization", + "arrestin", + "ligand", + "gprotein" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Harmon_2017", + "name": "Harmon 2017", + "description": "Antigen pulses", + "tags": [ + "published", + "immunology", + "harmon", + "2017" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "Hat_2016", + "name": "Hat 2016", + "description": "Nuclear transport", + "tags": [ + "published", + "hat", + "2016", + "dna_dsb", + "atm", + "siah1", + "hipk2", + "wip1", + "gene_wip1", + "mrna_wip1", + "p53" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "cell-cycle", + "multistage" + ], + "collectionId": null + }, + { + "id": "Haugh2b", + "name": "Haugh2b", + "description": "R(KD,Y1~U,Y2~U) 1.00", + "tags": [ + "validation", + "haugh2b", + "r", + "s1", + "s2", + "exclude_reactants", + "include_reactants" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "hedgehog-signaling-pathway", + "name": "hedgehog signaling pathway", + "description": "Hedgehog (Hh) Signaling: Ciliary translocation and Gli processing.", + "tags": [ + "hedgehog", + "signaling", + "pathway", + "hh", + "ptch", + "smo", + "gli", + "sufu" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "heise", + "name": "heise", + "description": "Validate state inheritance in a symmetric context", + "tags": [ + "validation", + "heise", + "a", + "b", + "generate_network", + "simulate_ode", + "setparameter" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "hematopoietic-growth-factor", + "name": "hematopoietic growth factor", + "description": "Kinetic Parameters", + "tags": [ + "hematopoietic", + "growth", + "factor", + "epo", + "epor", + "jak2", + "stat5" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "hif1a_degradation_loop", + "name": "hif1a degradation loop", + "description": "HIF-1alpha Oxygen Sensing: Hydroxylation and VHL-mediated decay.", + "tags": [ + "hif1a", + "degradation", + "loop", + "vhl", + "arnt", + "v_hydrox" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Hlavacek_1999", + "name": "Hlavacek 1999", + "description": "Steric effects", + "tags": [ + "published", + "physics", + "hlavacek", + "1999" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "Hlavacek_2001", + "name": "Hlavacek 2001", + "description": "Kinetic proofreading", + "tags": [ + "published", + "physics", + "hlavacek", + "2001" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "Hlavacek2018Egg_egg", + "name": "Hlavacek2018Egg", + "description": "End of permute change log", + "tags": [ + "a0__free", + "a1__free", + "a2__free", + "b1__free", + "b2__free", + "c0__free", + "c1__free", + "c2__free", + "d1__free", + "d2__free", + "a0", + "a1", + "a2", + "b1", + "b2", + "c0", + "c1", + "c2", + "d1", + "d2", + "period", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "Houston", + "name": "Houston", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "houston", + "counter", + "fdcs", + "s", + "sv", + "e", + "a", + "i", + "v" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": null + }, + { + "id": "hypoxia-response-signaling", + "name": "hypoxia response signaling", + "description": "Rate Constants", + "tags": [ + "hypoxia", + "response", + "signaling", + "oxygensensor", + "hif1", + "vegf" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "IGF1R_Model_receptor_activation_bnf", + "name": "IGF1R Model receptor activation bnf", + "description": "Author: William S. Hlavacek", + "tags": [ + "igf1r", + "model", + "receptor", + "activation", + "bnf", + "igf1" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "il1b-signaling", + "name": "il1b signaling", + "description": "IL-1beta Signaling: MyD88/IRAK assembly and NF-kB translocation.", + "tags": [ + "il1b", + "signaling", + "il1ri", + "myd88", + "irak", + "nfkb" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "il6-jak-stat-pathway", + "name": "il6 jak stat pathway", + "description": "IL-6 Signaling: gp130 hexamerization and pSTAT3 import.", + "tags": [ + "il6", + "jak", + "stat", + "pathway", + "gp130", + "stat3", + "socs" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "immune-synapse-formation", + "name": "immune synapse formation", + "description": "Kinetic Parameters", + "tags": [ + "immune", + "synapse", + "formation", + "tcr", + "pmhc", + "lck", + "zap70" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "inflammasome-activation", + "name": "inflammasome activation", + "description": "Rate Constants", + "tags": [ + "inflammasome", + "activation", + "sensor", + "asc", + "caspase1", + "il1b" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "innate_immunity", + "name": "Korwek 2023", + "description": "Immune response", + "tags": [ + "published", + "immunology", + "innate", + "immunity", + "polyic", + "rigi", + "mavs", + "pkr", + "oas3", + "rnasel", + "eif2a", + "rigi_mrna" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "inositol-phosphate-metabolism", + "name": "inositol phosphate metabolism", + "description": "Inositol Phosphate (IP) Metabolism: PLC signaling and branch points.", + "tags": [ + "inositol", + "phosphate", + "metabolism", + "pip2", + "ip3", + "ip4", + "calcium", + "agonist" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "insulin-glucose-homeostasis", + "name": "insulin glucose homeostasis", + "description": "Insulin-Glucose: Compartmentalized transport.", + "tags": [ + "insulin", + "glucose", + "homeostasis", + "ir", + "glut4", + "pancreas" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "interferon-signaling", + "name": "interferon signaling", + "description": "Rate Constants", + "tags": [ + "interferon", + "signaling", + "ifn", + "ifnar", + "tyk2", + "stat1" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "ire1a-xbp1-er-stress", + "name": "ire1a xbp1 er stress", + "description": "IRE1a/XBP1 ER Stress: Chaperone buffering and mRNA decay (RIDD).", + "tags": [ + "ire1a", + "xbp1", + "er", + "stress", + "ire1", + "bip", + "unfolded", + "ridd_target" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "issue_198_short", + "name": "issue_198_short", + "description": "No description available", + "tags": [ + "validation", + "issue", + "198", + "short", + "a", + "b", + "c", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "jak-stat-cytokine-signaling", + "name": "jak stat cytokine signaling", + "description": "Rate Constants", + "tags": [ + "jak", + "stat", + "cytokine", + "signaling", + "receptor" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "Jaruszewicz-Blonska_2023", + "name": "Jaruszewicz 2023", + "description": "T-cell discrimination", + "tags": [ + "published", + "immunology", + "jaruszewicz", + "blonska", + "2023", + "ikk", + "ikba", + "ikba_mrna", + "a20", + "nfkb" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "jnk-mapk-signaling", + "name": "jnk mapk signaling", + "description": "JNK MAPK Signaling: Scaffold-mediated activation and feedback.", + "tags": [ + "jnk", + "mapk", + "signaling", + "mkk7", + "jip1", + "v_dephos" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "jobs_ground", + "name": "30-jobs", + "description": "NFsim simulation of the job market", + "tags": [ + "other" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "jobs_tofit", + "name": "30-jobs", + "description": "NFsim simulation of the job market", + "tags": [ + "other" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "Jung_2017", + "name": "Jung 2017", + "description": "M1 receptor signaling", + "tags": [ + "published", + "jung", + "2017", + "m1r", + "oxo", + "arrestin", + "mek", + "erk", + "perk", + "oxo_ec", + "pp2a" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience" + ], + "collectionId": null + }, + { + "id": "Kesseler_2013", + "name": "Kesseler 2013", + "description": "G2/Mitosis transition", + "tags": [ + "published", + "kesseler", + "2013", + "mpf", + "cdc25", + "wee1", + "myt1", + "pin1", + "pp2a", + "prox", + "e33" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "collectionId": null + }, + { + "id": "Kiefhaber_emodel", + "name": "Kiefhaber_emodel", + "description": "Allow molar units to be used for bimolecular rate constants", + "tags": [ + "validation", + "kiefhaber", + "emodel", + "setoption", + "l", + "p", + "s", + "a" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "kir-channel-regulation", + "name": "kir channel regulation", + "description": "Kir Channel Regulation: PIP2 modulation and G-protein potentiation.", + "tags": [ + "kir", + "channel", + "regulation", + "pip2", + "gbg", + "v_opening", + "v_gbg_factor" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Kocieniewski_2012", + "name": "Kocieniewski 2012", + "description": "Actin dynamics", + "tags": [ + "published", + "kocieniewski", + "2012", + "map3k", + "map2k", + "mapk", + "scaff" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "Korwek_2023", + "name": "Korwek_2023", + "description": "This BioNetGen file features the article:", + "tags": [ + "validation", + "korwek", + "2023", + "polyic", + "rigi", + "mavs", + "pkr", + "oas3", + "rnasel", + "eif2a", + "rigi_mrna" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Kozer_2013", + "name": "Kozer 2013", + "description": "EGFR oligomerization", + "tags": [ + "published", + "kozer", + "2013", + "egf", + "egfr" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "Kozer_2014", + "name": "Kozer 2014", + "description": "Grb2-EGFR recruitment", + "tags": [ + "published", + "kozer", + "2014", + "egf", + "egfr", + "grb2" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "l-type-calcium-channel-dynamics", + "name": "l type calcium channel dynamics", + "description": "L-type Calcium Channel: Voltage gating and CDI (Calcium-dependent inactivation).", + "tags": [ + "l", + "type", + "calcium", + "channel", + "dynamics", + "ltcc", + "voltage", + "v_open", + "v_inact" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "lac-operon-regulation", + "name": "lac operon regulation", + "description": "Kinetic Parameters", + "tags": [ + "lac", + "operon", + "regulation", + "laci", + "promoter", + "mrna", + "betagal", + "lactose", + "allolactose" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "Lang_2024", + "name": "Lang 2024", + "description": "Cell cycle regulation", + "tags": [ + "published", + "lang", + "2024", + "e2f", + "rb1", + "ppp2r2b", + "ccnb_promoter", + "ccna", + "ccna_promoter", + "foxm1_promoter", + "ensa_arpp19" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "collectionId": null + }, + { + "id": "Ligon_2014", + "name": "Ligon 2014", + "description": "Lipoplex delivery", + "tags": [ + "published", + "nfsim", + "ligon", + "2014", + "lext", + "pit", + "lint" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "LilyIgE", + "name": "LilyIgE", + "description": "An example from a real application", + "tags": [ + "lilyige", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Lin_ERK_2019", + "name": "Lin 2019", + "description": "ERK signaling", + "tags": [ + "published", + "literature", + "signaling", + "lin", + "erk", + "2019", + "egfr", + "sos", + "ras", + "rasgap", + "raf", + "mek", + "ekar3" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "developmental" + ], + "collectionId": null + }, + { + "id": "Lin_Prion_2019", + "name": "Lin 2019", + "description": "Prion replication", + "tags": [ + "published", + "literature", + "prion", + "lin", + "2019", + "prp", + "scaledupspecies1", + "scaledupspecies2", + "scaledupspecies15", + "scaledupspecies30" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "neuroscience" + ], + "collectionId": null + }, + { + "id": "Lin_TCR_2019", + "name": "Lin 2019", + "description": "TCR signaling", + "tags": [ + "published", + "literature", + "immune", + "lin", + "tcr", + "2019", + "pmhc", + "lck", + "shp", + "zap", + "mek", + "erk" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "lipid-mediated-pip3-signaling", + "name": "lipid mediated pip3 signaling", + "description": "Kinetic Parameters", + "tags": [ + "lipid", + "mediated", + "pip3", + "signaling", + "pi3k", + "pip2", + "pten", + "pdk1" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Lisman", + "name": "Lisman", + "description": "title: auto.bngl", + "tags": [ + "lisman", + "k1", + "p", + "input", + "visualize", + "setparameter", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "Lisman_bifurcate", + "name": "Lisman bifurcate", + "description": "title: Lisman_bifurcate.bngl", + "tags": [ + "lisman", + "bifurcate", + "k1", + "p" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "localfunc", + "name": "localfunc", + "description": "Test local function expansion", + "tags": [ + "validation", + "localfunc", + "a", + "b", + "c", + "trash", + "f_synth" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "LR", + "name": "LR", + "description": "title: LR.bngl", + "tags": [ + "lr", + "l", + "r", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "LR_comp", + "name": "LR comp", + "description": "title: LR_comp.bngl", + "tags": [ + "lr", + "comp", + "l", + "r", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "LRR", + "name": "LRR", + "description": "title: LRR.bngl", + "tags": [ + "lrr", + "l", + "r" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "LRR_comp", + "name": "LRR comp", + "description": "title: LRR_comp.bngl", + "tags": [ + "lrr", + "comp", + "l", + "r", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "LV", + "name": "LV", + "description": "title: LV.bgl", + "tags": [ + "lv", + "s", + "w", + "generate_network", + "writesbml", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "LV_comp", + "name": "LV comp", + "description": "title: LV_comp.bgl", + "tags": [ + "lv", + "comp", + "k2", + "s", + "w" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "m1", + "name": "of a 3-step signaling cascade", + "description": "Toy model of a 3-step signaling cascade", + "tags": [ + "k1", + "k2", + "k3", + "ainit", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "m1_ground", + "name": "of a 3-step signaling cascade", + "description": "Toy model of a 3-step signaling cascade", + "tags": [ + "k1", + "k2", + "k3", + "ainit", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "machine_tofit", + "name": "translated into BNGL", + "description": "Ensemble model translated into BNGL", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "Macken_1982", + "name": "Macken 1982", + "description": "TLBR solution macken 1982", + "tags": [ + "published", + "physics", + "macken", + "1982" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "Mallela2021_Cities", + "name": "Mallela 2021 - COVID-19 City Models", + "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", + "tags": [ + "covid-19", + "epidemiology", + "parameter-estimation", + "pybionetgen" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": "Mallela2021_Cities" + }, + { + "id": "Mallela2021_States", + "name": "Mallela 2021 - COVID-19 State-Level Models", + "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", + "tags": [ + "covid-19", + "epidemiology", + "parameter-estimation", + "pybionetgen" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": "Mallela2021_States" + }, + { + "id": "Mallela2022_MSAs", + "name": "Mallela 2022 - COVID-19 MSA Models", + "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", + "tags": [ + "covid-19", + "epidemiology", + "parameter-estimation", + "pybionetgen" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": "Mallela2022_MSAs" + }, + { + "id": "mapk-dimers", + "name": "MAPK Dimers", + "description": "MAPK dimerization", + "tags": [ + "published", + "mapk", + "dimers", + "ste5", + "ste11", + "ste7", + "fus3" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "mapk-monomers", + "name": "MAPK Monomers", + "description": "MAPK cascade", + "tags": [ + "published", + "mapk", + "monomers", + "ste5", + "ste11", + "ste7", + "fus3" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "mapk-signaling-cascade", + "name": "mapk signaling cascade", + "description": "Rate Constants", + "tags": [ + "mapk", + "signaling", + "cascade", + "ligand", + "receptor", + "mapkkk", + "mapkk" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "Massole_2023", + "name": "Massole 2023", + "description": "Epo receptor signaling", + "tags": [ + "published", + "massole", + "2023" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental" + ], + "collectionId": null + }, + { + "id": "mCaMKII_Ca_Spike", + "name": "Ordyan 2020: mCaMKII Ca Spike", + "description": "mCaMKII Ca Spike model", + "tags": [ + "published", + "neuroscience", + "mcamkii", + "ca", + "spike", + "cam", + "ng", + "camkii", + "pp1", + "time_counter" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "collectionId": null + }, + { + "id": "McMillan_2021", + "name": "McMillan 2021", + "description": "TNF signaling", + "tags": [ + "published", + "nfsim", + "mcmillan", + "2021", + "r0_tot", + "t0_tot", + "r", + "t", + "generate_network", + "simulate_ode" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "Mertins_2023", + "name": "Mertins 2023", + "description": "DNA damage response", + "tags": [ + "published", + "mertins", + "2023", + "dnadsb", + "p53", + "mrna_bax", + "bax", + "bclxl", + "bad", + "fourteen_3_3", + "caspase" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "meta_formal_game_theory", + "name": "meta formal game theory", + "description": "Model: meta_formal_game_theory.bngl", + "tags": [ + "meta", + "formal", + "game", + "theory", + "hawk", + "dove", + "pop", + "payoffh", + "payoffd" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "meta_formal_molecular_clock", + "name": "meta formal molecular clock", + "description": "Model: meta_formal_molecular_clock.bngl", + "tags": [ + "meta", + "formal", + "molecular", + "clock", + "fasta", + "fastb", + "slowc", + "slowd" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "meta_formal_petri_net", + "name": "meta formal petri net", + "description": "Model: meta_formal_petri_net.bngl", + "tags": [ + "meta", + "formal", + "petri", + "net", + "p1", + "p2", + "p3", + "p4" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "michaelis-menten-kinetics", + "name": "michaelis menten kinetics", + "description": "Kinetic Constants", + "tags": [ + "michaelis", + "menten", + "kinetics", + "e", + "s", + "p", + "generate_network", + "simulate", + "writesbml" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "michment", + "name": "michment", + "description": "Michaelis Menten", + "tags": [ + "validation", + "michment", + "e", + "s", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "michment_cont", + "name": "michment_cont", + "description": "Michaelis Menten Continue", + "tags": [ + "validation", + "michment", + "cont", + "readfile", + "setconcentration", + "simulate_ode", + "addconcentration" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Miller2022_NavajoNation", + "name": "Miller 2022 - Navajo Nation Models", + "description": "COVID-19 epidemiological models fit to Navajo Nation regional data.", + "tags": [ + "covid-19", + "epidemiology", + "pybionetgen" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": "Miller2022_NavajoNation" + }, + { + "id": "Miller2025_MEK", + "name": "Miller 2025 - MEK Isoform Models", + "description": "MEK isoform variant models curated for PyBioNetGen.", + "tags": [ + "mek", + "isoforms", + "signaling", + "pybionetgen" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "collectionId": "Miller2025_MEK" + }, + { + "id": "Mitra2019_02_egfr_bnf1_InputFiles_egfr", + "name": "InputFiles", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "ml_gradient_descent", + "name": "ml gradient descent", + "description": "Gradient Descent Optimizer in BNGL", + "tags": [ + "ml", + "gradient", + "descent", + "posx", + "posy", + "velx", + "vely", + "loss" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "ml_hopfield", + "name": "ml hopfield", + "description": "Model: ml_hopfield.bngl", + "tags": [ + "ml", + "hopfield", + "neuron", + "net1", + "net2", + "net3", + "target1" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "ml_kmeans", + "name": "ml kmeans", + "description": "Model: ml_kmeans.bngl", + "tags": [ + "ml", + "kmeans", + "ax", + "ay", + "bx", + "by" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "ml_q_learning", + "name": "ml q learning", + "description": "Q-Learning Agent in BNGL", + "tags": [ + "ml", + "q", + "learning", + "pos", + "ql", + "qr", + "reward", + "action" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "ml_svm", + "name": "ml svm", + "description": "Model: ml_svm.bngl", + "tags": [ + "ml", + "svm", + "w1", + "w2", + "b", + "db_dt", + "dw1_dt" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "model", + "name": "model", + "description": "filename: model.bngl", + "tags": [ + "model", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "model", + "name": "model", + "description": "A model of IgE receptor signaling", + "tags": [ + "model", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "model_ground", + "name": "model_ground.bngl", + "description": "filename: model_ground.bngl", + "tags": [ + "x_tot__free", + "k_xoff__free", + "k_xon__free", + "kase__free", + "kdegx__free", + "kdegran__free", + "km_ship1__free", + "km_syk__free", + "km_x__free", + "koff__free", + "kp_ship1__free", + "kp_syk__free", + "kp_x__free", + "kpten__free", + "ksynth1__free", + "pase__free", + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "model_tofit", + "name": "model tofit", + "description": "A model of IgE receptor signaling", + "tags": [ + "model", + "tofit", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "Model_ZAP", + "name": "Model ZAP", + "description": "ZAP-70 recruitment", + "tags": [ + "published", + "immunology", + "nfsim", + "model", + "zap", + "kon", + "a", + "cbl", + "cd16", + "lck", + "ligand", + "zeta", + "dead" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "Motivating_example", + "name": "Motivating_example", + "description": "Signal Transduction with receptor internalization", + "tags": [ + "validation", + "motivating", + "example", + "l", + "r", + "tf", + "dna", + "mrna1", + "mrna2", + "p1", + "p2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Motivating_example_cBNGL", + "name": "Motivating_example_cBNGL", + "description": "Signal transduction with receptor internalization", + "tags": [ + "validation", + "motivating", + "example", + "cbngl", + "l", + "r", + "tf", + "dna", + "mrna1", + "mrna2", + "p1", + "p2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "motor", + "name": "motor", + "description": "Motor protein", + "tags": [ + "validation", + "motor", + "chey", + "kplus", + "kminus" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "mt_arithmetic_compiler", + "name": "mt arithmetic compiler", + "description": "Model: mt_arithmetic_compiler.bngl", + "tags": [ + "mt", + "arithmetic", + "compiler", + "node", + "target_add", + "target_mult" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "mt_bngl_interpreter", + "name": "mt bngl interpreter", + "description": "Model: mt_bngl_interpreter.bngl", + "tags": [ + "mt", + "bngl", + "interpreter", + "rule", + "species", + "exec_s1_s2", + "generate_network", + "simulate" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "mt_music_sequencer", + "name": "mt music sequencer", + "description": "Music Sequencer / Chord Synthesizer in BNGL", + "tags": [ + "mt", + "music", + "sequencer", + "v1s", + "v1c", + "v2s", + "v2c", + "v3s", + "v3c", + "mix", + "chordphase" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "mt_pascal_triangle", + "name": "mt pascal triangle", + "description": "Model: mt_pascal_triangle.bngl", + "tags": [ + "mt", + "pascal", + "triangle", + "node" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "mt_quine", + "name": "mt quine", + "description": "Model: mt_quine.bngl", + "tags": [ + "mt", + "quine", + "gene", + "protein" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "collectionId": null + }, + { + "id": "mtor-signaling", + "name": "mtor signaling", + "description": "mTOR Signaling Pathway", + "tags": [ + "mtor", + "signaling", + "rheb", + "mtorc1", + "s6k", + "ampk" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "mtorc2-signaling", + "name": "mtorc2 signaling", + "description": "mTORC2 signaling regulates cell survival and growth via AKT and SGK1.", + "tags": [ + "mtorc2", + "signaling", + "mtor", + "sin1", + "rictor", + "akt", + "sgk1", + "pip3" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Mukhopadhyay_2013", + "name": "Mukhopadhyay 2013", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "mukhopadhyay", + "2013", + "s", + "e", + "f", + "z" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "mwc", + "name": "mwc", + "description": "Monod-Wyman-Changeux model", + "tags": [ + "validation", + "mwc", + "setoption", + "h", + "ox", + "b" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "myogenic-differentiation", + "name": "myogenic differentiation", + "description": "Myogenic Differentiation", + "tags": [ + "myogenic", + "differentiation", + "myod", + "myog", + "mef2" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", + "name": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", + "description": "Runtime-only BNGL model migrated from public/models: Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", + "tags": [ + "myrtle", + "beach", + "conway", + "north", + "sc", + "nc" + ], + "category": "other", + "origin": "contributed", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "Nag_2009", + "name": "Nag 2009", + "description": "LAT-Grb2-SOS1 signaling", + "tags": [ + "published", + "nag", + "2009", + "lig", + "lyn", + "syk", + "rec", + "lat", + "grb", + "sos" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "negative-feedback-loop", + "name": "negative feedback loop", + "description": "Negative Feedback Loop", + "tags": [ + "negative", + "feedback", + "loop", + "gene", + "mrna", + "protein" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "neurotransmitter-release", + "name": "neurotransmitter release", + "description": "Neurotransmitter Release", + "tags": [ + "neurotransmitter", + "release", + "calcium", + "snare", + "vesicle", + "postsynaptic" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "nfkb", + "name": "nfkb", + "description": "NF-kB signaling pathway", + "tags": [ + "validation", + "nfkb", + "tnfr", + "ikkk", + "tnf", + "ikk", + "ikba", + "a20", + "competitor" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "nfkb_illustrating_protocols", + "name": "nfkb_illustrating_protocols", + "description": "NF-kB signaling pathway", + "tags": [ + "validation", + "nfkb", + "illustrating", + "protocols", + "tnfr", + "ikkk", + "tnf", + "ikk", + "ikba", + "a20", + "competitor" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "nfkb-feedback", + "name": "nfkb feedback", + "description": "TNFalpha-induced NF-kB signaling with IkappaB-alpha feedback.", + "tags": [ + "nfkb", + "feedback", + "ikb", + "ikk", + "a20" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "NFmodel", + "name": "NFmodel", + "description": "BioNetGen model: NFmodel", + "tags": [ + "nfmodel", + "ag", + "ab", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "nfsim_aggregation_gelation", + "name": "nfsim aggregation gelation", + "description": "Model: nfsim_aggregation_gelation.bngl", + "tags": [ + "nfsim", + "aggregation", + "gelation", + "m" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "nfsim_coarse_graining", + "name": "nfsim coarse graining", + "description": "Model: nfsim_coarse_graining.bngl", + "tags": [ + "nfsim", + "coarse", + "graining", + "droplet" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "nfsim_dynamic_compartments", + "name": "nfsim dynamic compartments", + "description": "Model: nfsim_dynamic_compartments.bngl", + "tags": [ + "nfsim", + "dynamic", + "compartments", + "cell", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "nfsim_hybrid_particle_field", + "name": "nfsim hybrid particle field", + "description": "Model: nfsim_hybrid_particle_field.bngl", + "tags": [ + "nfsim", + "hybrid", + "particle", + "field" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "nfsim_ring_closure_polymer", + "name": "nfsim ring closure polymer", + "description": "Model: nfsim_ring_closure_polymer.bngl", + "tags": [ + "nfsim", + "ring", + "closure", + "polymer", + "a", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "nn_xor", + "name": "nn xor", + "description": "Model: nn_xor.bngl", + "tags": [ + "nn", + "xor", + "input", + "hidden", + "output", + "target", + "weightih", + "weightho", + "dopamine" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "no_frees", + "name": "no frees", + "description": "Original values used to generate parabola.exp", + "tags": [ + "no", + "frees", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "no_generate_network", + "name": "no generate network", + "description": "Original values used to generate parabola.exp", + "tags": [ + "no", + "generate", + "network", + "counter", + "y", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "no_suffix", + "name": "no suffix", + "description": "Original values used to generate parabola.exp", + "tags": [ + "no", + "suffix", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "no-cgmp-signaling", + "name": "no cgmp signaling", + "description": "Nitric Oxide (NO) / cGMP signaling pathway.", + "tags": [ + "no", + "cgmp", + "signaling", + "sgc", + "pkg" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "collectionId": null + }, + { + "id": "Nosbisch_2022", + "name": "Nosbisch 2022", + "description": "RTK-PLCgamma1 signaling", + "tags": [ + "published", + "nosbisch", + "2022", + "rtk", + "plcgamma1", + "generate_network" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "notch", + "name": "Notch", + "description": "Notch signaling", + "tags": [ + "published", + "notch", + "icn", + "ofut1", + "fringe", + "furin", + "dsl", + "csl", + "maml" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "notch-delta-lateral-inhibition", + "name": "notch delta lateral inhibition", + "description": "Notch-Delta Lateral Inhibition", + "tags": [ + "notch", + "delta", + "lateral", + "inhibition", + "cellnotch", + "celldelta" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "NYC", + "name": "NYC", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "nyc", + "counter", + "fdcs", + "s", + "sv", + "e", + "a", + "i", + "v" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": null + }, + { + "id": "organelle_transport", + "name": "organelle transport", + "description": "title: organelle_transport.bngl", + "tags": [ + "organelle", + "transport", + "a", + "b", + "c", + "d", + "t1", + "at1", + "ct1", + "t2" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "organelle_transport_struct", + "name": "organelle transport struct", + "description": "title: organelle_transport_abcd.bngl", + "tags": [ + "organelle", + "transport", + "struct", + "a", + "b", + "t1", + "t2" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "oxidative-stress-response", + "name": "oxidative stress response", + "description": "Oxidative Stress Response (Keap1-Nrf2 Pathway)", + "tags": [ + "oxidative", + "stress", + "response", + "ros", + "keap1", + "nrf2", + "antioxidant" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "p38-mapk-signaling", + "name": "p38 mapk signaling", + "description": "p38 MAPK stress signaling cascade.", + "tags": [ + "p38", + "mapk", + "signaling", + "mkk3", + "mapkap2", + "v_thermal" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "p53-mdm2-oscillator", + "name": "p53 mdm2 oscillator", + "description": "BioNetGen model: p53 mdm2 oscillator", + "tags": [ + "p53", + "mdm2", + "oscillator", + "generate_network" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "parabola", + "name": "parabola", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "parabola", + "counter", + "par", + "line", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "parabola", + "name": "parabola", + "description": "Original values used to generate parabola.exp", + "tags": [ + "parabola", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "parabola", + "name": "parabola", + "description": "Original values used to generate parabola.exp", + "tags": [ + "parabola", + "counter", + "y", + "generate_network", + "simulate", + "resetconcentrations" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "parabola", + "name": "parabola", + "description": "Original values used to generate parabola.exp", + "tags": [ + "parabola", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "parabola", + "name": "parabola", + "description": "Original values used to generate parabola.exp", + "tags": [ + "parabola", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "parabola_ground", + "name": "parabola ground", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "parabola", + "ground", + "counter", + "par", + "line", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "parabola2", + "name": "parabola2", + "description": "A file for testing behavior with duplicate file names", + "tags": [ + "parabola2", + "counter", + "y", + "generate_network", + "simulate", + "resetconcentrations" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "ParamsEverywhere", + "name": "ParamsEverywhere", + "description": "An example from a real application", + "tags": [ + "paramseverywhere", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "parp1-mediated-dna-repair", + "name": "parp1 mediated dna repair", + "description": "PARP1-mediated DNA damage sensing and repair.", + "tags": [ + "parp1", + "mediated", + "dna", + "repair", + "par", + "nad", + "v_parylate" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "Pekalski_2013", + "name": "Pekalski 2013", + "description": "Spontaneous signaling", + "tags": [ + "published", + "pekalski", + "2013", + "tnfr", + "ikk", + "ikkk", + "ikba", + "ikba_mrna", + "a20", + "a20_mrna", + "nfkb" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "ph_lorenz_attractor", + "name": "ph lorenz attractor", + "description": "Lorenz Attractor in BNGL", + "tags": [ + "ph", + "lorenz", + "attractor", + "lx", + "ly", + "lz", + "x", + "y" + ], + "category": "physics", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "ph_nbody_gravity", + "name": "ph nbody gravity", + "description": "Model: ph_nbody_gravity.bngl", + "tags": [ + "ph", + "nbody", + "gravity", + "body", + "r2" + ], + "category": "physics", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "ph_schrodinger", + "name": "ph schrodinger", + "description": "Model: ph_schrodinger.bngl", + "tags": [ + "ph", + "schrodinger", + "psi" + ], + "category": "physics", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "ph_wave_equation", + "name": "ph wave equation", + "description": "Model: ph_wave_equation.bngl", + "tags": [ + "ph", + "wave", + "equation", + "node" + ], + "category": "physics", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "Phoenix", + "name": "Phoenix", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "phoenix", + "counter", + "fdcs", + "s", + "sv", + "e", + "a", + "i", + "v" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "collectionId": null + }, + { + "id": "phosphorelay-chain", + "name": "phosphorelay chain", + "description": "BioNetGen model: phosphorelay chain", + "tags": [ + "phosphorelay", + "chain", + "sensor", + "relay", + "output" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "platelet-activation", + "name": "platelet activation", + "description": "BioNetGen model: platelet activation", + "tags": [ + "platelet", + "activation", + "adp", + "p2y12", + "integrin", + "thromboxane" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "polymer", + "name": "polymer", + "description": "Polymerization model", + "tags": [ + "published", + "tutorials", + "nfsim", + "polymer", + "a", + "b", + "c", + "simulate_nf" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "tutorials" + ], + "collectionId": null + }, + { + "id": "polymer_draft", + "name": "polymer draft", + "description": "Polymerization (draft)", + "tags": [ + "published", + "tutorials", + "nfsim", + "polymer", + "draft", + "a", + "b", + "c", + "simulate_nf" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "tutorials" + ], + "collectionId": null + }, + { + "id": "polymer_fixed", + "name": "polymer_fixed", + "description": "Runtime-only BNGL model migrated from public/models: polymer_fixed", + "tags": [ + "polymer", + "fixed" + ], + "category": "other", + "origin": "contributed", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "polynomial", + "name": "polynomial", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "polynomial", + "counter", + "y1", + "y2", + "generate_network", + "simulate", + "setparameter", + "resetconcentrations" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "polynomial", + "name": "polynomial", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "polynomial", + "counter", + "y1", + "y2", + "generate_network", + "simulate", + "setparameter", + "resetconcentrations" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "polynomial", + "name": "polynomial", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "polynomial", + "counter", + "y1", + "y2", + "generate_network", + "simulate", + "setparameter", + "resetconcentrations" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "polynomial_ground", + "name": "polynomial ground", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "polynomial", + "ground", + "counter", + "y1", + "y2", + "generate_network", + "simulate", + "setparameter", + "resetconcentrations" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "Posner_1995", + "name": "Posner 1995", + "description": "BLBR rings", + "tags": [ + "published", + "physics", + "posner", + "1995" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "Posner_2004", + "name": "Posner 2004", + "description": "BLBR cooperativity", + "tags": [ + "published", + "physics", + "posner", + "2004" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "predator-prey-dynamics", + "name": "predator prey dynamics", + "description": "BioNetGen model: predator prey dynamics", + "tags": [ + "predator", + "prey", + "dynamics" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "prion_model", + "name": "ERK_model.bngl", + "description": "filename: ERK_model.bngl", + "tags": [ + "egf", + "erkpp_sos1_fb", + "erkpp_mek_fb", + "erkpp_raf1_fb", + "lambda", + "egfr_tot", + "ras_tot", + "sos_tot", + "rasgap_tot", + "raf_tot", + "mek_tot", + "erk_tot", + "ekar3_tot", + "erktr_tot", + "a1", + "d1", + "b1", + "u1a", + "u1b", + "b2a", + "u2a", + "b2b", + "u2b", + "k2a", + "k2b", + "b3", + "u3", + "k3", + "a2", + "d2", + "p1", + "q1", + "p2", + "q2", + "p3", + "q3", + "p4", + "q4", + "q5", + "p6", + "q6", + "a0_ekar3", + "d0_ekar3", + "a0_erktr", + "d0_erktr", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem_quant_model_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem16_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem16_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem32_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem32_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem4_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem4_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem64_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem64_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem8_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "problem8_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "process_actin_treadmilling", + "name": "process actin treadmilling", + "description": "Model: process_actin_treadmilling.bngl", + "tags": [ + "process", + "actin", + "treadmilling", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "process_autophagy_flux", + "name": "process autophagy flux", + "description": "Model: process_autophagy_flux.bngl", + "tags": [ + "process", + "autophagy", + "flux", + "phagophore", + "autophagosome", + "lysosome", + "autolysosome", + "cargo" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "process_cell_adhesion_strength", + "name": "process cell adhesion strength", + "description": "Model: process_cell_adhesion_strength.bngl", + "tags": [ + "process", + "cell", + "adhesion", + "strength", + "c1", + "c2", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "process_kinetic_proofreading_tcr", + "name": "process kinetic proofreading tcr", + "description": "Model: process_kinetic_proofreading_tcr.bngl", + "tags": [ + "process", + "kinetic", + "proofreading", + "tcr", + "l" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "process_quorum_sensing_switch", + "name": "process quorum sensing switch", + "description": "Model: process_quorum_sensing_switch.bngl", + "tags": [ + "process", + "quorum", + "sensing", + "switch", + "gene_ai", + "ai", + "r", + "gene_light" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "pt303", + "name": "pt303", + "description": "c = 0.20 /d t_1/2 = 3.5 d (inferred)", + "tags": [ + "pt303", + "counter", + "v", + "lnv", + "s", + "c", + "half_life", + "lnv_tangent" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "pt403", + "name": "pt403", + "description": "c = 0.23 /d t_1/2 = 3.0 d (inferred)", + "tags": [ + "pt403", + "counter", + "v", + "lnv", + "s", + "c", + "half_life", + "lnv_tangent" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "pt409", + "name": "pt409", + "description": "c = 0.39 /d t_1/2 = 1.8 d (inferred)", + "tags": [ + "pt409", + "counter", + "v", + "lnv", + "s", + "c", + "half_life", + "lnv_tangent" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "PyBNF_fitting_setup_190127_CHO_EGFR_forBNF", + "name": "PyBNF-fitting-setup", + "description": "BNGL model: 190127_CHO_EGFR_forBNF", + "tags": [ + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "quasi_equilibrium", + "name": "quasi equilibrium", + "description": "Quasi-equilibrium approximation", + "tags": [ + "published", + "toy models", + "quasi", + "equilibrium", + "a", + "b", + "c" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "quorum-sensing-circuit", + "name": "quorum sensing circuit", + "description": "BioNetGen model: quorum sensing circuit", + "tags": [ + "quorum", + "sensing", + "circuit", + "autoinducer", + "autoinducer_env", + "gene", + "protein" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "rab_mon1ccz1_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_mon1ccz1_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_rab5_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_rab5_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_rab7_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_rab7_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_wt", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab_wt", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "rab-gtpase-cycle", + "name": "rab gtpase cycle", + "description": "BioNetGen model: rab gtpase cycle", + "tags": [ + "rab", + "gtpase", + "cycle", + "gef", + "gap", + "effector" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "RAFi", + "name": "RAFi", + "description": "BioNetGen model: RAFi", + "tags": [ + "rafi", + "r", + "i", + "ybar", + "activity" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "RAFi_ground", + "name": "RAFi ground", + "description": "BioNetGen model: RAFi ground", + "tags": [ + "rafi", + "ground", + "r", + "i", + "ybar", + "activity" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "rankl-rank-signaling", + "name": "rankl rank signaling", + "description": "RANKL-RANK-OPG signaling in bone remodeling.", + "tags": [ + "rankl", + "rank", + "signaling", + "opg", + "nfat", + "traf6" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "ras-gef-gap-cycle", + "name": "ras gef gap cycle", + "description": "Ras-GEF-GAP cycle with explicit nucleotide exchange.", + "tags": [ + "ras", + "gef", + "gap", + "cycle", + "sos", + "rasgap", + "v_gef", + "v_gap" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "rec_dim", + "name": "rec_dim", + "description": "Ligand-receptor binding", + "tags": [ + "validation", + "rec", + "dim", + "lig", + "writemdl", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "rec_dim_comp", + "name": "rec_dim_comp", + "description": "name dimension volume contained_by", + "tags": [ + "validation", + "rec", + "dim", + "comp", + "kp1", + "kp2", + "lig", + "writemdl", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "receptor", + "name": "13-receptor", + "description": "A simple model", + "tags": [ + "ligand_ispresent", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "receptor", + "name": "receptor", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", + "tags": [ + "receptor", + "l", + "r", + "func" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "receptor_nf", + "name": "receptor nf", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", + "tags": [ + "receptor", + "nf", + "l", + "r" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "receptor_nf", + "name": "receptor nf", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", + "tags": [ + "receptor", + "nf", + "l", + "r" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Repressilator", + "name": "Repressilator", + "description": "Repressilator circuit", + "tags": [ + "published", + "tutorial", + "native", + "repressilator", + "gtetr", + "gci", + "glaci", + "mtetr", + "mci", + "mlaci", + "ptetr", + "pci" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "synbio", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "repressilator-oscillator", + "name": "repressilator oscillator", + "description": "BioNetGen model: repressilator oscillator", + "tags": [ + "repressilator", + "oscillator", + "genea", + "geneb", + "genec", + "mrna_a", + "mrna_b", + "mrna_c", + "proteina", + "proteinb" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "retinoic-acid-signaling", + "name": "retinoic acid signaling", + "description": "BioNetGen model: retinoic acid signaling", + "tags": [ + "retinoic", + "acid", + "signaling", + "ra", + "rarrxr", + "corepressor", + "targetgene" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "rho-gtpase-actin-cytoskeleton", + "name": "rho gtpase actin cytoskeleton", + "description": "RhoA-GTPase regulation of the actin cytoskeleton.", + "tags": [ + "rho", + "gtpase", + "actin", + "cytoskeleton", + "rhoa", + "rock", + "limk", + "cofilin" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Rule_based_egfr_compart", + "name": "Rule based egfr compart", + "description": "Compartmental EGFR model", + "tags": [ + "published", + "rule", + "based", + "egfr", + "compart", + "egf", + "grb2", + "shc", + "generate_network" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "collectionId": null + }, + { + "id": "Rule_based_egfr_tutorial", + "name": "Faeder 2009", + "description": "EGFR signaling", + "tags": [ + "published", + "rule", + "based", + "egfr", + "tutorial", + "egf", + "grb2", + "shc", + "generate_network" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "collectionId": null + }, + { + "id": "Rule_based_Ran_transport", + "name": "Rule based Ran transport", + "description": "Nuclear Ran transport", + "tags": [ + "published", + "rule", + "based", + "ran", + "transport", + "c", + "rcc1", + "generate_network" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "Rule_based_Ran_transport_draft", + "name": "Rule based Ran transport draft", + "description": "Ran transport (draft)", + "tags": [ + "published", + "rule", + "based", + "ran", + "transport", + "draft", + "c", + "rcc1", + "generate_network" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "Scaff-22_ground", + "name": "18-mapk", + "description": "For \"ground truth\" model, use median values such that hierarchy H1 occurs, as shown in Table 3.", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "Scaff-22_tofit", + "name": "18-mapk", + "description": "For \"ground truth\" model, use median values such that hierarchy H1 occurs, as shown in Table 3.", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "SHP2_base_model", + "name": "SHP2_base_model", + "description": "Base model of Shp2 regulation", + "tags": [ + "validation", + "shp2", + "base", + "model", + "r", + "s", + "exclude_reactants" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "shp2-phosphatase-regulation", + "name": "shp2 phosphatase regulation", + "description": "SHP2 phosphatase regulation via autoinhibition and SH2 binding.", + "tags": [ + "shp2", + "phosphatase", + "regulation", + "rtk", + "substrate", + "v_dephos" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "signal-amplification-cascade", + "name": "signal amplification cascade", + "description": "BioNetGen model: signal amplification cascade", + "tags": [ + "signal", + "amplification", + "cascade", + "ligand", + "receptor", + "effector", + "messenger" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "simple", + "name": "simple", + "description": "Simple binding model", + "tags": [ + "published", + "tutorials", + "simple", + "s", + "t", + "dnat", + "trash" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "collectionId": null + }, + { + "id": "Simple", + "name": "Simple", + "description": "An example from a real application", + "tags": [ + "simple", + "setoption", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Simple_AddActions", + "name": "Simple AddActions", + "description": "An example from a real application", + "tags": [ + "simple", + "addactions", + "setoption", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Simple_Answer", + "name": "Simple Answer", + "description": "An example from a real application", + "tags": [ + "simple", + "answer", + "setoption", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "Simple_GenOnly", + "name": "Simple GenOnly", + "description": "An example from a real application", + "tags": [ + "simple", + "genonly", + "setoption", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "simple_nf_seed", + "name": "simple nf seed", + "description": "BioNetGen model: simple nf seed", + "tags": [ + "simple", + "nf", + "seed", + "a", + "b", + "function1", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "simple_nfsim_test", + "name": "simple_nfsim_test", + "description": "Runtime-only BNGL model migrated from public/models: simple_nfsim_test", + "tags": [ + "simple", + "nfsim", + "test" + ], + "category": "other", + "origin": "contributed", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "Simple_nogen", + "name": "Simple nogen", + "description": "An example from a real application", + "tags": [ + "simple", + "nogen", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "simple_sbml_import", + "name": "simple_sbml_import", + "description": "SBML import test", + "tags": [ + "validation", + "simple", + "sbml", + "import", + "readfile", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "simple_system", + "name": "simple_system", + "description": "Simple binding system", + "tags": [ + "validation", + "simple", + "system", + "x", + "y" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "simple-dimerization", + "name": "simple dimerization", + "description": "BioNetGen model: simple dimerization", + "tags": [ + "simple", + "dimerization", + "a", + "b", + "generate_network", + "simulate" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "SIR", + "name": "SIR", + "description": "BioNetGen model: SIR", + "tags": [ + "sir", + "saveconcentrations", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "sir-epidemic-model", + "name": "sir epidemic model", + "description": "BioNetGen model: sir epidemic model", + "tags": [ + "sir", + "epidemic", + "model", + "human", + "generate_network", + "simulate" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "tutorials", + "test-models" + ], + "collectionId": null + }, + { + "id": "smad-tgf-beta-signaling", + "name": "smad tgf beta signaling", + "description": "BioNetGen model: smad tgf beta signaling", + "tags": [ + "smad", + "tgf", + "beta", + "signaling", + "tgfb", + "tgfbr", + "smad2", + "smad4" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "sonic-hedgehog-gradient", + "name": "sonic hedgehog gradient", + "description": "Sonic Hedgehog (Shh) morphogen gradient formation.", + "tags": [ + "sonic", + "hedgehog", + "gradient", + "shh", + "ptc1", + "v_prod" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "sp_fourier_synthesizer", + "name": "sp fourier synthesizer", + "description": "Fourier Series Synthesizer in BNGL", + "tags": [ + "sp", + "fourier", + "synthesizer", + "s1", + "s3", + "s5", + "s7", + "s9", + "wave", + "c1" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "sp_image_convolution", + "name": "sp image convolution", + "description": "Image Convolution Filter in BNGL", + "tags": [ + "sp", + "image", + "convolution", + "px", + "ex", + "sink" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "sp_kalman_filter", + "name": "sp kalman filter", + "description": "Kalman Filter in BNGL", + "tags": [ + "sp", + "kalman", + "filter", + "truex", + "obs", + "estx", + "estv", + "variance", + "innovation" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "collectionId": null + }, + { + "id": "stat3-mediated-transcription", + "name": "stat3 mediated transcription", + "description": "STAT3-mediated transcription and feedback.", + "tags": [ + "stat3", + "mediated", + "transcription", + "dna", + "pias3", + "mrna" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "stress-response-adaptation", + "name": "stress response adaptation", + "description": "BioNetGen model: stress response adaptation", + "tags": [ + "stress", + "response", + "adaptation", + "sensor", + "adapter", + "enzyme" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Suderman_2013", + "name": "Suderman 2013", + "description": "Ensemble model translated into BNGL", + "tags": [ + "suderman", + "2013", + "i", + "trash", + "pheromone", + "ste2", + "gpa1", + "ste4", + "sst2", + "ste20" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "synaptic-plasticity-ltp", + "name": "synaptic plasticity ltp", + "description": "Initial Concentrations", + "tags": [ + "synaptic", + "plasticity", + "ltp", + "glutamate", + "nmda", + "calcium", + "camkii", + "ampar", + "glusource" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "collectionId": null + }, + { + "id": "synbio_band_pass_filter", + "name": "synbio band pass filter", + "description": "Model: synbio_band_pass_filter.bngl", + "tags": [ + "synbio", + "band", + "pass", + "filter", + "i", + "a", + "r", + "out" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "collectionId": null + }, + { + "id": "synbio_counter_molecular", + "name": "synbio counter molecular", + "description": "Model: synbio_counter_molecular.bngl", + "tags": [ + "synbio", + "counter", + "molecular", + "state", + "input" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "collectionId": null + }, + { + "id": "synbio_edge_detector", + "name": "synbio edge detector", + "description": "Model: synbio_edge_detector.bngl", + "tags": [ + "synbio", + "edge", + "detector", + "x", + "y", + "z" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "collectionId": null + }, + { + "id": "synbio_logic_gates_enzymatic", + "name": "synbio logic gates enzymatic", + "description": "Model: synbio_logic_gates_enzymatic.bngl", + "tags": [ + "synbio", + "logic", + "gates", + "enzymatic", + "i1", + "i2", + "gateand", + "gateor", + "outand", + "outor" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "collectionId": null + }, + { + "id": "synbio_oscillator_synchronization", + "name": "synbio oscillator synchronization", + "description": "Model: synbio_oscillator_synchronization.bngl", + "tags": [ + "synbio", + "oscillator", + "synchronization", + "osc1", + "osc2", + "signal" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "collectionId": null + }, + { + "id": "t-cell-activation", + "name": "t cell activation", + "description": "BioNetGen model: t cell activation", + "tags": [ + "t", + "cell", + "activation", + "tcr", + "antigen", + "cytokine" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "tcr", + "name": "tcr", + "description": "A model of T cell receptor signaling", + "tags": [ + "tcr", + "lig1", + "lig2", + "lig3", + "cd28", + "lck", + "itk", + "zap70" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "collectionId": null + }, + { + "id": "TCR_model", + "name": "ERK_model.bngl", + "description": "filename: ERK_model.bngl", + "tags": [ + "egf", + "erkpp_sos1_fb", + "erkpp_mek_fb", + "erkpp_raf1_fb", + "lambda", + "egfr_tot", + "ras_tot", + "sos_tot", + "rasgap_tot", + "raf_tot", + "mek_tot", + "erk_tot", + "ekar3_tot", + "erktr_tot", + "a1", + "d1", + "b1", + "u1a", + "u1b", + "b2a", + "u2a", + "b2b", + "u2b", + "k2a", + "k2b", + "b3", + "u3", + "k3", + "a2", + "d2", + "p1", + "q1", + "p2", + "q2", + "p3", + "q3", + "p4", + "q4", + "q5", + "p6", + "q6", + "a0_ekar3", + "d0_ekar3", + "a0_erktr", + "d0_erktr", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "collectionId": null + }, + { + "id": "test_ANG_synthesis_simple", + "name": "test_ANG_synthesis_simple", + "description": "Synthesis network test", + "tags": [ + "validation", + "test", + "ang", + "synthesis", + "simple", + "a", + "b", + "c", + "source", + "source2", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_fixed", + "name": "test_fixed", + "description": "# actions ##", + "tags": [ + "validation", + "test", + "fixed", + "a", + "b", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_MM", + "name": "test_MM", + "description": "Kinetic constants", + "tags": [ + "validation", + "test", + "mm", + "e", + "s", + "p", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_mratio", + "name": "test_mratio", + "description": "Reaction ratio test", + "tags": [ + "validation", + "test", + "mratio", + "a", + "b", + "c_theory", + "c_upper", + "c_lower" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_network_gen", + "name": "test_network_gen", + "description": "fceri model with network generation", + "tags": [ + "validation", + "test", + "network", + "gen", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_sat", + "name": "test_sat", + "description": "Kinetic constants", + "tags": [ + "validation", + "test", + "sat", + "e", + "s", + "p", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_synthesis_cBNGL_simple", + "name": "test_synthesis_cBNGL_simple", + "description": "Compartmental synthesis", + "tags": [ + "validation", + "test", + "synthesis", + "cbngl", + "simple", + "a", + "a2", + "b", + "c", + "source", + "source2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_synthesis_complex", + "name": "test_synthesis_complex", + "description": "Complex synthesis test", + "tags": [ + "validation", + "test", + "synthesis", + "complex", + "a", + "b", + "c", + "receptor", + "source", + "source2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_synthesis_complex_0_cBNGL", + "name": "test_synthesis_complex_0_cBNGL", + "description": "volume-surface", + "tags": [ + "validation", + "test", + "synthesis", + "complex", + "0", + "cbngl", + "volume_molecule1", + "volume_molecule2", + "surface_molecule1", + "surface_molecule2", + "volume_molecule3", + "volume_molecule4", + "volume_receptor", + "surface_receptor" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_synthesis_complex_source_cBNGL", + "name": "test_synthesis_complex_source_cBNGL", + "description": "volume-surface", + "tags": [ + "validation", + "test", + "synthesis", + "complex", + "source", + "cbngl", + "volume_molecule1", + "volume_molecule2", + "surface_molecule1", + "surface_molecule2", + "volume_molecule3", + "volume_molecule4", + "volume_receptor", + "surface_receptor" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "test_synthesis_simple", + "name": "test_synthesis_simple", + "description": "Simple synthesis test", + "tags": [ + "validation", + "test", + "synthesis", + "simple", + "a", + "b", + "c", + "source", + "source2", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "tlbr", + "name": "tlbr", + "description": "A model of trivalent ligand, bivalent receptor", + "tags": [ + "tlbr", + "l", + "r", + "lambda", + "fl" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "tlbr", + "name": "TLBR Tutorial", + "description": "Ligand binding", + "tags": [ + "published", + "immunology", + "tlbr", + "l", + "r", + "simulate_rm" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "collectionId": null + }, + { + "id": "tlmr", + "name": "tlmr", + "description": "Trivalent ligand monovalent receptor", + "tags": [ + "validation", + "tlmr", + "l", + "r", + "generate_network", + "simulate_ode" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "tlr3-dsrna-sensing", + "name": "tlr3 dsrna sensing", + "description": "TLR3-mediated dsRNA sensing and TRIF pathway activation.", + "tags": [ + "tlr3", + "dsrna", + "sensing", + "trif", + "irf3", + "sarm" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "tnf-induced-apoptosis", + "name": "tnf induced apoptosis", + "description": "BioNetGen model: tnf induced apoptosis", + "tags": [ + "tnf", + "induced", + "apoptosis", + "tnfr", + "caspase8", + "bid", + "caspase3" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "collectionId": null + }, + { + "id": "toggle", + "name": "Toggle", + "description": "Toggle switch", + "tags": [ + "published", + "tutorial", + "native", + "toggle", + "x", + "y", + "generate_network", + "writemfile", + "setconcentration" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "synbio", + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "toy-jim", + "name": "toy-jim", + "description": "The model consists of a monovalent extracellular ligand,", + "tags": [ + "validation", + "toy", + "jim", + "l", + "r", + "a", + "k", + "null" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "toy1", + "name": "toy1", + "description": "Basic signaling toy", + "tags": [ + "published", + "tutorials", + "toy1", + "l", + "r", + "a", + "generate_network", + "writesbml", + "simulate_ode" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "collectionId": null + }, + { + "id": "toy2", + "name": "toy2", + "description": "Enzymatic reaction toy", + "tags": [ + "published", + "tutorials", + "toy2", + "l", + "r", + "a", + "k" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "collectionId": null + }, + { + "id": "translateSBML", + "name": "translateSBML", + "description": "title: translateSBML.bngl", + "tags": [ + "translatesbml", + "generate_network", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorial" + ], + "collectionId": null + }, + { + "id": "Tricky", + "name": "Tricky", + "description": "An example from a real application", + "tags": [ + "tricky", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "TrickyUS", + "name": "TrickyUS", + "description": "An example from a real application", + "tags": [ + "trickyus", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "trivial", + "name": "trivial", + "description": "A trivial model file for testing MCMC distributions.", + "tags": [ + "trivial", + "q", + "r", + "output", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "two-component-system", + "name": "two component system", + "description": "BioNetGen model: two component system", + "tags": [ + "two", + "component", + "system", + "kinase", + "regulator", + "target" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "univ_synth", + "name": "univ_synth", + "description": "example of universal synthesis", + "tags": [ + "validation", + "univ", + "synth", + "a", + "b", + "c", + "generate_network", + "simulate_ode" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "collectionId": null + }, + { + "id": "vegf-angiogenesis", + "name": "vegf angiogenesis", + "description": "VEGF-mediated signaling in angiogenesis.", + "tags": [ + "vegf", + "angiogenesis", + "vegfr2", + "vegfr1", + "erk", + "endothelial" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "collectionId": null + }, + { + "id": "vilar_2002", + "name": "Vilar 2002", + "description": "Genetic oscillator", + "tags": [ + "published", + "vilar", + "2002", + "dna", + "a", + "r" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "collectionId": null + }, + { + "id": "vilar_2002b", + "name": "Vilar 2002b", + "description": "Gene oscillator", + "tags": [ + "published", + "vilar", + "2002b", + "dna", + "a", + "r" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "collectionId": null + }, + { + "id": "vilar_2002c", + "name": "Vilar 2002c", + "description": "Gene oscillator", + "tags": [ + "published", + "vilar", + "2002c", + "dna", + "a", + "r" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "viral-sensing-innate-immunity", + "name": "viral sensing innate immunity", + "description": "BioNetGen model: viral sensing innate immunity", + "tags": [ + "viral", + "sensing", + "innate", + "immunity", + "viralrna", + "rigi", + "mavs", + "irf3", + "ifnb" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "collectionId": null + }, + { + "id": "visualize", + "name": "Visualize", + "description": "Visualization toy", + "tags": [ + "published", + "tutorial", + "native", + "visualize", + "x", + "a1", + "a2", + "b" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "collectionId": null + }, + { + "id": "wacky_alchemy_stone", + "name": "wacky alchemy stone", + "description": "Model: wacky_alchemy_stone.bngl", + "tags": [ + "wacky", + "alchemy", + "stone", + "lead", + "gold" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "collectionId": null + }, + { + "id": "wacky_black_hole", + "name": "wacky black hole", + "description": "Model: wacky_black_hole.bngl", + "tags": [ + "wacky", + "black", + "hole", + "m", + "bh", + "k_accrete", + "k_evap" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "wacky_bouncing_ball", + "name": "wacky bouncing ball", + "description": "Model: wacky_bouncing_ball.bngl", + "tags": [ + "wacky", + "bouncing", + "ball", + "height", + "velocity" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "wacky_traffic_jam_asep", + "name": "wacky traffic jam asep", + "description": "Model: wacky_traffic_jam_asep.bngl", + "tags": [ + "wacky", + "traffic", + "jam", + "asep", + "site", + "car", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "collectionId": null + }, + { + "id": "wacky_zombie_infection", + "name": "wacky zombie infection", + "description": "Model: wacky_zombie_infection.bngl", + "tags": [ + "wacky", + "zombie", + "infection", + "human" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "collectionId": null + }, + { + "id": "wnt", + "name": "Wnt Signaling", + "description": "Wnt signaling", + "tags": [ + "published", + "wnt", + "dsh", + "axc", + "frz", + "lrp5", + "bcat" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "collectionId": null + }, + { + "id": "wnt-beta-catenin-signaling", + "name": "wnt beta catenin signaling", + "description": "Wnt/Beta-Catenin signaling (Canonical pathway).", + "tags": [ + "wnt", + "beta", + "catenin", + "signaling", + "frizzled", + "dvl", + "dest_complex", + "betacatenin", + "tcf" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "collectionId": null + }, + { + "id": "wound-healing-pdgf-signaling", + "name": "wound healing pdgf signaling", + "description": "BioNetGen model: wound healing pdgf signaling", + "tags": [ + "wound", + "healing", + "pdgf", + "signaling", + "pdgfr", + "stat3", + "fibroblast" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "collectionId": null + }, + { + "id": "Yang_2008", + "name": "Yang 2008", + "description": "TLBR yang 2008", + "tags": [ + "published", + "physics", + "yang", + "2008" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "collectionId": null + }, + { + "id": "Zhang_2021", + "name": "Zhang 2021", + "description": "CAR-T signaling", + "tags": [ + "published", + "zhang", + "2021", + "tie2", + "tie1", + "ang1_4", + "ang2_2", + "ang2_3", + "ang2_4", + "veptp", + "pten" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental" + ], + "collectionId": null + }, + { + "id": "Zhang_2023", + "name": "Zhang 2023", + "description": "VEGF signaling", + "tags": [ + "published", + "zhang", + "2023", + "vegf", + "vegfr2", + "vegfr1", + "nrp1", + "pi", + "plcgamma", + "dag", + "ip3_cyto" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental" + ], + "collectionId": null + } +] \ No newline at end of file diff --git a/manifest.generated.json b/manifest.generated.json new file mode 100644 index 0000000..fe5e655 --- /dev/null +++ b/manifest.generated.json @@ -0,0 +1,18701 @@ +[ + { + "id": "03_fcerig_fceri_gamma2", + "name": "03-fcerig", + "description": "Added molecule type definition block so that the", + "tags": [ + "immunology" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/03-fcerig/fceri_gamma2.bngl", + "file": "fceri_gamma2.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "04_egfrnf_egfr_nf", + "name": "example2_starting_point.bngl", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "f", + "lt_nm", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "molecules" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/04-egfrnf/egfr_nf.bngl", + "file": "egfr_nf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "06_degranulation_model_tofit", + "name": "of IgE receptor signaling", + "description": "A model of IgE receptor signaling", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/06-degranulation/model_tofit.bngl", + "file": "model_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "07_egg_egg", + "name": "07-egg", + "description": "BNGL model: egg", + "tags": [ + "a0", + "a1", + "a2", + "b1", + "b2", + "c0", + "c1", + "c2", + "d1", + "d2", + "period", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/07-egg/egg.bngl", + "file": "egg.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "10_egfr_egfr_ode", + "name": "example1.bngl", + "description": "Filename: example1.bngl", + "tags": [ + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/10-egfr/egfr_ode.bngl", + "file": "egfr_ode.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "11_TLBR_tlbr", + "name": "11-TLBR", + "description": "BNGL model: tlbr", + "tags": [ + "alpha", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/11-TLBR/tlbr.bngl", + "file": "tlbr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "12_TCR_tcr", + "name": "of T cell receptor signaling", + "description": "A model of T cell receptor signaling", + "tags": [ + "immunology" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/12-TCR/tcr.bngl", + "file": "tcr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "14_receptor_nf_receptor_nf", + "name": "of ligand/receptor binding and receptor phosphorylation.", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", + "tags": [ + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/14-receptor-nf/receptor_nf.bngl", + "file": "receptor_nf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "15_igf1r_IGF1R_fit_all", + "name": "15-igf1r", + "description": "Author: William S. Hlavacek", + "tags": [ + "dilution", + "a1_permpers", + "a2_permpers", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/15-igf1r/IGF1R_fit_all.bngl", + "file": "IGF1R_fit_all.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "19_raf_constraint_RAFi", + "name": "19-raf-constraint", + "description": "BNGL model: RAFi", + "tags": [ + "k1", + "k2", + "k3", + "k5", + "kf1", + "kf2", + "kf3", + "kf4", + "kf5", + "kf6", + "rtot", + "ifree", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/19-raf-constraint/RAFi.bngl", + "file": "RAFi.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_CHO_EGFR_best-fit", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_CHO_EGFR_best-fit.bngl", + "file": "190127_CHO_EGFR_best-fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_CHO_EGFR_Epigen", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_CHO_EGFR_Epigen.bngl", + "file": "190127_CHO_EGFR_Epigen.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_CHO_EGFR_sensitivity", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_CHO_EGFR_sensitivity.bngl", + "file": "190127_CHO_EGFR_sensitivity.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_CHO_HA_EGFR_L858R", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_CHO_HA_EGFR_L858R.bngl", + "file": "190127_CHO_HA_EGFR_L858R.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_HeLa", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_HeLa.bngl", + "file": "190127_HeLa.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_HMEC", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_HMEC.bngl", + "file": "190127_HMEC.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_MCF10A", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_MCF10A.bngl", + "file": "190127_MCF10A.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "20_raf_constraint4_RAFi", + "name": "20-raf-constraint4", + "description": "BNGL model: RAFi", + "tags": [ + "k1", + "k2", + "k3", + "k5", + "kf1", + "kf2", + "kf3", + "kf4", + "kf5", + "kf6", + "rtot", + "ifree", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/20-raf-constraint4/RAFi.bngl", + "file": "RAFi.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "24_jnk_JNKmodel_180724_bnf", + "name": "24-jnk", + "description": "BNGL model: JNKmodel_180724_bnf", + "tags": [ + "scale_t", + "ani", + "k3_zakbyu1", + "k1_u1tozak", + "d3_zak", + "d1_zak", + "k3_mkk4byzak", + "k1_zaktomkk4", + "d3_mkk4", + "d1_mkk4", + "k3_mkk7byzak", + "k1_zaktomkk7", + "f3_mkk7byzak", + "d3_mkk7", + "d1_mkk7", + "k3_jnkbymkk4", + "k1_mkk4tojnk", + "k3_jnkbymkk7", + "k1_mkk7tojnk", + "f3_jnkbymkk7", + "d3_jnk", + "d1_jnk", + "k3_mkk7byjnk", + "k1_jnktomkk7", + "inh_jnk", + "d3_mkk7byjnkpt", + "d1_jnkpttomkk7", + "f1_zaktomkk7p", + "k1_zaktojnk", + "k3_mkk4byakt", + "k1_akttomkk4", + "k3_mkk7byakt", + "k1_akttomkk7", + "d3_mkk4byaktpt", + "d1_aktpttomkk4", + "d3_mkk7byaktpt", + "d1_aktpttomkk7", + "scale_ppmkk4", + "scale_ppmkk7", + "scale_ppjnk", + "pakt", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/24-jnk/JNKmodel_180724_bnf.bngl", + "file": "JNKmodel_180724_bnf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "26_tcr_sens_tcr_sens_tofit", + "name": "for the Manz/Groves 2011 data", + "description": "Modification of Mukhopadhyay/Dushek 2013 model for the Manz/Groves 2011 data", + "tags": [ + "immunology" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/26-tcr-sens/tcr_sens_tofit.bngl", + "file": "tcr_sens_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "31_elephant_elephant", + "name": "31-elephant", + "description": "BNGL model: elephant", + "tags": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10", + "a11", + "a12", + "a13", + "a14", + "a15", + "a16", + "a17", + "a18", + "a19", + "a20", + "b1", + "b2", + "b3", + "b4", + "b5", + "b6", + "b7", + "b8", + "b9", + "b10", + "b11", + "b12", + "b13", + "b14", + "b15", + "b16", + "b17", + "b18", + "b19", + "b20", + "c0", + "c1", + "c2", + "c3", + "c4", + "c5", + "c6", + "c7", + "c8", + "c9", + "c10", + "c11", + "c12", + "c13", + "c14", + "c15", + "c16", + "c17", + "c18", + "c19", + "c20", + "d1", + "d2", + "d3", + "d4", + "d5", + "d6", + "d7", + "d8", + "d9", + "d10", + "d11", + "d12", + "d13", + "d14", + "d15", + "d16", + "d17", + "d18", + "d19", + "d20", + "tmax", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/31-elephant/elephant.bngl", + "file": "elephant.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "AB", + "name": "AB", + "description": "BioNetGen model: AB", + "tags": [ + "ab", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/AB/AB.bngl", + "file": "AB.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "ABC", + "name": "ABC", + "description": "BioNetGen model: ABC", + "tags": [ + "abc", + "a", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABC/ABC.bngl", + "file": "ABC.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "ABC_scan", + "name": "ABC scan", + "description": "BioNetGen model: ABC scan", + "tags": [ + "abc", + "scan", + "a", + "generate_network", + "parameter_scan" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABCscan/ABC_scan.bngl", + "file": "ABC_scan.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ABC_ssa", + "name": "ABC ssa", + "description": "BioNetGen model: ABC ssa", + "tags": [ + "abc", + "ssa", + "a", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABCssa/ABC_ssa.bngl", + "file": "ABC_ssa.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ABp", + "name": "ABp", + "description": "title: ABp.bngl", + "tags": [ + "abp", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABp/ABp.bngl", + "file": "ABp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "ABp_approx", + "name": "ABp approx", + "description": "title: ABp.bngl", + "tags": [ + "abp", + "approx", + "km", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABpapprox/ABp_approx.bngl", + "file": "ABp_approx.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "actions_syntax", + "name": "actions syntax", + "description": "Original values used to generate parabola.exp", + "tags": [ + "actions", + "syntax", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/actionssyntax/actions_syntax.bngl", + "file": "actions_syntax.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "after_bunching", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/after_bunching.bngl", + "file": "after_bunching.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "after_decoupling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/after_decoupling.bngl", + "file": "after_decoupling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "after_scaling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/after_scaling.bngl", + "file": "after_scaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "akt-signaling", + "name": "akt signaling", + "description": "Signaling rates", + "tags": [ + "akt", + "signaling", + "growthfactor", + "rtk", + "pi3k", + "mtorc2", + "mtorc1", + "s6k" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/aktsignaling/akt-signaling.bngl", + "file": "akt-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Alabama", + "name": "Alabama", + "description": "reporting period (1 d)", + "tags": [ + "alabama", + "fdcs", + "counter", + "s", + "e1", + "e2", + "e3", + "e4", + "e5" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/Mallela2022/Alabama/Alabama.bngl", + "file": "Alabama.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "allosteric-activation", + "name": "allosteric activation", + "description": "Binding constants", + "tags": [ + "allosteric", + "activation", + "enzyme", + "substrate", + "activator", + "product" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/allostericactivation/allosteric-activation.bngl", + "file": "allosteric-activation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ampk-signaling", + "name": "ampk signaling", + "description": "AMPK signaling: The cellular energy sensor.", + "tags": [ + "ampk", + "signaling", + "amp", + "lkb1", + "ca", + "sik", + "crtc" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/ampksignaling/ampk-signaling.bngl", + "file": "ampk-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "An_2009", + "name": "An 2009", + "description": "TLR4 signaling", + "tags": [ + "published", + "immunology", + "an", + "2009", + "cd14", + "md2", + "tlr4", + "tram", + "trif", + "sarm", + "traf4", + "irak1" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/An2009/An_2009.bngl", + "file": "An_2009.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "apoptosis-cascade", + "name": "apoptosis cascade", + "description": "Apoptosis cascade: Integrated extrinsic and intrinsic death signaling.", + "tags": [ + "apoptosis", + "cascade", + "deathligand", + "caspase8", + "bid", + "mito", + "apaf1", + "caspase3", + "xiap", + "smac" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/apoptosiscascade/apoptosis-cascade.bngl", + "file": "apoptosis-cascade.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "auto-activation-loop", + "name": "auto activation loop", + "description": "Auto-activation loop: A positive feedback circuit.", + "tags": [ + "auto", + "activation", + "loop", + "gene", + "mrna", + "protein", + "rbp" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/autoactivationloop/auto-activation-loop.bngl", + "file": "auto-activation-loop.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "autophagy-regulation", + "name": "autophagy regulation", + "description": "Autophagy regulation: mTOR and AMPK competition on the ULK1 switch.", + "tags": [ + "autophagy", + "regulation", + "mtor", + "ampk", + "ulk1", + "lc3", + "p62" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/autophagyregulation/autophagy-regulation.bngl", + "file": "autophagy-regulation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "BAB", + "name": "BAB", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "tags": [ + "bab", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/BAB/BAB.bngl", + "file": "BAB.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "BAB_coop", + "name": "BAB coop", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "tags": [ + "bab", + "coop", + "a", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/BABcoop/BAB_coop.bngl", + "file": "BAB_coop.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "BAB_scan", + "name": "BAB scan", + "description": "Simple binding model with a bivalent A molecule that has two identical sites", + "tags": [ + "bab", + "scan", + "a", + "b", + "generate_network", + "parameter_scan" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/BABscan/BAB_scan.bngl", + "file": "BAB_scan.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Barua_2007", + "name": "Barua 2007", + "description": "Model from Haugh (2006)", + "tags": [ + "published", + "barua", + "2007", + "version", + "r", + "s" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Barua2007/Barua_2007.bngl", + "file": "Barua_2007.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Barua_2009", + "name": "Barua 2009", + "description": "JAK2-SH2B signaling", + "tags": [ + "published", + "barua", + "2009", + "s", + "j" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Barua2009/Barua_2009.bngl", + "file": "Barua_2009.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Barua_2013", + "name": "Barua 2013", + "description": "Beta-catenin destruction", + "tags": [ + "published", + "barua", + "2013", + "axin", + "gsk3b", + "apc", + "bcat", + "ck1a" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Barua2013/Barua_2013.bngl", + "file": "Barua_2013.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "BaruaBCR_2012", + "name": "Barua 2012", + "description": "BCR signaling", + "tags": [ + "published", + "immunology", + "baruabcr", + "2012", + "bcr", + "lyn", + "fyn", + "csk", + "pag", + "syk" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/BaruaBCR2012/BaruaBCR_2012.bngl", + "file": "BaruaBCR_2012.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "BaruaFceRI_2012", + "name": "BaruaFceRI 2012", + "description": "FcεRI signaling", + "tags": [ + "published", + "immunology", + "baruafceri", + "2012", + "r_o", + "rdimer_o", + "l_o", + "t_o", + "l", + "fcr", + "lyn", + "syk" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/BaruaFceRI2012/BaruaFceRI_2012.bngl", + "file": "BaruaFceRI_2012.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "bcr-signaling", + "name": "bcr signaling", + "description": "BCR signaling: The B-cell antigen receptor cascade.", + "tags": [ + "bcr", + "signaling", + "antigen", + "syk", + "plcg2", + "cd22", + "shp1", + "calcium" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/bcrsignaling/bcr-signaling.bngl", + "file": "bcr-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "before_bunching", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/before_bunching.bngl", + "file": "before_bunching.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "before_decoupling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/before_decoupling.bngl", + "file": "before_decoupling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "before_scaling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/before_scaling.bngl", + "file": "before_scaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "beta-adrenergic-response", + "name": "beta adrenergic response", + "description": "Beta-adrenergic signaling: GPCR pathway and desensitization.", + "tags": [ + "beta", + "adrenergic", + "response", + "epi", + "betar", + "gs", + "ac", + "arr", + "camp" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/betaadrenergicresponse/beta-adrenergic-response.bngl", + "file": "beta-adrenergic-response.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "birth-death", + "name": "Birth-Death", + "description": "Stochastic process", + "tags": [ + "published", + "tutorial", + "native", + "birth", + "death", + "a", + "generate_network", + "saveconcentrations", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/birthdeath/birth-death.bngl", + "file": "birth-death.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "bistable-toggle-switch", + "name": "bistable toggle switch", + "description": "Genetic Toggle Switch: Mutual repression circuit.", + "tags": [ + "bistable", + "toggle", + "switch", + "proml", + "promr", + "tf_l", + "tf_r", + "ind_l", + "ind_r" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/bistabletoggleswitch/bistable-toggle-switch.bngl", + "file": "bistable-toggle-switch.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "BLBR", + "name": "BLBR", + "description": "title: BLBR.bngl", + "tags": [ + "blbr", + "setoption", + "r", + "l", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode", + "nf" + ] + }, + "gallery": [ + "tutorial" + ], + "path": "Tutorials/NativeTutorials/BLBR/BLBR.bngl", + "file": "BLBR.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Blinov_2006", + "name": "Blinov 2006", + "description": "Phosphotyrosine signaling", + "tags": [ + "published", + "blinov", + "2006", + "egf", + "egfr", + "shc", + "grb2", + "sos" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "path": "Published/Blinov2006/Blinov_2006.bngl", + "file": "Blinov_2006.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Blinov_egfr", + "name": "Blinov egfr", + "description": "EGFR signaling model", + "tags": [ + "published", + "nfsim", + "blinov", + "egfr", + "egf", + "grb2", + "shc", + "simulate_nf" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Blinovegfr/Blinov_egfr.bngl", + "file": "Blinov_egfr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Blinov_ran", + "name": "Blinov ran", + "description": "Ran GTPase cycle", + "tags": [ + "published", + "nfsim", + "blinov", + "ran", + "c", + "rcc1", + "simulate_nf" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "cell-cycle" + ], + "path": "Published/Blinovran/Blinov_ran.bngl", + "file": "Blinov_ran.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "blood-coagulation-thrombin", + "name": "blood coagulation thrombin", + "description": "Blood coagulation: Thrombin burst and feedback propagation.", + "tags": [ + "blood", + "coagulation", + "thrombin", + "tf", + "factorx", + "factorv", + "prothrombin", + "fibrinogen", + "at" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin.bngl", + "file": "blood-coagulation-thrombin.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "bmp-signaling", + "name": "bmp signaling", + "description": "BMP-Smad signaling: Developmental gradient relay.", + "tags": [ + "bmp", + "signaling", + "noggin", + "receptor1", + "receptor2", + "smad1", + "smad4", + "smad6" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/bmpsignaling/bmp-signaling.bngl", + "file": "bmp-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "bng_error", + "name": "bng error", + "description": "Original values used to generate parabola.exp", + "tags": [ + "bng", + "error", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/bngerror/bng_error.bngl", + "file": "bng_error.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "brusselator-oscillator", + "name": "brusselator oscillator", + "description": "The Brusselator: Auto-catalytic chemical oscillator.", + "tags": [ + "brusselator", + "oscillator", + "a", + "b", + "x", + "y" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "path": "Examples/biology/brusselatoroscillator/brusselator-oscillator.bngl", + "file": "brusselator-oscillator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "calcineurin-nfat-pathway", + "name": "calcineurin nfat pathway", + "description": "NFAT Signaling: Calcium-dependent nuclear translocation.", + "tags": [ + "calcineurin", + "nfat", + "pathway", + "ca", + "cam", + "can", + "rcan1" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway.bngl", + "file": "calcineurin-nfat-pathway.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "calcium-spike-signaling", + "name": "calcium spike signaling", + "description": "Calcium spikes: Oscillations driven by IP3R and CICR feedback.", + "tags": [ + "calcium", + "spike", + "signaling", + "plc", + "ip3", + "ca", + "stim1" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/calciumspikesignaling/calcium-spike-signaling.bngl", + "file": "calcium-spike-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "CaMKII_holo", + "name": "Ordyan 2020: CaMKII holo", + "description": "CaMKII holo", + "tags": [ + "published", + "neuroscience", + "camkii", + "holo", + "ca", + "cam", + "ng", + "pp1", + "time_counter" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Ordyan2020/CaMKIIholo/CaMKII_holo.bngl", + "file": "CaMKII_holo.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "CaOscillate_Func", + "name": "CaOscillate_Func", + "description": "Calcium oscillations (func)", + "tags": [ + "validation", + "caoscillate", + "func", + "null", + "ga", + "plc", + "ca" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "path": "Tutorials/CaOscillateFunc/CaOscillate_Func.bngl", + "file": "CaOscillate_Func.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "CaOscillate_Sat", + "name": "CaOscillate_Sat", + "description": "Calcium oscillations (sat)", + "tags": [ + "validation", + "caoscillate", + "sat", + "null", + "ga", + "plc", + "ca" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/CaOscillateSat/CaOscillate_Sat.bngl", + "file": "CaOscillate_Sat.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "caspase-activation-loop", + "name": "caspase activation loop", + "description": "Caspase activation loop: The executioner feedback system.", + "tags": [ + "caspase", + "activation", + "loop", + "deathligand", + "caspase8", + "caspase3", + "iap", + "flip" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/caspaseactivationloop/caspase-activation-loop.bngl", + "file": "caspase-activation-loop.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "catalysis", + "name": "catalysis", + "description": "Catalysis in energy BNG", + "tags": [ + "validation", + "catalysis", + "version", + "setoption", + "s", + "kinase", + "pptase", + "atp", + "adp" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/catalysis/catalysis.bngl", + "file": "catalysis.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "cBNGL_simple", + "name": "cBNGL simple", + "description": "A simplified signal transduction model including the following processes:", + "tags": [ + "cbngl", + "simple", + "l", + "r", + "tf", + "dna", + "mrna", + "p" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/cBNGLsimple/cBNGL_simple.bngl", + "file": "cBNGL_simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "cd40-signaling", + "name": "cd40 signaling", + "description": "CD40 Signaling: B-cell activation and TRAF-mediated relay.", + "tags": [ + "cd40", + "signaling", + "cd40l", + "traf", + "ikk", + "nik", + "nfkb", + "relb" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/cd40signaling/cd40-signaling.bngl", + "file": "cd40-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "cell-cycle-checkpoint", + "name": "cell cycle checkpoint", + "description": "Cell cycle checkpoint: Mitotic entry switch (CDK1).", + "tags": [ + "cell", + "cycle", + "checkpoint", + "cyclin", + "cdk", + "cdc25", + "wee1", + "apc", + "p21" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint.bngl", + "file": "cell-cycle-checkpoint.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Chattaraj_2021", + "name": "Chattaraj 2021", + "description": "NFkB oscillations", + "tags": [ + "published", + "chattaraj", + "2021", + "nephrin", + "nck", + "nwasp", + "writexml" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience" + ], + "path": "Published/Chattaraj2021/Chattaraj_2021.bngl", + "file": "Chattaraj_2021.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "check_scaling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/check_scaling.bngl", + "file": "check_scaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "checkpoint-kinase-signaling", + "name": "checkpoint kinase signaling", + "description": "DNA Checkpoint: ATM/ATR mediated damage sensing.", + "tags": [ + "checkpoint", + "kinase", + "signaling", + "dna", + "atm", + "atr", + "chk1", + "chk2", + "p53", + "cdc25" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling.bngl", + "file": "checkpoint-kinase-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Cheemalavagu_JAK_STAT", + "name": "Cheemalavagu 2024", + "description": "JAK-STAT signaling", + "tags": [ + "published", + "literature", + "signaling", + "cheemalavagu", + "jak", + "stat", + "l1", + "il6r", + "gp130", + "l2", + "il10r1", + "il10r2", + "jak1", + "jak2" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/CheemalavaguJAKSTAT/Cheemalavagu_JAK_STAT.bngl", + "file": "Cheemalavagu_JAK_STAT.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "chemistry", + "name": "chemistry", + "description": "Basic chemical reactions", + "tags": [ + "published", + "tutorials", + "chemistry", + "a", + "b", + "c", + "d", + "e" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "path": "Tutorials/General/chemistry/chemistry.bngl", + "file": "chemistry.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "chemotaxis-signal-transduction", + "name": "chemotaxis signal transduction", + "description": "Bacterial Chemotaxis: Adaptation through methylation.", + "tags": [ + "chemotaxis", + "signal", + "transduction", + "attr", + "mcp", + "chea", + "chey", + "cheb", + "motor" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction.bngl", + "file": "chemotaxis-signal-transduction.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Chylek_library", + "name": "Chylek library", + "description": "Created by BioNetGen 2.2.6", + "tags": [ + "chylek", + "library", + "kflatplcg", + "kfgrb2gab2", + "kflcp2plcg1", + "kd1", + "kd2", + "sink", + "pre", + "pag1" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/Chyleklibrary/Chylek_library.bngl", + "file": "Chylek_library.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ChylekFceRI_2014", + "name": "Chylek 2014 (FceRI)", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "chylekfceri", + "2014", + "lig", + "rec", + "lyn", + "fyn", + "syk", + "pag1", + "csk", + "lat" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/ChylekFceRI2014/ChylekFceRI_2014.bngl", + "file": "ChylekFceRI_2014.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ChylekTCR_2014", + "name": "Chylek 2014 (TCR)", + "description": "TCR signaling", + "tags": [ + "published", + "immunology", + "chylektcr", + "2014", + "lig1", + "lig2", + "lig3", + "tcr", + "cd28", + "lck", + "itk", + "zap70" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/ChylekTCR2014/ChylekTCR_2014.bngl", + "file": "ChylekTCR_2014.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "circadian-oscillator", + "name": "circadian oscillator", + "description": "title: Vilar Circadian Oscillator Model", + "tags": [ + "circadian", + "oscillator", + "a", + "r", + "pa", + "pr", + "mrna_a", + "mrna_r" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/circadianoscillator/circadian-oscillator.bngl", + "file": "circadian-oscillator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "CircadianOscillator", + "name": "CircadianOscillator", + "description": "Circadian rhythm", + "tags": [ + "published", + "tutorial", + "native", + "circadianoscillator", + "a", + "r", + "pa", + "pr", + "mrna_a", + "mrna_r" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "cell-cycle", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/CircadianOscillator/CircadianOscillator.bngl", + "file": "CircadianOscillator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "clock-bmal1-gene-circuit", + "name": "clock bmal1 gene circuit", + "description": "BMAL1-CLOCK: The master activator of the circadian circuit.", + "tags": [ + "clock", + "bmal1", + "gene", + "circuit", + "ror", + "reverb", + "dna" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit.bngl", + "file": "clock-bmal1-gene-circuit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "compartment_endocytosis", + "name": "compartment endocytosis", + "description": "Model: compartment_endocytosis.bngl", + "tags": [ + "compartment", + "endocytosis", + "l", + "r", + "t" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl", + "file": "compartment_endocytosis.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "compartment_membrane_bound", + "name": "compartment membrane bound", + "description": "Model: compartment_membrane_bound.bngl", + "tags": [ + "compartment", + "membrane", + "bound", + "p", + "lipid", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl", + "file": "compartment_membrane_bound.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "compartment_nested_transport", + "name": "compartment nested transport", + "description": "Model: compartment_nested_transport.bngl", + "tags": [ + "compartment", + "nested", + "transport", + "s", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl", + "file": "compartment_nested_transport.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "compartment_nuclear_transport", + "name": "compartment nuclear transport", + "description": "Model: compartment_nuclear_transport.bngl", + "tags": [ + "compartment", + "nuclear", + "transport", + "tf", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl", + "file": "compartment_nuclear_transport.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "compartment_organelle_exchange", + "name": "compartment organelle exchange", + "description": "Model: compartment_organelle_exchange.bngl", + "tags": [ + "compartment", + "organelle", + "exchange", + "cargo", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl", + "file": "compartment_organelle_exchange.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "competitive-enzyme-inhibition", + "name": "competitive enzyme inhibition", + "description": "Competitive inhibition: Inhibitor (I) and Substrate (S) compete for the same", + "tags": [ + "competitive", + "enzyme", + "inhibition", + "substrate1", + "substrate2", + "inhibitor", + "product" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition.bngl", + "file": "competitive-enzyme-inhibition.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "complement-activation-cascade", + "name": "complement activation cascade", + "description": "Complement System: Pathogen opsonization and the Alternative Pathway.", + "tags": [ + "complement", + "activation", + "cascade", + "c3", + "fb", + "c5", + "mac", + "surf" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/complementactivationcascade/complement-activation-cascade.bngl", + "file": "complement-activation-cascade.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ComplexDegradation", + "name": "ComplexDegradation", + "description": "Degradation model", + "tags": [ + "published", + "tutorial", + "native", + "complexdegradation", + "a", + "b", + "c", + "generate_network" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ComplexDegradation/ComplexDegradation.bngl", + "file": "ComplexDegradation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "contact-inhibition-hippo-yap", + "name": "contact inhibition hippo yap", + "description": "Hippo Pathway: Contact inhibition and YAP regulation.", + "tags": [ + "contact", + "inhibition", + "hippo", + "yap", + "mst", + "lats", + "tead" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl", + "file": "contact-inhibition-hippo-yap.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "continue", + "name": "continue", + "description": "Test trajectory continuation", + "tags": [ + "validation", + "continue", + "a", + "b", + "c", + "trash" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/continue/continue.bngl", + "file": "continue.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "cooperative-binding", + "name": "cooperative binding", + "description": "Cooperative binding: The binding of the first ligand molecule increases", + "tags": [ + "cooperative", + "binding", + "receptor", + "ligand", + "competitor" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/cooperativebinding/cooperative-binding.bngl", + "file": "cooperative-binding.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Creamer_2012", + "name": "Creamer 2012", + "description": "Initial values", + "tags": [ + "creamer", + "2012", + "egf", + "hrg", + "egfr", + "erbb2", + "erbb3", + "erbb4", + "p52shc1", + "grb2" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/Creamer2012/Creamer_2012.bngl", + "file": "Creamer_2012.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "cs_diffie_hellman", + "name": "cs diffie hellman", + "description": "Model: cs_diffie_hellman.bngl", + "tags": [ + "cs", + "diffie", + "hellman", + "agent", + "target", + "dshareda_dt", + "dsharedb_dt" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl", + "file": "cs_diffie_hellman.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "cs_hash_function", + "name": "cs hash function", + "description": "Cryptographic Hash Function in BNGL", + "tags": [ + "cs", + "hash", + "function", + "b0", + "b1", + "b2", + "b3", + "h0", + "h1", + "h2", + "h3" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/cs/cshashfunction/cs_hash_function.bngl", + "file": "cs_hash_function.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "cs_huffman", + "name": "cs huffman", + "description": "Model: cs_huffman.bngl", + "tags": [ + "cs", + "huffman", + "char", + "hnode", + "generate_network", + "simulate" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/cs/cshuffman/cs_huffman.bngl", + "file": "cs_huffman.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "cs_monte_carlo_pi", + "name": "cs monte carlo pi", + "description": "Model: cs_monte_carlo_pi.bngl", + "tags": [ + "cs", + "monte", + "carlo", + "pi", + "trial", + "pi_estimate", + "generate_network", + "simulate" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl", + "file": "cs_monte_carlo_pi.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "cs_pagerank", + "name": "cs pagerank", + "description": "Model: cs_pagerank.bngl", + "tags": [ + "cs", + "pagerank", + "teleport", + "page" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/cs/cspagerank/cs_pagerank.bngl", + "file": "cs_pagerank.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "cs_pid_controller", + "name": "cs pid controller", + "description": "PID Controller in BNGL", + "tags": [ + "cs", + "pid", + "controller", + "sensor", + "accumulator", + "leakyerror", + "actuator", + "disturbance" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/cs/cspidcontroller/cs_pid_controller.bngl", + "file": "cs_pid_controller.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "cs_regex_nfa", + "name": "cs regex nfa", + "description": "Model: cs_regex_nfa.bngl", + "tags": [ + "cs", + "regex", + "nfa", + "state", + "char", + "generate_network", + "simulate", + "setparameter" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/cs/csregexnfa/cs_regex_nfa.bngl", + "file": "cs_regex_nfa.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Dallas", + "name": "Dallas", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "dallas", + "counter", + "fdcs", + "s", + "sv", + "e", + "a", + "i", + "v" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/VaxAndVariants/Dallas/Dallas.bngl", + "file": "Dallas.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "degranulation_model", + "name": "PyBNG: Degranulation model", + "description": "Degranulation model", + "tags": [ + "published", + "pybng", + "degranulation", + "model", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/PyBioNetGen/core/degranulationmodel/degranulation_model.bngl", + "file": "degranulation_model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Dembo_1978", + "name": "Dembo 1978", + "description": "BLBR dembo 1978", + "tags": [ + "published", + "physics", + "dembo", + "1978" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "path": "Published/Dembo1978/blbr_dembo1978.bngl", + "file": "blbr_dembo1978.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "dna-damage-repair", + "name": "dna damage repair", + "description": "DNA damage sensing and repair pathway (ATM-CHK2-p53 axis)", + "tags": [ + "dna", + "damage", + "repair", + "mrn", + "atm", + "chk2", + "repaircomplex" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/dnadamagerepair/dna-damage-repair.bngl", + "file": "dna-damage-repair.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "dna-methylation-dynamics", + "name": "dna methylation dynamics", + "description": "DNA Methylation: Maintenance and de novo dynamics.", + "tags": [ + "dna", + "methylation", + "dynamics", + "cpg", + "dnmt1", + "tet", + "v_maint", + "v_erase" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/dnamethylationdynamics/dna-methylation-dynamics.bngl", + "file": "dna-methylation-dynamics.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Dolan_2015", + "name": "Dolan 2015", + "description": "Insulin signaling", + "tags": [ + "published", + "literature", + "signaling", + "dolan", + "2015", + "time", + "t", + "p", + "e", + "ir", + "d", + "p53_mrna", + "p53" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism" + ], + "path": "Published/Dolan2015/Dolan_2015.bngl", + "file": "Dolan_2015.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Dolan2015", + "name": "Dolan 2015", + "description": "Insulin signaling", + "tags": [ + "published", + "literature", + "signaling", + "dolan", + "2015", + "time", + "t", + "p", + "e", + "ir", + "d", + "p53_mrna", + "p53" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism" + ], + "path": "Published/Dolan2015/Dolan2015.bngl", + "file": "Dolan2015.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "dr5-apoptosis-signaling", + "name": "dr5 apoptosis signaling", + "description": "DR5 (TRAIL) Signaling: Extrinsic apoptosis and DISC formation.", + "tags": [ + "dr5", + "apoptosis", + "signaling", + "trail", + "fadd", + "caspase8", + "flip", + "death_signal" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling.bngl", + "file": "dr5-apoptosis-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Dreisigmeyer_2008", + "name": "Dreisigmeyer 2008", + "description": "Lac operon", + "tags": [ + "published", + "gene-expression", + "dreisigmeyer", + "2008" + ], + "category": "gene-expression", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "gene-expression" + ], + "path": "Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl", + "file": "lac_operon_dreisigmeyer2008.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "dual-site-phosphorylation", + "name": "dual site phosphorylation", + "description": "Dual-site phosphorylation: Requires two sequential modifications for activity.", + "tags": [ + "dual", + "site", + "phosphorylation", + "kinase", + "phosphatase", + "substrate" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/dualsitephosphorylation/dual-site-phosphorylation.bngl", + "file": "dual-site-phosphorylation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Dushek_2011", + "name": "Dushek 2011", + "description": "TCR signaling", + "tags": [ + "published", + "dushek", + "2011", + "s" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/Dushek2011/Dushek_2011.bngl", + "file": "Dushek_2011.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Dushek_2014", + "name": "Dushek 2014", + "description": "TCR signaling dynamics", + "tags": [ + "published", + "dushek", + "2014", + "e", + "f", + "b" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/Dushek2014/Dushek_2014.bngl", + "file": "Dushek_2014.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "e2f-rb-cell-cycle-switch", + "name": "e2f rb cell cycle switch", + "description": "E2F/Rb Switch: The G1/S transition gate.", + "tags": [ + "e2f", + "rb", + "cell", + "cycle", + "switch", + "mitogen", + "cycd", + "cyce", + "p27" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch.bngl", + "file": "e2f-rb-cell-cycle-switch.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "eco_coevolution_host_parasite", + "name": "eco coevolution host parasite", + "description": "Model: eco_coevolution_host_parasite.bngl", + "tags": [ + "eco", + "coevolution", + "host", + "parasite" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "path": "Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl", + "file": "eco_coevolution_host_parasite.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "eco_food_web_chaos_3sp", + "name": "eco food web chaos 3sp", + "description": "Model: eco_food_web_chaos_3sp.bngl", + "tags": [ + "eco", + "food", + "web", + "chaos", + "3sp", + "r", + "c", + "p", + "k_eat_r", + "k_eat_c" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "path": "Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl", + "file": "eco_food_web_chaos_3sp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "eco_lotka_volterra_grid", + "name": "eco lotka volterra grid", + "description": "Model: eco_lotka_volterra_grid.bngl", + "tags": [ + "eco", + "lotka", + "volterra", + "grid", + "prey", + "pred" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "path": "Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl", + "file": "eco_lotka_volterra_grid.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "eco_mutualism_obligate", + "name": "eco mutualism obligate", + "description": "Model: eco_mutualism_obligate.bngl", + "tags": [ + "eco", + "mutualism", + "obligate", + "a", + "b" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "path": "Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl", + "file": "eco_mutualism_obligate.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "eco_rock_paper_scissors_spatial", + "name": "eco rock paper scissors spatial", + "description": "Model: eco_rock_paper_scissors_spatial.bngl", + "tags": [ + "eco", + "rock", + "paper", + "scissors", + "spatial", + "s", + "generate_network" + ], + "category": "ecology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "path": "Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl", + "file": "eco_rock_paper_scissors_spatial.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "egfr", + "name": "02-egfr", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/02-egfr/egfr.bngl", + "file": "egfr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "egfr", + "name": "17-egfr-ssa", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/17-egfr-ssa/egfr.bngl", + "file": "egfr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "egfr", + "name": "egfr", + "description": "Blinov et al. 2006. Biosystems, 83:136", + "tags": [ + "egfr", + "egf", + "grb2", + "shc", + "sos" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/egfr/egfr.bngl", + "file": "egfr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "egfr_ground", + "name": "02-egfr", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/02-egfr/egfr_ground.bngl", + "file": "egfr_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "egfr_ground", + "name": "17-egfr-ssa", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/17-egfr-ssa/egfr_ground.bngl", + "file": "egfr_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "egfr_ground", + "name": "egfr ground", + "description": "Blinov et al. 2006. Biosystems, 83:136", + "tags": [ + "egfr", + "ground", + "egf", + "grb2", + "shc", + "sos" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/egfrground/egfr_ground.bngl", + "file": "egfr_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "egfr_net", + "name": "egfr_net", + "description": "check detailed balanced", + "tags": [ + "validation", + "egfr", + "net", + "egf", + "shc", + "grb2", + "sos" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/egfrnet/egfr_net.bngl", + "file": "egfr_net.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "egfr_net_red", + "name": "egfr_net_red", + "description": "Reduced state-space version of EGFR_NET.BNGL with equivalent ODE dynamics", + "tags": [ + "validation", + "egfr", + "net", + "red", + "egf", + "egfr_1", + "egfr_2", + "egfr_3", + "grb2", + "shc", + "sos" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/egfrnetred/egfr_net_red.bngl", + "file": "egfr_net_red.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "egfr_nf", + "name": "egfr nf", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "egfr", + "nf", + "egf", + "clusters", + "pre1_dose", + "pre2_time" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/egfrnf/egfr_nf.bngl", + "file": "egfr_nf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "egfr_ode", + "name": "egfr ode", + "description": "Filename: example1.bngl", + "tags": [ + "egfr", + "ode", + "egf", + "pre1_dose", + "pre2_time", + "pre3_dose" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/PyBioNetGen/core/egfrode/egfr_ode.bngl", + "file": "egfr_ode.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "egfr_ode", + "name": "PyBNG: EGFR ODE", + "description": "EGFR ODE", + "tags": [ + "published", + "pybng", + "egfr", + "ode", + "egf", + "pre1_dose", + "pre2_time", + "pre3_dose" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode.bngl", + "file": "egfr_ode.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "egfr_path", + "name": "egfr_path", + "description": "The primary focus of the model developed by Kholodenko", + "tags": [ + "validation", + "egfr", + "path", + "generate_network", + "setconcentration", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/egfrpath/egfr_path.bngl", + "file": "egfr_path.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "egfr_simple", + "name": "egfr simple", + "description": "This is a demo model of EGFR signaling.", + "tags": [ + "egfr", + "simple", + "egf", + "grb2", + "sos1" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/egfrsimple/egfr_simple.bngl", + "file": "egfr_simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "egfr-signaling-pathway", + "name": "egfr signaling pathway", + "description": "Enhanced EGFR Signaling: Combinatorial complexity with multiple phosphorylation sites.", + "tags": [ + "egfr", + "signaling", + "pathway", + "egf", + "grb2", + "shc" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/egfrsignalingpathway/egfr-signaling-pathway.bngl", + "file": "egfr-signaling-pathway.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "egg", + "name": "egg", + "description": "BioNetGen model: egg", + "tags": [ + "egg", + "x", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/egg/egg.bngl", + "file": "egg.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "eif2a-stress-response", + "name": "eif2a stress response", + "description": "Integrated Stress Response: eIF2alpha and the translational gate.", + "tags": [ + "eif2a", + "stress", + "response", + "eif2b", + "perk", + "gadd34" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/eif2astressresponse/eif2a-stress-response.bngl", + "file": "eif2a-stress-response.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "elephant_EFA", + "name": "Hlavacek2018Elephant", + "description": "BNGL model: elephant_EFA", + "tags": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10", + "a11", + "a12", + "a13", + "a14", + "a15", + "a16", + "a17", + "a18", + "a19", + "a20", + "b0", + "b1", + "b2", + "b3", + "b4", + "b5", + "b6", + "b7", + "b8", + "b9", + "b10", + "b11", + "b12", + "b13", + "b14", + "b15", + "b16", + "b17", + "b18", + "b19", + "b20", + "c0", + "c1", + "c2", + "c3", + "c4", + "c5", + "c6", + "c7", + "c8", + "c9", + "c10", + "c11", + "c12", + "c13", + "c14", + "c15", + "c16", + "c17", + "c18", + "c19", + "c20", + "d0", + "d1", + "d2", + "d3", + "d4", + "d5", + "d6", + "d7", + "d8", + "d9", + "d10", + "d11", + "d12", + "d13", + "d14", + "d15", + "d16", + "d17", + "d18", + "d19", + "d20", + "period", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Elephant/elephant_EFA.bngl", + "file": "elephant_EFA.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "elephant_fit", + "name": "Hlavacek2018Elephant", + "description": "BNGL model: elephant_EFA", + "tags": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10", + "a11", + "a12", + "a13", + "a14", + "a15", + "a16", + "a17", + "a18", + "a19", + "a20", + "b0", + "b1", + "b2", + "b3", + "b4", + "b5", + "b6", + "b7", + "b8", + "b9", + "b10", + "b11", + "b12", + "b13", + "b14", + "b15", + "b16", + "b17", + "b18", + "b19", + "b20", + "c0", + "c1", + "c2", + "c3", + "c4", + "c5", + "c6", + "c7", + "c8", + "c9", + "c10", + "c11", + "c12", + "c13", + "c14", + "c15", + "c16", + "c17", + "c18", + "c19", + "c20", + "d0", + "d1", + "d2", + "d3", + "d4", + "d5", + "d6", + "d7", + "d8", + "d9", + "d10", + "d11", + "d12", + "d13", + "d14", + "d15", + "d16", + "d17", + "d18", + "d19", + "d20", + "period", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Elephant/elephant_fit.bngl", + "file": "elephant_fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "endosomal-sorting-rab", + "name": "endosomal sorting rab", + "description": "Endosomal Sorting: Rab GTPase conversion and effector recruitment.", + "tags": [ + "endosomal", + "sorting", + "rab", + "rab5", + "rab7", + "effector", + "v_gef", + "v_gap_drive" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/endosomalsortingrab/endosomal-sorting-rab.bngl", + "file": "endosomal-sorting-rab.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "energy_allostery_mwc", + "name": "energy allostery mwc", + "description": "Model: energy_allostery_mwc.bngl", + "tags": [ + "energy", + "allostery", + "mwc", + "p", + "l" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl", + "file": "energy_allostery_mwc.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "energy_catalysis_mm", + "name": "energy catalysis mm", + "description": "Model: energy_catalysis_mm.bngl", + "tags": [ + "energy", + "catalysis", + "mm", + "e", + "s", + "p" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/energy/energycatalysismm/energy_catalysis_mm.bngl", + "file": "energy_catalysis_mm.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "energy_cooperativity_adh", + "name": "energy cooperativity adh", + "description": "Model: energy_cooperativity_adh.bngl", + "tags": [ + "energy", + "cooperativity", + "adh", + "r", + "l" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/energy/energycooperativityadh/energy_cooperativity_adh.bngl", + "file": "energy_cooperativity_adh.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "energy_example1", + "name": "energy_example1", + "description": "Illustration of energy modeling approach w/ a simple protein scaffold model", + "tags": [ + "validation", + "energy", + "example1", + "version", + "setoption", + "s", + "a", + "b", + "c" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/energyexample1/energy_example1.bngl", + "file": "energy_example1.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "energy_linear_chain", + "name": "energy linear chain", + "description": "Model: energy_linear_chain.bngl", + "tags": [ + "energy", + "linear", + "chain", + "m", + "generate_network" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/energy/energylinearchain/energy_linear_chain.bngl", + "file": "energy_linear_chain.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "energy_transport_pump", + "name": "energy transport pump", + "description": "Model: energy_transport_pump.bngl", + "tags": [ + "energy", + "transport", + "pump", + "a", + "atp", + "adp", + "pi", + "t" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/energy/energytransportpump/energy_transport_pump.bngl", + "file": "energy_transport_pump.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ensemble_tofit", + "name": "translated into BNGL", + "description": "Ensemble model translated into BNGL", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/28-mapk/ensemble_tofit.bngl", + "file": "ensemble_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "er-stress-response", + "name": "er stress response", + "description": "Rate Constants", + "tags": [ + "er", + "stress", + "response", + "unfoldedprotein", + "perk", + "eif2a", + "chaperone" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/erstressresponse/er-stress-response.bngl", + "file": "er-stress-response.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Erdem_2021", + "name": "Erdem 2021", + "description": "InsR/IGF1R signaling", + "tags": [ + "published", + "erdem", + "2021", + "igf1", + "ins", + "igf1r", + "insr", + "irs", + "sos", + "ras", + "raf" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism" + ], + "path": "Published/Erdem2021/Erdem_2021.bngl", + "file": "Erdem_2021.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ERK_model", + "name": "ERK_model.bngl", + "description": "filename: ERK_model.bngl", + "tags": [ + "egf", + "erkpp_sos1_fb", + "erkpp_mek_fb", + "erkpp_raf1_fb", + "lambda", + "egfr_tot", + "ras_tot", + "sos_tot", + "rasgap_tot", + "raf_tot", + "mek_tot", + "erk_tot", + "ekar3_tot", + "erktr_tot", + "a1", + "d1", + "b1", + "u1a", + "u1b", + "b2a", + "u2a", + "b2b", + "u2b", + "k2a", + "k2b", + "b3", + "u3", + "k3", + "a2", + "d2", + "p1", + "q1", + "p2", + "q2", + "p3", + "q3", + "p4", + "q4", + "q5", + "p6", + "q6", + "a0_ekar3", + "d0_ekar3", + "a0_erktr", + "d0_erktr", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "path": "Published/Lin2019/ERK_model.bngl", + "file": "ERK_model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "erk-nuclear-translocation", + "name": "erk nuclear translocation", + "description": "ERK Translocation: Spatial signaling and transcriptional assembly.", + "tags": [ + "erk", + "nuclear", + "translocation", + "mek", + "elk1", + "dusp", + "transcription_signal" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/erknucleartranslocation/erk-nuclear-translocation.bngl", + "file": "erk-nuclear-translocation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ErrNoFrees", + "name": "ErrNoFrees", + "description": "An example from a real application", + "tags": [ + "errnofrees", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/ErrNoFrees/ErrNoFrees.bngl", + "file": "ErrNoFrees.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example1", + "name": "example1", + "description": "Filename: example1.bngl", + "tags": [ + "example1", + "egf", + "egfr", + "pre1_dose", + "pre2_time", + "pre3_dose" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/example1/example1.bngl", + "file": "example1.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "example1", + "name": "example1", + "description": "Example file for BNG2 tutorial.", + "tags": [ + "validation", + "example1", + "version", + "generate_network", + "simulate_ode" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/example1/example1.bngl", + "file": "example1.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example1_BNFfiles_example1", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example1_BNFfiles/example1.bngl", + "file": "example1.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example1_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example1_fit.bngl", + "file": "example1_fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example2_BNFfiles_example2", + "name": "example2_starting_point.bngl", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "f", + "lt_nm", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example2_BNFfiles/example2.bngl", + "file": "example2.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example2_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example2_fit.bngl", + "file": "example2_fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example2_starting_point", + "name": "example2 starting point", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "example2", + "starting", + "point", + "egf", + "egfr", + "clusters", + "pre1_dose", + "pre2_time" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/example2startingpoint/example2_starting_point.bngl", + "file": "example2_starting_point.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "example3_BNFfiles_example3", + "name": "example3 BNFfiles", + "description": "BNGL model: example3", + "tags": [ + "alpha", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example3_BNFfiles/example3.bngl", + "file": "example3.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example3_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example3_fit.bngl", + "file": "example3_fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example4_BNFfiles_example4", + "name": "in BNGL. For a description of BNGL, see:", + "description": "Supplementary File A in File S1", + "tags": [ + "other" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example4_BNFfiles/example4.bngl", + "file": "example4.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example4_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example4_fit.bngl", + "file": "example4_fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example5_BNFfiles_example5", + "name": "example5 BNFfiles", + "description": "A simple model", + "tags": [ + "ligand_ispresent", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example5_BNFfiles/example5.bngl", + "file": "example5.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example5_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example5_fit.bngl", + "file": "example5_fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example5_ground_truth", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example5_ground_truth.bngl", + "file": "example5_ground_truth.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example5_starting_point", + "name": "13-receptor", + "description": "A simple model", + "tags": [ + "ligand_ispresent", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/13-receptor/example5_starting_point.bngl", + "file": "example5_starting_point.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example6_BNFfiles_example6", + "name": "example6 BNFfiles", + "description": "A simple model", + "tags": [ + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example6_BNFfiles/example6.bngl", + "file": "example6.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example6_ground_truth", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example6_ground_truth.bngl", + "file": "example6_ground_truth.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "extra_CaMKII_Holo", + "name": "Ordyan 2020: extra CaMKII holo", + "description": "Extra CaMKII holo (supplement)", + "tags": [ + "published", + "neuroscience", + "extra", + "camkii", + "holo", + "t1", + "t2", + "t3", + "t4", + "t5", + "t6", + "t7", + "t8" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "path": "Published/Ordyan2020/extraCaMKIIHolo/extra_CaMKII_Holo.bngl", + "file": "extra_CaMKII_Holo.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Faeder_2003", + "name": "Faeder 2003", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "faeder", + "2003", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/Faeder2003/Faeder_2003.bngl", + "file": "Faeder_2003.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "fceri_fyn", + "name": "FceRI Fyn", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "fceri", + "fyn", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/fcerifyn/fceri_fyn.bngl", + "file": "fceri_fyn.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "fceri_gamma2", + "name": "fceri gamma2", + "description": "BioNetGen model: fceri gamma2", + "tags": [ + "fceri", + "gamma2", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/fcerigamma2/fceri_gamma2.bngl", + "file": "fceri_gamma2.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "fceri_gamma2_ground_truth", + "name": "fceri gamma2 ground truth", + "description": "BioNetGen model: fceri gamma2 ground truth", + "tags": [ + "fceri", + "gamma2", + "ground", + "truth", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth.bngl", + "file": "fceri_gamma2_ground_truth.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "fceri_ji", + "name": "Faeder 2003", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "faeder", + "2003", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/Faeder2003/fceri_ji.bngl", + "file": "fceri_ji.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "FceRI_ji", + "name": "FceRI ji", + "description": "title: FceRI_ji.bngl", + "tags": [ + "fceri", + "ji", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/FceRIji/FceRI_ji.bngl", + "file": "FceRI_ji.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "fceri_ji_comp", + "name": "fceri_ji_comp", + "description": "Ligand-receptor binding", + "tags": [ + "validation", + "fceri", + "ji", + "comp", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/fcerijicomp/fceri_ji_comp.bngl", + "file": "fceri_ji_comp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "FceRI_viz", + "name": "FceRI Viz", + "description": "FcεRI (viz)", + "tags": [ + "published", + "tutorial", + "native", + "fceri", + "viz", + "fcr", + "ige", + "lat", + "lyn", + "syk", + "pb", + "pg", + "sykp" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/FceRIviz/FceRI_viz.bngl", + "file": "FceRI_viz.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "feature_functional_rates_volume", + "name": "feature functional rates volume", + "description": "Model: feature_functional_rates_volume.bngl", + "tags": [ + "feature", + "functional", + "rates", + "volume", + "a", + "b", + "c" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume.bngl", + "file": "feature_functional_rates_volume.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "feature_global_functions_scan", + "name": "feature global functions scan", + "description": "Model: feature_global_functions_scan.bngl", + "tags": [ + "feature", + "global", + "functions", + "scan", + "signal", + "response", + "stimulus" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl", + "file": "feature_global_functions_scan.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "feature_local_functions_explicit", + "name": "feature local functions explicit", + "description": "Model: feature_local_functions_explicit.bngl", + "tags": [ + "feature", + "local", + "functions", + "explicit", + "s", + "p", + "e", + "mm_rate", + "ratelaw" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit.bngl", + "file": "feature_local_functions_explicit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "feature_symmetry_factors_cyclic", + "name": "feature symmetry factors cyclic", + "description": "Model: feature_symmetry_factors_cyclic.bngl", + "tags": [ + "feature", + "symmetry", + "factors", + "cyclic", + "x", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic.bngl", + "file": "feature_symmetry_factors_cyclic.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "feature_synthesis_degradation_ss", + "name": "feature synthesis degradation ss", + "description": "Model: feature_synthesis_degradation_ss.bngl", + "tags": [ + "feature", + "synthesis", + "degradation", + "ss", + "m", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss.bngl", + "file": "feature_synthesis_degradation_ss.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "fgf-signaling-pathway", + "name": "fgf signaling pathway", + "description": "FGF Signaling: FGFR dimerization and FRS2-Ras/PI3K relay.", + "tags": [ + "fgf", + "signaling", + "pathway", + "fgfr", + "frs2", + "spry", + "rasgef", + "internalized_rec" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/fgfsignalingpathway/fgf-signaling-pathway.bngl", + "file": "fgf-signaling-pathway.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "free_missing", + "name": "free missing", + "description": "Original values used to generate parabola.exp", + "tags": [ + "free", + "missing", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/freemissing/free_missing.bngl", + "file": "free_missing.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Gardner_2000", + "name": "Gardner 2000", + "description": "Genetic toggle switch", + "tags": [ + "published", + "synthetic-biology", + "gardner", + "2000" + ], + "category": "synthetic-biology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synthetic-biology" + ], + "path": "Published/Gardner2000/genetic_switch_gardner2000.bngl", + "file": "genetic_switch_gardner2000.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "gas6-axl-signaling", + "name": "gas6 axl signaling", + "description": "GAS6/AXL Signaling: AKT activation and SOCS feedback.", + "tags": [ + "gas6", + "axl", + "signaling", + "pi3k", + "akt", + "socs", + "survival_burst" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/gas6axlsignaling/gas6-axl-signaling.bngl", + "file": "gas6-axl-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "gene-expression-toggle", + "name": "gene expression toggle", + "description": "Kinetic Parameters", + "tags": [ + "gene", + "expression", + "toggle", + "mrna", + "protein" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/geneexpressiontoggle/gene-expression-toggle.bngl", + "file": "gene-expression-toggle.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "genetic_bistability_energy", + "name": "genetic bistability energy", + "description": "Model: genetic_bistability_energy.bngl", + "tags": [ + "genetic", + "bistability", + "energy", + "genea", + "geneb", + "prota", + "protb" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy.bngl", + "file": "genetic_bistability_energy.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "genetic_dna_replication_stochastic", + "name": "genetic dna replication stochastic", + "description": "Model: genetic_dna_replication_stochastic.bngl", + "tags": [ + "genetic", + "dna", + "replication", + "stochastic", + "pol", + "n", + "generate_network" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic.bngl", + "file": "genetic_dna_replication_stochastic.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "genetic_goodwin_oscillator", + "name": "genetic goodwin oscillator", + "description": "Model: genetic_goodwin_oscillator.bngl", + "tags": [ + "genetic", + "goodwin", + "oscillator", + "gene", + "mrna", + "protein", + "repressor" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator.bngl", + "file": "genetic_goodwin_oscillator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "genetic_translation_kinetics", + "name": "genetic translation kinetics", + "description": "Model: genetic_translation_kinetics.bngl", + "tags": [ + "genetic", + "translation", + "kinetics", + "mrna", + "rib", + "protein" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics.bngl", + "file": "genetic_translation_kinetics.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "genetic_turing_pattern_1d", + "name": "genetic turing pattern 1d", + "description": "Model: genetic_turing_pattern_1d.bngl", + "tags": [ + "genetic", + "turing", + "pattern", + "1d", + "a", + "b" + ], + "category": "gene-expression", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d.bngl", + "file": "genetic_turing_pattern_1d.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "GK", + "name": "GK", + "description": "title: GK.bngl", + "tags": [ + "gk", + "b", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/GK/GK.bngl", + "file": "GK.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "glioblastoma-egfrviii-signaling", + "name": "glioblastoma egfrviii signaling", + "description": "EGFRvIII in Glioblastoma: Constitutive AKT drive and escape from decay.", + "tags": [ + "glioblastoma", + "egfrviii", + "signaling", + "pi3k", + "akt", + "oncogenic_output", + "v_viii_act" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling.bngl", + "file": "glioblastoma-egfrviii-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "glycolysis-branch-point", + "name": "glycolysis branch point", + "description": "BioNetGen model: glycolysis branch point", + "tags": [ + "glycolysis", + "branch", + "point", + "glucose", + "atp", + "biomass" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/glycolysisbranchpoint/glycolysis-branch-point.bngl", + "file": "glycolysis-branch-point.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "gm_game_of_life", + "name": "gm game of life", + "description": "Model: gm_game_of_life.bngl", + "tags": [ + "gm", + "game", + "of", + "life", + "cell" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/generative/gmgameoflife/gm_game_of_life.bngl", + "file": "gm_game_of_life.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "gm_ray_marcher", + "name": "gm ray marcher", + "description": "Ray Marching Renderer in BNGL", + "tags": [ + "gm", + "ray", + "marcher", + "ray0", + "hit0", + "bright0", + "sdf0", + "sdf1", + "sdf2", + "sdf3", + "speed0" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/generative/gmraymarcher/gm_ray_marcher.bngl", + "file": "gm_ray_marcher.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Goldstein_1980", + "name": "Goldstein 1980", + "description": "BLBR heterogeneity", + "tags": [ + "published", + "physics", + "goldstein", + "1980" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "path": "Published/Goldstein1980/blbr_heterogeneity_goldstein1980.bngl", + "file": "blbr_heterogeneity_goldstein1980.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "gpcr-desensitization-arrestin", + "name": "gpcr desensitization arrestin", + "description": "GPCR Desensitization: Arrestin-mediated spatial sequestration.", + "tags": [ + "gpcr", + "desensitization", + "arrestin", + "ligand", + "gprotein" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin.bngl", + "file": "gpcr-desensitization-arrestin.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Harmon_2017", + "name": "Harmon 2017", + "description": "Antigen pulses", + "tags": [ + "published", + "immunology", + "harmon", + "2017" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/Harmon2017/antigen_pulses_harmon2017.bngl", + "file": "antigen_pulses_harmon2017.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Hat_2016", + "name": "Hat 2016", + "description": "Nuclear transport", + "tags": [ + "published", + "hat", + "2016", + "dna_dsb", + "atm", + "siah1", + "hipk2", + "wip1", + "gene_wip1", + "mrna_wip1", + "p53" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "cell-cycle", + "multistage" + ], + "path": "Published/Hat2016/Hat_2016.bngl", + "file": "Hat_2016.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Haugh2b", + "name": "Haugh2b", + "description": "R(KD,Y1~U,Y2~U) 1.00", + "tags": [ + "validation", + "haugh2b", + "r", + "s1", + "s2", + "exclude_reactants", + "include_reactants" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/Haugh2b/Haugh2b.bngl", + "file": "Haugh2b.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "hedgehog-signaling-pathway", + "name": "hedgehog signaling pathway", + "description": "Hedgehog (Hh) Signaling: Ciliary translocation and Gli processing.", + "tags": [ + "hedgehog", + "signaling", + "pathway", + "hh", + "ptch", + "smo", + "gli", + "sufu" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/hedgehogsignalingpathway/hedgehog-signaling-pathway.bngl", + "file": "hedgehog-signaling-pathway.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "heise", + "name": "heise", + "description": "Validate state inheritance in a symmetric context", + "tags": [ + "validation", + "heise", + "a", + "b", + "generate_network", + "simulate_ode", + "setparameter" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/heise/heise.bngl", + "file": "heise.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "hematopoietic-growth-factor", + "name": "hematopoietic growth factor", + "description": "Kinetic Parameters", + "tags": [ + "hematopoietic", + "growth", + "factor", + "epo", + "epor", + "jak2", + "stat5" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/hematopoieticgrowthfactor/hematopoietic-growth-factor.bngl", + "file": "hematopoietic-growth-factor.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "hif1a_degradation_loop", + "name": "hif1a degradation loop", + "description": "HIF-1alpha Oxygen Sensing: Hydroxylation and VHL-mediated decay.", + "tags": [ + "hif1a", + "degradation", + "loop", + "vhl", + "arnt", + "v_hydrox" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/hif1adegradationloop/hif1a_degradation_loop.bngl", + "file": "hif1a_degradation_loop.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Hlavacek_1999", + "name": "Hlavacek 1999", + "description": "Steric effects", + "tags": [ + "published", + "physics", + "hlavacek", + "1999" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "path": "Published/Hlavacek1999/steric_effects_hlavacek1999.bngl", + "file": "steric_effects_hlavacek1999.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Hlavacek_2001", + "name": "Hlavacek 2001", + "description": "Kinetic proofreading", + "tags": [ + "published", + "physics", + "hlavacek", + "2001" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "path": "Published/Hlavacek2001/kinetic_proofreading_hlavacek2001.bngl", + "file": "kinetic_proofreading_hlavacek2001.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Hlavacek2018Egg_egg", + "name": "Hlavacek2018Egg", + "description": "End of permute change log", + "tags": [ + "a0__free", + "a1__free", + "a2__free", + "b1__free", + "b2__free", + "c0__free", + "c1__free", + "c2__free", + "d1__free", + "d2__free", + "a0", + "a1", + "a2", + "b1", + "b2", + "c0", + "c1", + "c2", + "d1", + "d2", + "period", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Egg/egg.bngl", + "file": "egg.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Houston", + "name": "Houston", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "houston", + "counter", + "fdcs", + "s", + "sv", + "e", + "a", + "i", + "v" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/VaxAndVariants/Houston/Houston.bngl", + "file": "Houston.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "hypoxia-response-signaling", + "name": "hypoxia response signaling", + "description": "Rate Constants", + "tags": [ + "hypoxia", + "response", + "signaling", + "oxygensensor", + "hif1", + "vegf" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/hypoxiaresponsesignaling/hypoxia-response-signaling.bngl", + "file": "hypoxia-response-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "IGF1R_Model_receptor_activation_bnf", + "name": "IGF1R Model receptor activation bnf", + "description": "Author: William S. Hlavacek", + "tags": [ + "igf1r", + "model", + "receptor", + "activation", + "bnf", + "igf1" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/IGF1R_Model_receptor_activation_bnf.bngl", + "file": "IGF1R_Model_receptor_activation_bnf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "il1b-signaling", + "name": "il1b signaling", + "description": "IL-1beta Signaling: MyD88/IRAK assembly and NF-kB translocation.", + "tags": [ + "il1b", + "signaling", + "il1ri", + "myd88", + "irak", + "nfkb" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/il1bsignaling/il1b-signaling.bngl", + "file": "il1b-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "il6-jak-stat-pathway", + "name": "il6 jak stat pathway", + "description": "IL-6 Signaling: gp130 hexamerization and pSTAT3 import.", + "tags": [ + "il6", + "jak", + "stat", + "pathway", + "gp130", + "stat3", + "socs" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/il6jakstatpathway/il6-jak-stat-pathway.bngl", + "file": "il6-jak-stat-pathway.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "immune-synapse-formation", + "name": "immune synapse formation", + "description": "Kinetic Parameters", + "tags": [ + "immune", + "synapse", + "formation", + "tcr", + "pmhc", + "lck", + "zap70" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/immunesynapseformation/immune-synapse-formation.bngl", + "file": "immune-synapse-formation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "inflammasome-activation", + "name": "inflammasome activation", + "description": "Rate Constants", + "tags": [ + "inflammasome", + "activation", + "sensor", + "asc", + "caspase1", + "il1b" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/inflammasomeactivation/inflammasome-activation.bngl", + "file": "inflammasome-activation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "innate_immunity", + "name": "Korwek 2023", + "description": "Immune response", + "tags": [ + "published", + "immunology", + "innate", + "immunity", + "polyic", + "rigi", + "mavs", + "pkr", + "oas3", + "rnasel", + "eif2a", + "rigi_mrna" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/innateimmunity/innate_immunity.bngl", + "file": "innate_immunity.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "inositol-phosphate-metabolism", + "name": "inositol phosphate metabolism", + "description": "Inositol Phosphate (IP) Metabolism: PLC signaling and branch points.", + "tags": [ + "inositol", + "phosphate", + "metabolism", + "pip2", + "ip3", + "ip4", + "calcium", + "agonist" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/inositolphosphatemetabolism/inositol-phosphate-metabolism.bngl", + "file": "inositol-phosphate-metabolism.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "insulin-glucose-homeostasis", + "name": "insulin glucose homeostasis", + "description": "Insulin-Glucose: Compartmentalized transport.", + "tags": [ + "insulin", + "glucose", + "homeostasis", + "ir", + "glut4", + "pancreas" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis.bngl", + "file": "insulin-glucose-homeostasis.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "interferon-signaling", + "name": "interferon signaling", + "description": "Rate Constants", + "tags": [ + "interferon", + "signaling", + "ifn", + "ifnar", + "tyk2", + "stat1" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/interferonsignaling/interferon-signaling.bngl", + "file": "interferon-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ire1a-xbp1-er-stress", + "name": "ire1a xbp1 er stress", + "description": "IRE1a/XBP1 ER Stress: Chaperone buffering and mRNA decay (RIDD).", + "tags": [ + "ire1a", + "xbp1", + "er", + "stress", + "ire1", + "bip", + "unfolded", + "ridd_target" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl", + "file": "ire1a-xbp1-er-stress.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "issue_198_short", + "name": "issue_198_short", + "description": "No description available", + "tags": [ + "validation", + "issue", + "198", + "short", + "a", + "b", + "c", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/issue198short/issue_198_short.bngl", + "file": "issue_198_short.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "jak-stat-cytokine-signaling", + "name": "jak stat cytokine signaling", + "description": "Rate Constants", + "tags": [ + "jak", + "stat", + "cytokine", + "signaling", + "receptor" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling.bngl", + "file": "jak-stat-cytokine-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Jaruszewicz-Blonska_2023", + "name": "Jaruszewicz 2023", + "description": "T-cell discrimination", + "tags": [ + "published", + "immunology", + "jaruszewicz", + "blonska", + "2023", + "ikk", + "ikba", + "ikba_mrna", + "a20", + "nfkb" + ], + "category": "immunology", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/JaruszewiczBlonska2023/Jaruszewicz-Blonska_2023.bngl", + "file": "Jaruszewicz-Blonska_2023.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "jnk-mapk-signaling", + "name": "jnk mapk signaling", + "description": "JNK MAPK Signaling: Scaffold-mediated activation and feedback.", + "tags": [ + "jnk", + "mapk", + "signaling", + "mkk7", + "jip1", + "v_dephos" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/jnkmapksignaling/jnk-mapk-signaling.bngl", + "file": "jnk-mapk-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "jobs_ground", + "name": "30-jobs", + "description": "NFsim simulation of the job market", + "tags": [ + "other" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/30-jobs/jobs_ground.bngl", + "file": "jobs_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "jobs_tofit", + "name": "30-jobs", + "description": "NFsim simulation of the job market", + "tags": [ + "other" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/30-jobs/jobs_tofit.bngl", + "file": "jobs_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Jung_2017", + "name": "Jung 2017", + "description": "M1 receptor signaling", + "tags": [ + "published", + "jung", + "2017", + "m1r", + "oxo", + "arrestin", + "mek", + "erk", + "perk", + "oxo_ec", + "pp2a" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience" + ], + "path": "Published/Jung2017/Jung_2017.bngl", + "file": "Jung_2017.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Kesseler_2013", + "name": "Kesseler 2013", + "description": "G2/Mitosis transition", + "tags": [ + "published", + "kesseler", + "2013", + "mpf", + "cdc25", + "wee1", + "myt1", + "pin1", + "pp2a", + "prox", + "e33" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "path": "Published/Kesseler2013/Kesseler_2013.bngl", + "file": "Kesseler_2013.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Kiefhaber_emodel", + "name": "Kiefhaber_emodel", + "description": "Allow molar units to be used for bimolecular rate constants", + "tags": [ + "validation", + "kiefhaber", + "emodel", + "setoption", + "l", + "p", + "s", + "a" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/Kiefhaberemodel/Kiefhaber_emodel.bngl", + "file": "Kiefhaber_emodel.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "kir-channel-regulation", + "name": "kir channel regulation", + "description": "Kir Channel Regulation: PIP2 modulation and G-protein potentiation.", + "tags": [ + "kir", + "channel", + "regulation", + "pip2", + "gbg", + "v_opening", + "v_gbg_factor" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/kirchannelregulation/kir-channel-regulation.bngl", + "file": "kir-channel-regulation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Kocieniewski_2012", + "name": "Kocieniewski 2012", + "description": "Actin dynamics", + "tags": [ + "published", + "kocieniewski", + "2012", + "map3k", + "map2k", + "mapk", + "scaff" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "path": "Published/Kocieniewski2012/Kocieniewski_2012.bngl", + "file": "Kocieniewski_2012.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Korwek_2023", + "name": "Korwek_2023", + "description": "This BioNetGen file features the article:", + "tags": [ + "validation", + "korwek", + "2023", + "polyic", + "rigi", + "mavs", + "pkr", + "oas3", + "rnasel", + "eif2a", + "rigi_mrna" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/Korwek2023/Korwek_2023.bngl", + "file": "Korwek_2023.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Kozer_2013", + "name": "Kozer 2013", + "description": "EGFR oligomerization", + "tags": [ + "published", + "kozer", + "2013", + "egf", + "egfr" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Kozer2013/Kozer_2013.bngl", + "file": "Kozer_2013.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Kozer_2014", + "name": "Kozer 2014", + "description": "Grb2-EGFR recruitment", + "tags": [ + "published", + "kozer", + "2014", + "egf", + "egfr", + "grb2" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Kozer2014/Kozer_2014.bngl", + "file": "Kozer_2014.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "l-type-calcium-channel-dynamics", + "name": "l type calcium channel dynamics", + "description": "L-type Calcium Channel: Voltage gating and CDI (Calcium-dependent inactivation).", + "tags": [ + "l", + "type", + "calcium", + "channel", + "dynamics", + "ltcc", + "voltage", + "v_open", + "v_inact" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics.bngl", + "file": "l-type-calcium-channel-dynamics.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "lac-operon-regulation", + "name": "lac operon regulation", + "description": "Kinetic Parameters", + "tags": [ + "lac", + "operon", + "regulation", + "laci", + "promoter", + "mrna", + "betagal", + "lactose", + "allolactose" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/lacoperonregulation/lac-operon-regulation.bngl", + "file": "lac-operon-regulation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Lang_2024", + "name": "Lang 2024", + "description": "Cell cycle regulation", + "tags": [ + "published", + "lang", + "2024", + "e2f", + "rb1", + "ppp2r2b", + "ccnb_promoter", + "ccna", + "ccna_promoter", + "foxm1_promoter", + "ensa_arpp19" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "path": "Published/Lang2024/Lang_2024.bngl", + "file": "Lang_2024.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Ligon_2014", + "name": "Ligon 2014", + "description": "Lipoplex delivery", + "tags": [ + "published", + "nfsim", + "ligon", + "2014", + "lext", + "pit", + "lint" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Ligon2014/Ligon_2014.bngl", + "file": "Ligon_2014.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "LilyIgE", + "name": "LilyIgE", + "description": "An example from a real application", + "tags": [ + "lilyige", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/LilyIgE/LilyIgE.bngl", + "file": "LilyIgE.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Lin_ERK_2019", + "name": "Lin 2019", + "description": "ERK signaling", + "tags": [ + "published", + "literature", + "signaling", + "lin", + "erk", + "2019", + "egfr", + "sos", + "ras", + "rasgap", + "raf", + "mek", + "ekar3" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "developmental" + ], + "path": "Published/LinERK2019/Lin_ERK_2019.bngl", + "file": "Lin_ERK_2019.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Lin_Prion_2019", + "name": "Lin 2019", + "description": "Prion replication", + "tags": [ + "published", + "literature", + "prion", + "lin", + "2019", + "prp", + "scaledupspecies1", + "scaledupspecies2", + "scaledupspecies15", + "scaledupspecies30" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "neuroscience" + ], + "path": "Published/LinPrion2019/Lin_Prion_2019.bngl", + "file": "Lin_Prion_2019.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Lin_TCR_2019", + "name": "Lin 2019", + "description": "TCR signaling", + "tags": [ + "published", + "literature", + "immune", + "lin", + "tcr", + "2019", + "pmhc", + "lck", + "shp", + "zap", + "mek", + "erk" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/LinTCR2019/Lin_TCR_2019.bngl", + "file": "Lin_TCR_2019.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "lipid-mediated-pip3-signaling", + "name": "lipid mediated pip3 signaling", + "description": "Kinetic Parameters", + "tags": [ + "lipid", + "mediated", + "pip3", + "signaling", + "pi3k", + "pip2", + "pten", + "pdk1" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl", + "file": "lipid-mediated-pip3-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Lisman", + "name": "Lisman", + "description": "title: auto.bngl", + "tags": [ + "lisman", + "k1", + "p", + "input", + "visualize", + "setparameter", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/Lisman/Lisman.bngl", + "file": "Lisman.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Lisman_bifurcate", + "name": "Lisman bifurcate", + "description": "title: Lisman_bifurcate.bngl", + "tags": [ + "lisman", + "bifurcate", + "k1", + "p" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/Lismanbifurcate/Lisman_bifurcate.bngl", + "file": "Lisman_bifurcate.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "localfunc", + "name": "localfunc", + "description": "Test local function expansion", + "tags": [ + "validation", + "localfunc", + "a", + "b", + "c", + "trash", + "f_synth" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/localfunc/localfunc.bngl", + "file": "localfunc.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "LR", + "name": "LR", + "description": "title: LR.bngl", + "tags": [ + "lr", + "l", + "r", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/LR/LR.bngl", + "file": "LR.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "LR_comp", + "name": "LR comp", + "description": "title: LR_comp.bngl", + "tags": [ + "lr", + "comp", + "l", + "r", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/LRcomp/LR_comp.bngl", + "file": "LR_comp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "LRR", + "name": "LRR", + "description": "title: LRR.bngl", + "tags": [ + "lrr", + "l", + "r" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/LRR/LRR.bngl", + "file": "LRR.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "LRR_comp", + "name": "LRR comp", + "description": "title: LRR_comp.bngl", + "tags": [ + "lrr", + "comp", + "l", + "r", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/LRRcomp/LRR_comp.bngl", + "file": "LRR_comp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "LV", + "name": "LV", + "description": "title: LV.bgl", + "tags": [ + "lv", + "s", + "w", + "generate_network", + "writesbml", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/LV/LV.bngl", + "file": "LV.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "LV_comp", + "name": "LV comp", + "description": "title: LV_comp.bgl", + "tags": [ + "lv", + "comp", + "k2", + "s", + "w" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/LVcomp/LV_comp.bngl", + "file": "LV_comp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "m1", + "name": "of a 3-step signaling cascade", + "description": "Toy model of a 3-step signaling cascade", + "tags": [ + "k1", + "k2", + "k3", + "ainit", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/05-threestep/m1.bngl", + "file": "m1.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "m1_ground", + "name": "of a 3-step signaling cascade", + "description": "Toy model of a 3-step signaling cascade", + "tags": [ + "k1", + "k2", + "k3", + "ainit", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/05-threestep/m1_ground.bngl", + "file": "m1_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "machine_tofit", + "name": "translated into BNGL", + "description": "Ensemble model translated into BNGL", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/28-mapk/machine_tofit.bngl", + "file": "machine_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Macken_1982", + "name": "Macken 1982", + "description": "TLBR solution macken 1982", + "tags": [ + "published", + "physics", + "macken", + "1982" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "path": "Published/Macken1982/tlbr_solution_macken1982.bngl", + "file": "tlbr_solution_macken1982.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Mallela2021_Cities", + "name": "Mallela 2021 - COVID-19 City Models", + "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", + "tags": [ + "covid-19", + "epidemiology", + "parameter-estimation", + "pybionetgen" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/Mallela2021_Cities/Beantown_m11.bngl", + "file": "Beantown_m11.bngl", + "collectionId": "Mallela2021_Cities", + "collection": { + "type": "geographic-variants", + "count": 15, + "variant_key": "city", + "variants": [ + { + "id": "Beantown_m11", + "file": "Beantown_m11.bngl" + }, + { + "id": "BigApple_m1", + "file": "BigApple_m1.bngl" + }, + { + "id": "BigD_m4", + "file": "BigD_m4.bngl" + }, + { + "id": "BrotherlyLove_m8", + "file": "BrotherlyLove_m8.bngl" + }, + { + "id": "DC_m6", + "file": "DC_m6.bngl" + }, + { + "id": "EmeraldCity_m15", + "file": "EmeraldCity_m15.bngl" + }, + { + "id": "Frisco_m12", + "file": "Frisco_m12.bngl" + }, + { + "id": "HTown_m5", + "file": "HTown_m5.bngl" + }, + { + "id": "Hotlanta_m9", + "file": "Hotlanta_m9.bngl" + }, + { + "id": "InlandEmpire_m13", + "file": "InlandEmpire_m13.bngl" + }, + { + "id": "LaLaLand_m2", + "file": "LaLaLand_m2.bngl" + }, + { + "id": "MagicCity_m7", + "file": "MagicCity_m7.bngl" + }, + { + "id": "MotorCity_m14", + "file": "MotorCity_m14.bngl" + }, + { + "id": "Valley_of_the_Sun_m10", + "file": "Valley_of_the_Sun_m10.bngl" + }, + { + "id": "WindyCity_m3", + "file": "WindyCity_m3.bngl" + } + ] + }, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Mallela2021_States", + "name": "Mallela 2021 - COVID-19 State-Level Models", + "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", + "tags": [ + "covid-19", + "epidemiology", + "parameter-estimation", + "pybionetgen" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/Mallela2021/SI_files_Alabama_Alabama.bngl", + "file": "SI_files_Alabama_Alabama.bngl", + "collectionId": "Mallela2021_States", + "collection": { + "type": "geographic-variants", + "count": 50, + "variant_key": "us_state", + "variants": [ + { + "id": "SI_files_Alabama_Alabama", + "file": "SI_files_Alabama_Alabama.bngl" + }, + { + "id": "SI_files_Alaska_Alaska", + "file": "SI_files_Alaska_Alaska.bngl" + }, + { + "id": "SI_files_Arizona_Arizona", + "file": "SI_files_Arizona_Arizona.bngl" + }, + { + "id": "SI_files_Arkansas_Arkansas", + "file": "SI_files_Arkansas_Arkansas.bngl" + }, + { + "id": "SI_files_California_California", + "file": "SI_files_California_California.bngl" + }, + { + "id": "SI_files_Colorado_Colorado", + "file": "SI_files_Colorado_Colorado.bngl" + }, + { + "id": "SI_files_Connecticut_Connecticut", + "file": "SI_files_Connecticut_Connecticut.bngl" + }, + { + "id": "SI_files_Delaware_Delaware", + "file": "SI_files_Delaware_Delaware.bngl" + }, + { + "id": "SI_files_Florida_Florida", + "file": "SI_files_Florida_Florida.bngl" + }, + { + "id": "SI_files_Georgia_Georgia", + "file": "SI_files_Georgia_Georgia.bngl" + }, + { + "id": "SI_files_Hawaii_Hawaii", + "file": "SI_files_Hawaii_Hawaii.bngl" + }, + { + "id": "SI_files_Idaho_Idaho", + "file": "SI_files_Idaho_Idaho.bngl" + }, + { + "id": "SI_files_Illinois_Illinois", + "file": "SI_files_Illinois_Illinois.bngl" + }, + { + "id": "SI_files_Indiana_Indiana", + "file": "SI_files_Indiana_Indiana.bngl" + }, + { + "id": "SI_files_Iowa_Iowa", + "file": "SI_files_Iowa_Iowa.bngl" + }, + { + "id": "SI_files_Kansas_Kansas", + "file": "SI_files_Kansas_Kansas.bngl" + }, + { + "id": "SI_files_Kentucky_Kentucky", + "file": "SI_files_Kentucky_Kentucky.bngl" + }, + { + "id": "SI_files_Louisiana_Louisiana", + "file": "SI_files_Louisiana_Louisiana.bngl" + }, + { + "id": "SI_files_Maine_Maine", + "file": "SI_files_Maine_Maine.bngl" + }, + { + "id": "SI_files_Maryland_Maryland", + "file": "SI_files_Maryland_Maryland.bngl" + }, + { + "id": "SI_files_Massachusetts_Massachusetts", + "file": "SI_files_Massachusetts_Massachusetts.bngl" + }, + { + "id": "SI_files_Michigan_Michigan", + "file": "SI_files_Michigan_Michigan.bngl" + }, + { + "id": "SI_files_Minnesota_Minnesota", + "file": "SI_files_Minnesota_Minnesota.bngl" + }, + { + "id": "SI_files_Mississippi_Mississippi", + "file": "SI_files_Mississippi_Mississippi.bngl" + }, + { + "id": "SI_files_Missouri_Missouri", + "file": "SI_files_Missouri_Missouri.bngl" + }, + { + "id": "SI_files_Montana_Montana", + "file": "SI_files_Montana_Montana.bngl" + }, + { + "id": "SI_files_Nebraska_Nebraska", + "file": "SI_files_Nebraska_Nebraska.bngl" + }, + { + "id": "SI_files_Nevada_Nevada", + "file": "SI_files_Nevada_Nevada.bngl" + }, + { + "id": "SI_files_NewHampshire_NewHampshire", + "file": "SI_files_NewHampshire_NewHampshire.bngl" + }, + { + "id": "SI_files_NewJersey_NewJersey", + "file": "SI_files_NewJersey_NewJersey.bngl" + }, + { + "id": "SI_files_NewMexico_NewMexico", + "file": "SI_files_NewMexico_NewMexico.bngl" + }, + { + "id": "SI_files_NewYork_NewYork", + "file": "SI_files_NewYork_NewYork.bngl" + }, + { + "id": "SI_files_NorthCarolina_NorthCarolina", + "file": "SI_files_NorthCarolina_NorthCarolina.bngl" + }, + { + "id": "SI_files_NorthDakota_NorthDakota", + "file": "SI_files_NorthDakota_NorthDakota.bngl" + }, + { + "id": "SI_files_Ohio_Ohio", + "file": "SI_files_Ohio_Ohio.bngl" + }, + { + "id": "SI_files_Oklahoma_Oklahoma", + "file": "SI_files_Oklahoma_Oklahoma.bngl" + }, + { + "id": "SI_files_Oregon_Oregon", + "file": "SI_files_Oregon_Oregon.bngl" + }, + { + "id": "SI_files_Pennsylvania_Pennsylvania", + "file": "SI_files_Pennsylvania_Pennsylvania.bngl" + }, + { + "id": "SI_files_RhodeIsland_RhodeIsland", + "file": "SI_files_RhodeIsland_RhodeIsland.bngl" + }, + { + "id": "SI_files_SouthCarolina_SouthCarolina", + "file": "SI_files_SouthCarolina_SouthCarolina.bngl" + }, + { + "id": "SI_files_SouthDakota_SouthDakota", + "file": "SI_files_SouthDakota_SouthDakota.bngl" + }, + { + "id": "SI_files_Tennessee_Tennessee", + "file": "SI_files_Tennessee_Tennessee.bngl" + }, + { + "id": "SI_files_Texas_Texas", + "file": "SI_files_Texas_Texas.bngl" + }, + { + "id": "SI_files_Utah_Utah", + "file": "SI_files_Utah_Utah.bngl" + }, + { + "id": "SI_files_Vermont_Vermont", + "file": "SI_files_Vermont_Vermont.bngl" + }, + { + "id": "SI_files_Virginia_Virginia", + "file": "SI_files_Virginia_Virginia.bngl" + }, + { + "id": "SI_files_Washington_Washington", + "file": "SI_files_Washington_Washington.bngl" + }, + { + "id": "SI_files_WestVirginia_WestVirginia", + "file": "SI_files_WestVirginia_WestVirginia.bngl" + }, + { + "id": "SI_files_Wisconsin_Wisconsin", + "file": "SI_files_Wisconsin_Wisconsin.bngl" + }, + { + "id": "SI_files_Wyoming_Wyoming", + "file": "SI_files_Wyoming_Wyoming.bngl" + } + ] + }, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Mallela2022_MSAs", + "name": "Mallela 2022 - COVID-19 MSA Models", + "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", + "tags": [ + "covid-19", + "epidemiology", + "parameter-estimation", + "pybionetgen" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/Mallela2022_MSAs/Abilene_TX_Abilene_TX.bngl", + "file": "Abilene_TX_Abilene_TX.bngl", + "collectionId": "Mallela2022_MSAs", + "collection": { + "type": "geographic-variants", + "count": 281, + "variant_key": "metropolitan_area", + "variants": [ + { + "id": "Abilene_TX_Abilene_TX", + "file": "Abilene_TX_Abilene_TX.bngl" + }, + { + "id": "Akron_OH_Akron_OH", + "file": "Akron_OH_Akron_OH.bngl" + }, + { + "id": "Albany-Schenectady-Troy_NY_Albany-Schenectady-Troy_NY", + "file": "Albany-Schenectady-Troy_NY_Albany-Schenectady-Troy_NY.bngl" + }, + { + "id": "Albany_GA_Albany_GA", + "file": "Albany_GA_Albany_GA.bngl" + }, + { + "id": "Albuquerque_NM_Albuquerque_NM", + "file": "Albuquerque_NM_Albuquerque_NM.bngl" + }, + { + "id": "Alexandria_LA_Alexandria_LA", + "file": "Alexandria_LA_Alexandria_LA.bngl" + }, + { + "id": "Allentown-Bethlehem-Easton_PA-NJ_Allentown-Bethlehem-Easton_PA-NJ", + "file": "Allentown-Bethlehem-Easton_PA-NJ_Allentown-Bethlehem-Easton_PA-NJ.bngl" + }, + { + "id": "Amarillo_TX_Amarillo_TX", + "file": "Amarillo_TX_Amarillo_TX.bngl" + }, + { + "id": "Anchorage_AK_Anchorage_AK", + "file": "Anchorage_AK_Anchorage_AK.bngl" + }, + { + "id": "Ann_Arbor_MI_Ann_Arbor_MI", + "file": "Ann_Arbor_MI_Ann_Arbor_MI.bngl" + }, + { + "id": "Appleton_WI_Appleton_WI", + "file": "Appleton_WI_Appleton_WI.bngl" + }, + { + "id": "Asheville_NC_Asheville_NC", + "file": "Asheville_NC_Asheville_NC.bngl" + }, + { + "id": "Athens-Clarke_County_GA_Athens-Clarke_County_GA", + "file": "Athens-Clarke_County_GA_Athens-Clarke_County_GA.bngl" + }, + { + "id": "Atlanta-Sandy_Springs-Alpharetta_GA_Atlanta-Sandy_Springs-Alpharetta_GA", + "file": "Atlanta-Sandy_Springs-Alpharetta_GA_Atlanta-Sandy_Springs-Alpharetta_GA.bngl" + }, + { + "id": "Atlantic_City-Hammonton_NJ_Atlantic_City-Hammonton_NJ", + "file": "Atlantic_City-Hammonton_NJ_Atlantic_City-Hammonton_NJ.bngl" + }, + { + "id": "Auburn-Opelika_AL_Auburn-Opelika_AL", + "file": "Auburn-Opelika_AL_Auburn-Opelika_AL.bngl" + }, + { + "id": "Augusta-Richmond_County_GA-SC_Augusta-Richmond_County_GA-SC", + "file": "Augusta-Richmond_County_GA-SC_Augusta-Richmond_County_GA-SC.bngl" + }, + { + "id": "Austin-Round_Rock_TX_Austin-Round_Rock_TX", + "file": "Austin-Round_Rock_TX_Austin-Round_Rock_TX.bngl" + }, + { + "id": "Bakersfield_CA_Bakersfield_CA", + "file": "Bakersfield_CA_Bakersfield_CA.bngl" + }, + { + "id": "Baltimore-Columbia-Towson_MD_Baltimore-Columbia-Towson_MD", + "file": "Baltimore-Columbia-Towson_MD_Baltimore-Columbia-Towson_MD.bngl" + }, + { + "id": "Barnstable_Town_MA_Barnstable_Town_MA", + "file": "Barnstable_Town_MA_Barnstable_Town_MA.bngl" + }, + { + "id": "Baton_Rouge_LA_Baton_Rouge_LA", + "file": "Baton_Rouge_LA_Baton_Rouge_LA.bngl" + }, + { + "id": "Battle_Creek_MI_Battle_Creek_MI", + "file": "Battle_Creek_MI_Battle_Creek_MI.bngl" + }, + { + "id": "Bay_City_MI_Bay_City_MI", + "file": "Bay_City_MI_Bay_City_MI.bngl" + }, + { + "id": "Beaumont-Port_Arthur_TX_Beaumont-Port_Arthur_TX", + "file": "Beaumont-Port_Arthur_TX_Beaumont-Port_Arthur_TX.bngl" + }, + { + "id": "Bellingham_WA_Bellingham_WA", + "file": "Bellingham_WA_Bellingham_WA.bngl" + }, + { + "id": "Binghamton_NY_Binghamton_NY", + "file": "Binghamton_NY_Binghamton_NY.bngl" + }, + { + "id": "Birmingham-Hoover_AL_Birmingham-Hoover_AL", + "file": "Birmingham-Hoover_AL_Birmingham-Hoover_AL.bngl" + }, + { + "id": "Bloomington_IN_Bloomington_IN", + "file": "Bloomington_IN_Bloomington_IN.bngl" + }, + { + "id": "Bloomsburg-Berwick_PA_Bloomsburg-Berwick_PA", + "file": "Bloomsburg-Berwick_PA_Bloomsburg-Berwick_PA.bngl" + }, + { + "id": "Boise_City_ID_Boise_City_ID", + "file": "Boise_City_ID_Boise_City_ID.bngl" + }, + { + "id": "Boston-Cambridge-Newton_MA-NH_Boston-Cambridge-Newton_MA-NH", + "file": "Boston-Cambridge-Newton_MA-NH_Boston-Cambridge-Newton_MA-NH.bngl" + }, + { + "id": "Boulder_CO_Boulder_CO", + "file": "Boulder_CO_Boulder_CO.bngl" + }, + { + "id": "Bowling_Green_KY_Bowling_Green_KY", + "file": "Bowling_Green_KY_Bowling_Green_KY.bngl" + }, + { + "id": "Bridgeport-Stamford-Norwalk_CT_Bridgeport-Stamford-Norwalk_CT", + "file": "Bridgeport-Stamford-Norwalk_CT_Bridgeport-Stamford-Norwalk_CT.bngl" + }, + { + "id": "Brownsville-Harlingen_TX_Brownsville-Harlingen_TX", + "file": "Brownsville-Harlingen_TX_Brownsville-Harlingen_TX.bngl" + }, + { + "id": "Buffalo-Niagara_Falls_NY_Buffalo-Niagara_Falls_NY", + "file": "Buffalo-Niagara_Falls_NY_Buffalo-Niagara_Falls_NY.bngl" + }, + { + "id": "Burlington-South_Burlington_VT_Burlington-South_Burlington_VT", + "file": "Burlington-South_Burlington_VT_Burlington-South_Burlington_VT.bngl" + }, + { + "id": "Burlington_NC_Burlington_NC", + "file": "Burlington_NC_Burlington_NC.bngl" + }, + { + "id": "California-Lexington_Park_MD_California-Lexington_Park_MD", + "file": "California-Lexington_Park_MD_California-Lexington_Park_MD.bngl" + }, + { + "id": "Canton-Massillon_OH_Canton-Massillon_OH", + "file": "Canton-Massillon_OH_Canton-Massillon_OH.bngl" + }, + { + "id": "Cape_Coral-Fort_Myers_FL_Cape_Coral-Fort_Myers_FL", + "file": "Cape_Coral-Fort_Myers_FL_Cape_Coral-Fort_Myers_FL.bngl" + }, + { + "id": "Carbondale-Marion_IL_Carbondale-Marion_IL", + "file": "Carbondale-Marion_IL_Carbondale-Marion_IL.bngl" + }, + { + "id": "Cedar_Rapids_IA_Cedar_Rapids_IA", + "file": "Cedar_Rapids_IA_Cedar_Rapids_IA.bngl" + }, + { + "id": "Chambersburg-Waynesboro_PA_Chambersburg-Waynesboro_PA", + "file": "Chambersburg-Waynesboro_PA_Chambersburg-Waynesboro_PA.bngl" + }, + { + "id": "Champaign-Urbana_IL_Champaign-Urbana_IL", + "file": "Champaign-Urbana_IL_Champaign-Urbana_IL.bngl" + }, + { + "id": "Charleston-North_Charleston_SC_Charleston-North_Charleston_SC", + "file": "Charleston-North_Charleston_SC_Charleston-North_Charleston_SC.bngl" + }, + { + "id": "Charleston_WV_Charleston_WV", + "file": "Charleston_WV_Charleston_WV.bngl" + }, + { + "id": "Charlotte-Concord-Gastonia_NC-SC_Charlotte-Concord-Gastonia_NC-SC", + "file": "Charlotte-Concord-Gastonia_NC-SC_Charlotte-Concord-Gastonia_NC-SC.bngl" + }, + { + "id": "Charlottesville_VA_Charlottesville_VA", + "file": "Charlottesville_VA_Charlottesville_VA.bngl" + }, + { + "id": "Chattanooga_TN-GA_Chattanooga_TN-GA", + "file": "Chattanooga_TN-GA_Chattanooga_TN-GA.bngl" + }, + { + "id": "Chicago-Naperville-Elgin_IL-IN-WI_Chicago-Naperville-Elgin_IL-IN-WI", + "file": "Chicago-Naperville-Elgin_IL-IN-WI_Chicago-Naperville-Elgin_IL-IN-WI.bngl" + }, + { + "id": "Cincinnati_OH-KY-IN_Cincinnati_OH-KY-IN", + "file": "Cincinnati_OH-KY-IN_Cincinnati_OH-KY-IN.bngl" + }, + { + "id": "Clarksville_TN-KY_Clarksville_TN-KY", + "file": "Clarksville_TN-KY_Clarksville_TN-KY.bngl" + }, + { + "id": "Cleveland-Elyria_OH_Cleveland-Elyria_OH", + "file": "Cleveland-Elyria_OH_Cleveland-Elyria_OH.bngl" + }, + { + "id": "College_Station-Bryan_TX_College_Station-Bryan_TX", + "file": "College_Station-Bryan_TX_College_Station-Bryan_TX.bngl" + }, + { + "id": "Colorado_Springs_CO_Colorado_Springs_CO", + "file": "Colorado_Springs_CO_Colorado_Springs_CO.bngl" + }, + { + "id": "Columbia_SC_Columbia_SC", + "file": "Columbia_SC_Columbia_SC.bngl" + }, + { + "id": "Columbus_GA-AL_Columbus_GA-AL", + "file": "Columbus_GA-AL_Columbus_GA-AL.bngl" + }, + { + "id": "Columbus_IN_Columbus_IN", + "file": "Columbus_IN_Columbus_IN.bngl" + }, + { + "id": "Columbus_OH_Columbus_OH", + "file": "Columbus_OH_Columbus_OH.bngl" + }, + { + "id": "Corpus_Christi_TX_Corpus_Christi_TX", + "file": "Corpus_Christi_TX_Corpus_Christi_TX.bngl" + }, + { + "id": "Crestview-Fort_Walton_Beach-Destin_FL_Crestview-Fort_Walton_Beach-Destin_FL", + "file": "Crestview-Fort_Walton_Beach-Destin_FL_Crestview-Fort_Walton_Beach-Destin_FL.bngl" + }, + { + "id": "Cumberland_MD-WV_Cumberland_MD-WV", + "file": "Cumberland_MD-WV_Cumberland_MD-WV.bngl" + }, + { + "id": "Dallas-Fort_Worth-Arlington_TX_Dallas-Fort_Worth-Arlington_TX", + "file": "Dallas-Fort_Worth-Arlington_TX_Dallas-Fort_Worth-Arlington_TX.bngl" + }, + { + "id": "Dalton_GA_Dalton_GA", + "file": "Dalton_GA_Dalton_GA.bngl" + }, + { + "id": "Daphne-Fairhope-Foley_AL_Daphne-Fairhope-Foley_AL", + "file": "Daphne-Fairhope-Foley_AL_Daphne-Fairhope-Foley_AL.bngl" + }, + { + "id": "Davenport-Moline-Rock_Island_IA-IL_Davenport-Moline-Rock_Island_IA-IL", + "file": "Davenport-Moline-Rock_Island_IA-IL_Davenport-Moline-Rock_Island_IA-IL.bngl" + }, + { + "id": "Dayton_OH_Dayton_OH", + "file": "Dayton_OH_Dayton_OH.bngl" + }, + { + "id": "Deltona-Daytona_Beach-Ormond_Beach_FL_Deltona-Daytona_Beach-Ormond_Beach_FL", + "file": "Deltona-Daytona_Beach-Ormond_Beach_FL_Deltona-Daytona_Beach-Ormond_Beach_FL.bngl" + }, + { + "id": "Denver-Aurora-Lakewood_CO_Denver-Aurora-Lakewood_CO", + "file": "Denver-Aurora-Lakewood_CO_Denver-Aurora-Lakewood_CO.bngl" + }, + { + "id": "Des_Moines-West_Des_Moines_IA_Des_Moines-West_Des_Moines_IA", + "file": "Des_Moines-West_Des_Moines_IA_Des_Moines-West_Des_Moines_IA.bngl" + }, + { + "id": "Detroit-Warren-Dearborn_MI_Detroit-Warren-Dearborn_MI", + "file": "Detroit-Warren-Dearborn_MI_Detroit-Warren-Dearborn_MI.bngl" + }, + { + "id": "Detroit_Warren_Dearborn_MI_Detroit_Warren_Dearborn_MI", + "file": "Detroit_Warren_Dearborn_MI_Detroit_Warren_Dearborn_MI.bngl" + }, + { + "id": "Dothan_AL_Dothan_AL", + "file": "Dothan_AL_Dothan_AL.bngl" + }, + { + "id": "Dover_DE_Dover_DE", + "file": "Dover_DE_Dover_DE.bngl" + }, + { + "id": "Dubuque_IA_Dubuque_IA", + "file": "Dubuque_IA_Dubuque_IA.bngl" + }, + { + "id": "Durham-Chapel_Hill_NC_Durham-Chapel_Hill_NC", + "file": "Durham-Chapel_Hill_NC_Durham-Chapel_Hill_NC.bngl" + }, + { + "id": "East_Stroudsburg_PA_East_Stroudsburg_PA", + "file": "East_Stroudsburg_PA_East_Stroudsburg_PA.bngl" + }, + { + "id": "El_Centro_CA_El_Centro_CA", + "file": "El_Centro_CA_El_Centro_CA.bngl" + }, + { + "id": "El_Paso_TX_El_Paso_TX", + "file": "El_Paso_TX_El_Paso_TX.bngl" + }, + { + "id": "Elkhart-Goshen_IN_Elkhart-Goshen_IN", + "file": "Elkhart-Goshen_IN_Elkhart-Goshen_IN.bngl" + }, + { + "id": "Evansville_IN-KY_Evansville_IN-KY", + "file": "Evansville_IN-KY_Evansville_IN-KY.bngl" + }, + { + "id": "Fargo_ND-MN_Fargo_ND-MN", + "file": "Fargo_ND-MN_Fargo_ND-MN.bngl" + }, + { + "id": "Farmington_NM_Farmington_NM", + "file": "Farmington_NM_Farmington_NM.bngl" + }, + { + "id": "Fayetteville-Springdale-Rogers_AR_Fayetteville-Springdale-Rogers_AR", + "file": "Fayetteville-Springdale-Rogers_AR_Fayetteville-Springdale-Rogers_AR.bngl" + }, + { + "id": "Fayetteville_NC_Fayetteville_NC", + "file": "Fayetteville_NC_Fayetteville_NC.bngl" + }, + { + "id": "Flagstaff_AZ_Flagstaff_AZ", + "file": "Flagstaff_AZ_Flagstaff_AZ.bngl" + }, + { + "id": "Flint_MI_Flint_MI", + "file": "Flint_MI_Flint_MI.bngl" + }, + { + "id": "Florence-Muscle_Shoals_AL_Florence-Muscle_Shoals_AL", + "file": "Florence-Muscle_Shoals_AL_Florence-Muscle_Shoals_AL.bngl" + }, + { + "id": "Florence_SC_Florence_SC", + "file": "Florence_SC_Florence_SC.bngl" + }, + { + "id": "Fort_Collins_CO_Fort_Collins_CO", + "file": "Fort_Collins_CO_Fort_Collins_CO.bngl" + }, + { + "id": "Fort_Wayne_IN_Fort_Wayne_IN", + "file": "Fort_Wayne_IN_Fort_Wayne_IN.bngl" + }, + { + "id": "Fresno_CA_Fresno_CA", + "file": "Fresno_CA_Fresno_CA.bngl" + }, + { + "id": "Gadsden_AL_Gadsden_AL", + "file": "Gadsden_AL_Gadsden_AL.bngl" + }, + { + "id": "Gainesville_FL_Gainesville_FL", + "file": "Gainesville_FL_Gainesville_FL.bngl" + }, + { + "id": "Gainesville_GA_Gainesville_GA", + "file": "Gainesville_GA_Gainesville_GA.bngl" + }, + { + "id": "Glens_Falls_NY_Glens_Falls_NY", + "file": "Glens_Falls_NY_Glens_Falls_NY.bngl" + }, + { + "id": "Goldsboro_NC_Goldsboro_NC", + "file": "Goldsboro_NC_Goldsboro_NC.bngl" + }, + { + "id": "Grand_Forks_ND-MN_Grand_Forks_ND-MN", + "file": "Grand_Forks_ND-MN_Grand_Forks_ND-MN.bngl" + }, + { + "id": "Grand_Island_NE_Grand_Island_NE", + "file": "Grand_Island_NE_Grand_Island_NE.bngl" + }, + { + "id": "Grand_Rapids-Kentwood_MI_Grand_Rapids-Kentwood_MI", + "file": "Grand_Rapids-Kentwood_MI_Grand_Rapids-Kentwood_MI.bngl" + }, + { + "id": "Greeley_CO_Greeley_CO", + "file": "Greeley_CO_Greeley_CO.bngl" + }, + { + "id": "Green_Bay_WI_Green_Bay_WI", + "file": "Green_Bay_WI_Green_Bay_WI.bngl" + }, + { + "id": "Greensboro-High_Point_NC_Greensboro-High_Point_NC", + "file": "Greensboro-High_Point_NC_Greensboro-High_Point_NC.bngl" + }, + { + "id": "Greenville-Anderson_SC_Greenville-Anderson_SC", + "file": "Greenville-Anderson_SC_Greenville-Anderson_SC.bngl" + }, + { + "id": "Greenville_NC_Greenville_NC", + "file": "Greenville_NC_Greenville_NC.bngl" + }, + { + "id": "Gulfport-Biloxi_MS_Gulfport-Biloxi_MS", + "file": "Gulfport-Biloxi_MS_Gulfport-Biloxi_MS.bngl" + }, + { + "id": "Hagerstown-Martinsburg_MD-WV_Hagerstown-Martinsburg_MD-WV", + "file": "Hagerstown-Martinsburg_MD-WV_Hagerstown-Martinsburg_MD-WV.bngl" + }, + { + "id": "Hammond_LA_Hammond_LA", + "file": "Hammond_LA_Hammond_LA.bngl" + }, + { + "id": "Hanford-Corcoran_CA_Hanford-Corcoran_CA", + "file": "Hanford-Corcoran_CA_Hanford-Corcoran_CA.bngl" + }, + { + "id": "Harrisburg-Carlisle_PA_Harrisburg-Carlisle_PA", + "file": "Harrisburg-Carlisle_PA_Harrisburg-Carlisle_PA.bngl" + }, + { + "id": "Harrisonburg_VA_Harrisonburg_VA", + "file": "Harrisonburg_VA_Harrisonburg_VA.bngl" + }, + { + "id": "Hartford-East_Hartford-Middletown_CT_Hartford-East_Hartford-Middletown_CT", + "file": "Hartford-East_Hartford-Middletown_CT_Hartford-East_Hartford-Middletown_CT.bngl" + }, + { + "id": "Hattiesburg_MS_Hattiesburg_MS", + "file": "Hattiesburg_MS_Hattiesburg_MS.bngl" + }, + { + "id": "Hickory-Lenoir-Morganton_NC_Hickory-Lenoir-Morganton_NC", + "file": "Hickory-Lenoir-Morganton_NC_Hickory-Lenoir-Morganton_NC.bngl" + }, + { + "id": "Hilton_Head_Island-Bluffton-Beaufort_SC_Hilton_Head_Island-Bluffton-Beaufort_SC", + "file": "Hilton_Head_Island-Bluffton-Beaufort_SC_Hilton_Head_Island-Bluffton-Beaufort_SC.bngl" + }, + { + "id": "Houma-Thibodaux_LA_Houma-Thibodaux_LA", + "file": "Houma-Thibodaux_LA_Houma-Thibodaux_LA.bngl" + }, + { + "id": "Houston-The_Woodlands-Sugar_Land_TX_Houston-The_Woodlands-Sugar_Land_TX", + "file": "Houston-The_Woodlands-Sugar_Land_TX_Houston-The_Woodlands-Sugar_Land_TX.bngl" + }, + { + "id": "Huntington-Ashland_WV-KY-OH_Huntington-Ashland_WV-KY-OH", + "file": "Huntington-Ashland_WV-KY-OH_Huntington-Ashland_WV-KY-OH.bngl" + }, + { + "id": "Huntsville_AL_Huntsville_AL", + "file": "Huntsville_AL_Huntsville_AL.bngl" + }, + { + "id": "Indianapolis-Carmel-Anderson_IN_Indianapolis-Carmel-Anderson_IN", + "file": "Indianapolis-Carmel-Anderson_IN_Indianapolis-Carmel-Anderson_IN.bngl" + }, + { + "id": "Iowa_City_IA_Iowa_City_IA", + "file": "Iowa_City_IA_Iowa_City_IA.bngl" + }, + { + "id": "Jackson_MI_Jackson_MI", + "file": "Jackson_MI_Jackson_MI.bngl" + }, + { + "id": "Jackson_MS_Jackson_MS", + "file": "Jackson_MS_Jackson_MS.bngl" + }, + { + "id": "Jacksonville_FL_Jacksonville_FL", + "file": "Jacksonville_FL_Jacksonville_FL.bngl" + }, + { + "id": "Janesville-Beloit_WI_Janesville-Beloit_WI", + "file": "Janesville-Beloit_WI_Janesville-Beloit_WI.bngl" + }, + { + "id": "Kalamazoo-Portage_MI_Kalamazoo-Portage_MI", + "file": "Kalamazoo-Portage_MI_Kalamazoo-Portage_MI.bngl" + }, + { + "id": "Kankakee_IL_Kankakee_IL", + "file": "Kankakee_IL_Kankakee_IL.bngl" + }, + { + "id": "Kansas_City_MO-KS_Kansas_City_MO-KS", + "file": "Kansas_City_MO-KS_Kansas_City_MO-KS.bngl" + }, + { + "id": "Kennewick-Richland_WA_Kennewick-Richland_WA", + "file": "Kennewick-Richland_WA_Kennewick-Richland_WA.bngl" + }, + { + "id": "Killeen-Temple_TX_Killeen-Temple_TX", + "file": "Killeen-Temple_TX_Killeen-Temple_TX.bngl" + }, + { + "id": "Kingston_NY_Kingston_NY", + "file": "Kingston_NY_Kingston_NY.bngl" + }, + { + "id": "Knoxville_TN_Knoxville_TN", + "file": "Knoxville_TN_Knoxville_TN.bngl" + }, + { + "id": "Kokomo_IN_Kokomo_IN", + "file": "Kokomo_IN_Kokomo_IN.bngl" + }, + { + "id": "Lafayette-West_Lafayette_IN_Lafayette-West_Lafayette_IN", + "file": "Lafayette-West_Lafayette_IN_Lafayette-West_Lafayette_IN.bngl" + }, + { + "id": "Lafayette_LA_Lafayette_LA", + "file": "Lafayette_LA_Lafayette_LA.bngl" + }, + { + "id": "Lake_Charles_LA_Lake_Charles_LA", + "file": "Lake_Charles_LA_Lake_Charles_LA.bngl" + }, + { + "id": "Lake_Havasu_City-Kingman_AZ_Lake_Havasu_City-Kingman_AZ", + "file": "Lake_Havasu_City-Kingman_AZ_Lake_Havasu_City-Kingman_AZ.bngl" + }, + { + "id": "Lakeland-Winter_Haven_FL_Lakeland-Winter_Haven_FL", + "file": "Lakeland-Winter_Haven_FL_Lakeland-Winter_Haven_FL.bngl" + }, + { + "id": "Lancaster_PA_Lancaster_PA", + "file": "Lancaster_PA_Lancaster_PA.bngl" + }, + { + "id": "Lansing-East_Lansing_MI_Lansing-East_Lansing_MI", + "file": "Lansing-East_Lansing_MI_Lansing-East_Lansing_MI.bngl" + }, + { + "id": "Laredo_TX_Laredo_TX", + "file": "Laredo_TX_Laredo_TX.bngl" + }, + { + "id": "Las_Cruces_NM_Las_Cruces_NM", + "file": "Las_Cruces_NM_Las_Cruces_NM.bngl" + }, + { + "id": "Las_Vegas-Henderson-Paradise_NV_Las_Vegas-Henderson-Paradise_NV", + "file": "Las_Vegas-Henderson-Paradise_NV_Las_Vegas-Henderson-Paradise_NV.bngl" + }, + { + "id": "Lawton_OK_Lawton_OK", + "file": "Lawton_OK_Lawton_OK.bngl" + }, + { + "id": "Lebanon_PA_Lebanon_PA", + "file": "Lebanon_PA_Lebanon_PA.bngl" + }, + { + "id": "Lexington-Fayette_KY_Lexington-Fayette_KY", + "file": "Lexington-Fayette_KY_Lexington-Fayette_KY.bngl" + }, + { + "id": "Lincoln_NE_Lincoln_NE", + "file": "Lincoln_NE_Lincoln_NE.bngl" + }, + { + "id": "Little_Rock-North_Little_Rock-Conway_AR_Little_Rock-North_Little_Rock-Conway_AR", + "file": "Little_Rock-North_Little_Rock-Conway_AR_Little_Rock-North_Little_Rock-Conway_AR.bngl" + }, + { + "id": "Longview_TX_Longview_TX", + "file": "Longview_TX_Longview_TX.bngl" + }, + { + "id": "Los_Angeles-Long_Beach-Anaheim_CA_Los_Angeles-Long_Beach-Anaheim_CA", + "file": "Los_Angeles-Long_Beach-Anaheim_CA_Los_Angeles-Long_Beach-Anaheim_CA.bngl" + }, + { + "id": "Louisville_Jefferson_County_KY-IN_Louisville_Jefferson_County_KY-IN", + "file": "Louisville_Jefferson_County_KY-IN_Louisville_Jefferson_County_KY-IN.bngl" + }, + { + "id": "Lubbock_TX_Lubbock_TX", + "file": "Lubbock_TX_Lubbock_TX.bngl" + }, + { + "id": "Macon-Bibb_County_GA_Macon-Bibb_County_GA", + "file": "Macon-Bibb_County_GA_Macon-Bibb_County_GA.bngl" + }, + { + "id": "Madison_WI_Madison_WI", + "file": "Madison_WI_Madison_WI.bngl" + }, + { + "id": "Manchester-Nashua_NH_Manchester-Nashua_NH", + "file": "Manchester-Nashua_NH_Manchester-Nashua_NH.bngl" + }, + { + "id": "McAllen-Edinburg-Mission_TX_McAllen-Edinburg-Mission_TX", + "file": "McAllen-Edinburg-Mission_TX_McAllen-Edinburg-Mission_TX.bngl" + }, + { + "id": "Memphis_TN-MS-AR_Memphis_TN-MS-AR", + "file": "Memphis_TN-MS-AR_Memphis_TN-MS-AR.bngl" + }, + { + "id": "Merced_CA_Merced_CA", + "file": "Merced_CA_Merced_CA.bngl" + }, + { + "id": "Miami-Fort_Lauderdale-West_Palm_Beach_FL_Miami-Fort_Lauderdale-West_Palm_Beach_FL", + "file": "Miami-Fort_Lauderdale-West_Palm_Beach_FL_Miami-Fort_Lauderdale-West_Palm_Beach_FL.bngl" + }, + { + "id": "Michigan_City-La_Porte_IN_Michigan_City-La_Porte_IN", + "file": "Michigan_City-La_Porte_IN_Michigan_City-La_Porte_IN.bngl" + }, + { + "id": "Milwaukee-Waukesha_WI_Milwaukee-Waukesha_WI", + "file": "Milwaukee-Waukesha_WI_Milwaukee-Waukesha_WI.bngl" + }, + { + "id": "Minneapolis-St._Paul-Bloomington_MN-WI_Minneapolis-St._Paul-Bloomington_MN-WI", + "file": "Minneapolis-St._Paul-Bloomington_MN-WI_Minneapolis-St._Paul-Bloomington_MN-WI.bngl" + }, + { + "id": "Mobile_AL_Mobile_AL", + "file": "Mobile_AL_Mobile_AL.bngl" + }, + { + "id": "Modesto_CA_Modesto_CA", + "file": "Modesto_CA_Modesto_CA.bngl" + }, + { + "id": "Monroe_LA_Monroe_LA", + "file": "Monroe_LA_Monroe_LA.bngl" + }, + { + "id": "Monroe_MI_Monroe_MI", + "file": "Monroe_MI_Monroe_MI.bngl" + }, + { + "id": "Montgomery_AL_Montgomery_AL", + "file": "Montgomery_AL_Montgomery_AL.bngl" + }, + { + "id": "Mount_Vernon-Anacortes_WA_Mount_Vernon-Anacortes_WA", + "file": "Mount_Vernon-Anacortes_WA_Mount_Vernon-Anacortes_WA.bngl" + }, + { + "id": "Muncie_IN_Muncie_IN", + "file": "Muncie_IN_Muncie_IN.bngl" + }, + { + "id": "Muskegon_MI_Muskegon_MI", + "file": "Muskegon_MI_Muskegon_MI.bngl" + }, + { + "id": "Naples-Marco_Island_FL_Naples-Marco_Island_FL", + "file": "Naples-Marco_Island_FL_Naples-Marco_Island_FL.bngl" + }, + { + "id": "Nashville-Davidson-Murfreesboro-Franklin_TN_Nashville-Davidson-Murfreesboro-Franklin_TN", + "file": "Nashville-Davidson-Murfreesboro-Franklin_TN_Nashville-Davidson-Murfreesboro-Franklin_TN.bngl" + }, + { + "id": "New_Haven-Milford_CT_New_Haven-Milford_CT", + "file": "New_Haven-Milford_CT_New_Haven-Milford_CT.bngl" + }, + { + "id": "New_Orleans-Metairie_LA_New_Orleans-Metairie_LA", + "file": "New_Orleans-Metairie_LA_New_Orleans-Metairie_LA.bngl" + }, + { + "id": "New_York-Newark-Jersey_City_NY-NJ-PA_New_York-Newark-Jersey_City_NY-NJ-PA", + "file": "New_York-Newark-Jersey_City_NY-NJ-PA_New_York-Newark-Jersey_City_NY-NJ-PA.bngl" + }, + { + "id": "Niles_MI_Niles_MI", + "file": "Niles_MI_Niles_MI.bngl" + }, + { + "id": "North_Port-Sarasota-Bradenton_FL_North_Port-Sarasota-Bradenton_FL", + "file": "North_Port-Sarasota-Bradenton_FL_North_Port-Sarasota-Bradenton_FL.bngl" + }, + { + "id": "Norwich-New_London_CT_Norwich-New_London_CT", + "file": "Norwich-New_London_CT_Norwich-New_London_CT.bngl" + }, + { + "id": "Ocala_FL_Ocala_FL", + "file": "Ocala_FL_Ocala_FL.bngl" + }, + { + "id": "Ocean_City_NJ_Ocean_City_NJ", + "file": "Ocean_City_NJ_Ocean_City_NJ.bngl" + }, + { + "id": "Ogden-Clearfield_UT_Ogden-Clearfield_UT", + "file": "Ogden-Clearfield_UT_Ogden-Clearfield_UT.bngl" + }, + { + "id": "Oklahoma_City_OK_Oklahoma_City_OK", + "file": "Oklahoma_City_OK_Oklahoma_City_OK.bngl" + }, + { + "id": "Omaha-Council_Bluffs_NE-IA_Omaha-Council_Bluffs_NE-IA", + "file": "Omaha-Council_Bluffs_NE-IA_Omaha-Council_Bluffs_NE-IA.bngl" + }, + { + "id": "Orlando-Kissimmee-Sanford_FL_Orlando-Kissimmee-Sanford_FL", + "file": "Orlando-Kissimmee-Sanford_FL_Orlando-Kissimmee-Sanford_FL.bngl" + }, + { + "id": "Owensboro_KY_Owensboro_KY", + "file": "Owensboro_KY_Owensboro_KY.bngl" + }, + { + "id": "Oxnard-Thousand_Oaks-Ventura_CA_Oxnard-Thousand_Oaks-Ventura_CA", + "file": "Oxnard-Thousand_Oaks-Ventura_CA_Oxnard-Thousand_Oaks-Ventura_CA.bngl" + }, + { + "id": "Palm_Bay-Melbourne-Titusville_FL_Palm_Bay-Melbourne-Titusville_FL", + "file": "Palm_Bay-Melbourne-Titusville_FL_Palm_Bay-Melbourne-Titusville_FL.bngl" + }, + { + "id": "Pensacola-Ferry_Pass-Brent_FL_Pensacola-Ferry_Pass-Brent_FL", + "file": "Pensacola-Ferry_Pass-Brent_FL_Pensacola-Ferry_Pass-Brent_FL.bngl" + }, + { + "id": "Peoria_IL_Peoria_IL", + "file": "Peoria_IL_Peoria_IL.bngl" + }, + { + "id": "Philadelphia-Camden-Wilmington_PA-NJ-DE-MD_Philadelphia-Camden-Wilmington_PA-NJ-DE-MD", + "file": "Philadelphia-Camden-Wilmington_PA-NJ-DE-MD_Philadelphia-Camden-Wilmington_PA-NJ-DE-MD.bngl" + }, + { + "id": "Phoenix-Mesa-Chandler_AZ_Phoenix-Mesa-Chandler_AZ", + "file": "Phoenix-Mesa-Chandler_AZ_Phoenix-Mesa-Chandler_AZ.bngl" + }, + { + "id": "Pine_Bluff_AR_Pine_Bluff_AR", + "file": "Pine_Bluff_AR_Pine_Bluff_AR.bngl" + }, + { + "id": "Pittsburgh_PA_Pittsburgh_PA", + "file": "Pittsburgh_PA_Pittsburgh_PA.bngl" + }, + { + "id": "Pittsfield_MA_Pittsfield_MA", + "file": "Pittsfield_MA_Pittsfield_MA.bngl" + }, + { + "id": "Port_St._Lucie_FL_Port_St._Lucie_FL", + "file": "Port_St._Lucie_FL_Port_St._Lucie_FL.bngl" + }, + { + "id": "Portland-South_Portland_ME_Portland-South_Portland_ME", + "file": "Portland-South_Portland_ME_Portland-South_Portland_ME.bngl" + }, + { + "id": "Portland-Vancouver-Hillsboro_OR-WA_Portland-Vancouver-Hillsboro_OR-WA", + "file": "Portland-Vancouver-Hillsboro_OR-WA_Portland-Vancouver-Hillsboro_OR-WA.bngl" + }, + { + "id": "Poughkeepsie-Newburgh-Middletown_NY_Poughkeepsie-Newburgh-Middletown_NY", + "file": "Poughkeepsie-Newburgh-Middletown_NY_Poughkeepsie-Newburgh-Middletown_NY.bngl" + }, + { + "id": "Prescott_Valley-Prescott_AZ_Prescott_Valley-Prescott_AZ", + "file": "Prescott_Valley-Prescott_AZ_Prescott_Valley-Prescott_AZ.bngl" + }, + { + "id": "Providence-Warwick_RI-MA_Providence-Warwick_RI-MA", + "file": "Providence-Warwick_RI-MA_Providence-Warwick_RI-MA.bngl" + }, + { + "id": "Provo-Orem_UT_Provo-Orem_UT", + "file": "Provo-Orem_UT_Provo-Orem_UT.bngl" + }, + { + "id": "Pueblo_CO_Pueblo_CO", + "file": "Pueblo_CO_Pueblo_CO.bngl" + }, + { + "id": "Punta_Gorda_FL_Punta_Gorda_FL", + "file": "Punta_Gorda_FL_Punta_Gorda_FL.bngl" + }, + { + "id": "Racine_WI_Racine_WI", + "file": "Racine_WI_Racine_WI.bngl" + }, + { + "id": "Raleigh-Cary_NC_Raleigh-Cary_NC", + "file": "Raleigh-Cary_NC_Raleigh-Cary_NC.bngl" + }, + { + "id": "Reading_PA_Reading_PA", + "file": "Reading_PA_Reading_PA.bngl" + }, + { + "id": "Reno_NV_Reno_NV", + "file": "Reno_NV_Reno_NV.bngl" + }, + { + "id": "Richmond_VA_Richmond_VA", + "file": "Richmond_VA_Richmond_VA.bngl" + }, + { + "id": "Riverside-San_Bernardino-Ontario_CA_Riverside-San_Bernardino-Ontario_CA", + "file": "Riverside-San_Bernardino-Ontario_CA_Riverside-San_Bernardino-Ontario_CA.bngl" + }, + { + "id": "Roanoke_VA_Roanoke_VA", + "file": "Roanoke_VA_Roanoke_VA.bngl" + }, + { + "id": "Rochester_MN_Rochester_MN", + "file": "Rochester_MN_Rochester_MN.bngl" + }, + { + "id": "Rochester_NY_Rochester_NY", + "file": "Rochester_NY_Rochester_NY.bngl" + }, + { + "id": "Rockford_IL_Rockford_IL", + "file": "Rockford_IL_Rockford_IL.bngl" + }, + { + "id": "Rocky_Mount_NC_Rocky_Mount_NC", + "file": "Rocky_Mount_NC_Rocky_Mount_NC.bngl" + }, + { + "id": "Rome_GA_Rome_GA", + "file": "Rome_GA_Rome_GA.bngl" + }, + { + "id": "Sacramento-Roseville-Folsom_CA_Sacramento-Roseville-Folsom_CA", + "file": "Sacramento-Roseville-Folsom_CA_Sacramento-Roseville-Folsom_CA.bngl" + }, + { + "id": "Saginaw_MI_Saginaw_MI", + "file": "Saginaw_MI_Saginaw_MI.bngl" + }, + { + "id": "Salem_OR_Salem_OR", + "file": "Salem_OR_Salem_OR.bngl" + }, + { + "id": "Salinas_CA_Salinas_CA", + "file": "Salinas_CA_Salinas_CA.bngl" + }, + { + "id": "Salisbury_MD-DE_Salisbury_MD-DE", + "file": "Salisbury_MD-DE_Salisbury_MD-DE.bngl" + }, + { + "id": "Salt_Lake_City_UT_Salt_Lake_City_UT", + "file": "Salt_Lake_City_UT_Salt_Lake_City_UT.bngl" + }, + { + "id": "San_Antonio-New_Braunfels_TX_San_Antonio-New_Braunfels_TX", + "file": "San_Antonio-New_Braunfels_TX_San_Antonio-New_Braunfels_TX.bngl" + }, + { + "id": "San_Diego-Chula_Vista-Carlsbad_CA_San_Diego-Chula_Vista-Carlsbad_CA", + "file": "San_Diego-Chula_Vista-Carlsbad_CA_San_Diego-Chula_Vista-Carlsbad_CA.bngl" + }, + { + "id": "San_Francisco-Oakland-Berkeley_CA_San_Francisco-Oakland-Berkeley_CA", + "file": "San_Francisco-Oakland-Berkeley_CA_San_Francisco-Oakland-Berkeley_CA.bngl" + }, + { + "id": "San_Jose-Sunnyvale-Santa_Clara_CA_San_Jose-Sunnyvale-Santa_Clara_CA", + "file": "San_Jose-Sunnyvale-Santa_Clara_CA_San_Jose-Sunnyvale-Santa_Clara_CA.bngl" + }, + { + "id": "San_Luis_Obispo-Paso_Robles_CA_San_Luis_Obispo-Paso_Robles_CA", + "file": "San_Luis_Obispo-Paso_Robles_CA_San_Luis_Obispo-Paso_Robles_CA.bngl" + }, + { + "id": "Santa_Maria-Santa_Barbara_CA_Santa_Maria-Santa_Barbara_CA", + "file": "Santa_Maria-Santa_Barbara_CA_Santa_Maria-Santa_Barbara_CA.bngl" + }, + { + "id": "Santa_Rosa-Petaluma_CA_Santa_Rosa-Petaluma_CA", + "file": "Santa_Rosa-Petaluma_CA_Santa_Rosa-Petaluma_CA.bngl" + }, + { + "id": "Savannah_GA_Savannah_GA", + "file": "Savannah_GA_Savannah_GA.bngl" + }, + { + "id": "Scranton-Wilkes-Barre_PA_Scranton-Wilkes-Barre_PA", + "file": "Scranton-Wilkes-Barre_PA_Scranton-Wilkes-Barre_PA.bngl" + }, + { + "id": "Scranton_Wilkes-Barre_PA_Scranton_Wilkes-Barre_PA", + "file": "Scranton_Wilkes-Barre_PA_Scranton_Wilkes-Barre_PA.bngl" + }, + { + "id": "Seattle-Tacoma-Bellevue_WA_Seattle-Tacoma-Bellevue_WA", + "file": "Seattle-Tacoma-Bellevue_WA_Seattle-Tacoma-Bellevue_WA.bngl" + }, + { + "id": "Shreveport-Bossier_City_LA_Shreveport-Bossier_City_LA", + "file": "Shreveport-Bossier_City_LA_Shreveport-Bossier_City_LA.bngl" + }, + { + "id": "Sioux_City_IA-NE-SD_Sioux_City_IA-NE-SD", + "file": "Sioux_City_IA-NE-SD_Sioux_City_IA-NE-SD.bngl" + }, + { + "id": "Sioux_Falls_SD_Sioux_Falls_SD", + "file": "Sioux_Falls_SD_Sioux_Falls_SD.bngl" + }, + { + "id": "South_Bend-Mishawaka_IN-MI_South_Bend-Mishawaka_IN-MI", + "file": "South_Bend-Mishawaka_IN-MI_South_Bend-Mishawaka_IN-MI.bngl" + }, + { + "id": "Spartanburg_SC_Spartanburg_SC", + "file": "Spartanburg_SC_Spartanburg_SC.bngl" + }, + { + "id": "Spokane-Spokane_Valley_WA_Spokane-Spokane_Valley_WA", + "file": "Spokane-Spokane_Valley_WA_Spokane-Spokane_Valley_WA.bngl" + }, + { + "id": "Springfield_IL_Springfield_IL", + "file": "Springfield_IL_Springfield_IL.bngl" + }, + { + "id": "Springfield_MA_Springfield_MA", + "file": "Springfield_MA_Springfield_MA.bngl" + }, + { + "id": "St._Cloud_MN_St._Cloud_MN", + "file": "St._Cloud_MN_St._Cloud_MN.bngl" + }, + { + "id": "St._George_UT_St._George_UT", + "file": "St._George_UT_St._George_UT.bngl" + }, + { + "id": "St._Joseph_MO-KS_St._Joseph_MO-KS", + "file": "St._Joseph_MO-KS_St._Joseph_MO-KS.bngl" + }, + { + "id": "St._Louis_MO-IL_St._Louis_MO-IL", + "file": "St._Louis_MO-IL_St._Louis_MO-IL.bngl" + }, + { + "id": "Stockton_CA_Stockton_CA", + "file": "Stockton_CA_Stockton_CA.bngl" + }, + { + "id": "Sumter_SC_Sumter_SC", + "file": "Sumter_SC_Sumter_SC.bngl" + }, + { + "id": "Syracuse_NY_Syracuse_NY", + "file": "Syracuse_NY_Syracuse_NY.bngl" + }, + { + "id": "Tallahassee_FL_Tallahassee_FL", + "file": "Tallahassee_FL_Tallahassee_FL.bngl" + }, + { + "id": "Tampa-St._Petersburg-Clearwater_FL_Tampa-St._Petersburg-Clearwater_FL", + "file": "Tampa-St._Petersburg-Clearwater_FL_Tampa-St._Petersburg-Clearwater_FL.bngl" + }, + { + "id": "Texarkana_TX-AR_Texarkana_TX-AR", + "file": "Texarkana_TX-AR_Texarkana_TX-AR.bngl" + }, + { + "id": "The_Villages_FL_The_Villages_FL", + "file": "The_Villages_FL_The_Villages_FL.bngl" + }, + { + "id": "Toledo_OH_Toledo_OH", + "file": "Toledo_OH_Toledo_OH.bngl" + }, + { + "id": "Topeka_KS_Topeka_KS", + "file": "Topeka_KS_Topeka_KS.bngl" + }, + { + "id": "Trenton-Princeton_NJ_Trenton-Princeton_NJ", + "file": "Trenton-Princeton_NJ_Trenton-Princeton_NJ.bngl" + }, + { + "id": "Tucson_AZ_Tucson_AZ", + "file": "Tucson_AZ_Tucson_AZ.bngl" + }, + { + "id": "Tulsa_OK_Tulsa_OK", + "file": "Tulsa_OK_Tulsa_OK.bngl" + }, + { + "id": "Tuscaloosa_AL_Tuscaloosa_AL", + "file": "Tuscaloosa_AL_Tuscaloosa_AL.bngl" + }, + { + "id": "Twin_Falls_ID_Twin_Falls_ID", + "file": "Twin_Falls_ID_Twin_Falls_ID.bngl" + }, + { + "id": "Urban_Honolulu_HI_Urban_Honolulu_HI", + "file": "Urban_Honolulu_HI_Urban_Honolulu_HI.bngl" + }, + { + "id": "Utica-Rome_NY_Utica-Rome_NY", + "file": "Utica-Rome_NY_Utica-Rome_NY.bngl" + }, + { + "id": "Valdosta_GA_Valdosta_GA", + "file": "Valdosta_GA_Valdosta_GA.bngl" + }, + { + "id": "Vallejo_CA_Vallejo_CA", + "file": "Vallejo_CA_Vallejo_CA.bngl" + }, + { + "id": "Victoria_TX_Victoria_TX", + "file": "Victoria_TX_Victoria_TX.bngl" + }, + { + "id": "Vineland-Bridgeton_NJ_Vineland-Bridgeton_NJ", + "file": "Vineland-Bridgeton_NJ_Vineland-Bridgeton_NJ.bngl" + }, + { + "id": "Virginia_Beach-Norfolk-Newport_News_VA-NC_Virginia_Beach-Norfolk-Newport_News_VA-NC", + "file": "Virginia_Beach-Norfolk-Newport_News_VA-NC_Virginia_Beach-Norfolk-Newport_News_VA-NC.bngl" + }, + { + "id": "Visalia_CA_Visalia_CA", + "file": "Visalia_CA_Visalia_CA.bngl" + }, + { + "id": "Warner_Robins_GA_Warner_Robins_GA", + "file": "Warner_Robins_GA_Warner_Robins_GA.bngl" + }, + { + "id": "Washington-Arlington-Alexandria_DC-VA-MD-WV_Washington-Arlington-Alexandria_DC-VA-MD-WV", + "file": "Washington-Arlington-Alexandria_DC-VA-MD-WV_Washington-Arlington-Alexandria_DC-VA-MD-WV.bngl" + }, + { + "id": "Waterloo-Cedar_Falls_IA_Waterloo-Cedar_Falls_IA", + "file": "Waterloo-Cedar_Falls_IA_Waterloo-Cedar_Falls_IA.bngl" + }, + { + "id": "Wenatchee_WA_Wenatchee_WA", + "file": "Wenatchee_WA_Wenatchee_WA.bngl" + }, + { + "id": "Wheeling_WV-OH_Wheeling_WV-OH", + "file": "Wheeling_WV-OH_Wheeling_WV-OH.bngl" + }, + { + "id": "Wichita_KS_Wichita_KS", + "file": "Wichita_KS_Wichita_KS.bngl" + }, + { + "id": "Winchester_VA-WV_Winchester_VA-WV", + "file": "Winchester_VA-WV_Winchester_VA-WV.bngl" + }, + { + "id": "Winston-Salem_NC_Winston-Salem_NC", + "file": "Winston-Salem_NC_Winston-Salem_NC.bngl" + }, + { + "id": "Worcester_MA-CT_Worcester_MA-CT", + "file": "Worcester_MA-CT_Worcester_MA-CT.bngl" + }, + { + "id": "Yakima_WA_Yakima_WA", + "file": "Yakima_WA_Yakima_WA.bngl" + }, + { + "id": "York-Hanover_PA_York-Hanover_PA", + "file": "York-Hanover_PA_York-Hanover_PA.bngl" + }, + { + "id": "Youngstown-Warren-Boardman_OH-PA_Youngstown-Warren-Boardman_OH-PA", + "file": "Youngstown-Warren-Boardman_OH-PA_Youngstown-Warren-Boardman_OH-PA.bngl" + }, + { + "id": "Yuma_AZ_Yuma_AZ", + "file": "Yuma_AZ_Yuma_AZ.bngl" + } + ] + }, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "mapk-dimers", + "name": "MAPK Dimers", + "description": "MAPK dimerization", + "tags": [ + "published", + "mapk", + "dimers", + "ste5", + "ste11", + "ste7", + "fus3" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/mapkdimers/mapk-dimers.bngl", + "file": "mapk-dimers.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "mapk-monomers", + "name": "MAPK Monomers", + "description": "MAPK cascade", + "tags": [ + "published", + "mapk", + "monomers", + "ste5", + "ste11", + "ste7", + "fus3" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/mapkmonomers/mapk-monomers.bngl", + "file": "mapk-monomers.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "mapk-signaling-cascade", + "name": "mapk signaling cascade", + "description": "Rate Constants", + "tags": [ + "mapk", + "signaling", + "cascade", + "ligand", + "receptor", + "mapkkk", + "mapkk" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/mapksignalingcascade/mapk-signaling-cascade.bngl", + "file": "mapk-signaling-cascade.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Massole_2023", + "name": "Massole 2023", + "description": "Epo receptor signaling", + "tags": [ + "published", + "massole", + "2023" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental" + ], + "path": "Published/Massole2023/Massole_2023.bngl", + "file": "Massole_2023.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "mCaMKII_Ca_Spike", + "name": "Ordyan 2020: mCaMKII Ca Spike", + "description": "mCaMKII Ca Spike model", + "tags": [ + "published", + "neuroscience", + "mcamkii", + "ca", + "spike", + "cam", + "ng", + "camkii", + "pp1", + "time_counter" + ], + "category": "signaling", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "path": "Published/Ordyan2020/mCaMKIICaSpike/mCaMKII_Ca_Spike.bngl", + "file": "mCaMKII_Ca_Spike.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "McMillan_2021", + "name": "McMillan 2021", + "description": "TNF signaling", + "tags": [ + "published", + "nfsim", + "mcmillan", + "2021", + "r0_tot", + "t0_tot", + "r", + "t", + "generate_network", + "simulate_ode" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/McMillan2021/McMillan_2021.bngl", + "file": "McMillan_2021.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Mertins_2023", + "name": "Mertins 2023", + "description": "DNA damage response", + "tags": [ + "published", + "mertins", + "2023", + "dnadsb", + "p53", + "mrna_bax", + "bax", + "bclxl", + "bad", + "fourteen_3_3", + "caspase" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Mertins2023/Mertins_2023.bngl", + "file": "Mertins_2023.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "meta_formal_game_theory", + "name": "meta formal game theory", + "description": "Model: meta_formal_game_theory.bngl", + "tags": [ + "meta", + "formal", + "game", + "theory", + "hawk", + "dove", + "pop", + "payoffh", + "payoffd" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/meta/metaformalgametheory/meta_formal_game_theory.bngl", + "file": "meta_formal_game_theory.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "meta_formal_molecular_clock", + "name": "meta formal molecular clock", + "description": "Model: meta_formal_molecular_clock.bngl", + "tags": [ + "meta", + "formal", + "molecular", + "clock", + "fasta", + "fastb", + "slowc", + "slowd" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/meta/metaformalmolecularclock/meta_formal_molecular_clock.bngl", + "file": "meta_formal_molecular_clock.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "meta_formal_petri_net", + "name": "meta formal petri net", + "description": "Model: meta_formal_petri_net.bngl", + "tags": [ + "meta", + "formal", + "petri", + "net", + "p1", + "p2", + "p3", + "p4" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/meta/metaformalpetrinet/meta_formal_petri_net.bngl", + "file": "meta_formal_petri_net.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "michaelis-menten-kinetics", + "name": "michaelis menten kinetics", + "description": "Kinetic Constants", + "tags": [ + "michaelis", + "menten", + "kinetics", + "e", + "s", + "p", + "generate_network", + "simulate", + "writesbml" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/michaelismentenkinetics/michaelis-menten-kinetics.bngl", + "file": "michaelis-menten-kinetics.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "michment", + "name": "michment", + "description": "Michaelis Menten", + "tags": [ + "validation", + "michment", + "e", + "s", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/michment/michment.bngl", + "file": "michment.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "michment_cont", + "name": "michment_cont", + "description": "Michaelis Menten Continue", + "tags": [ + "validation", + "michment", + "cont", + "readfile", + "setconcentration", + "simulate_ode", + "addconcentration" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/michmentcont/michment_cont.bngl", + "file": "michment_cont.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Miller2022_NavajoNation", + "name": "Miller 2022 - Navajo Nation Models", + "description": "COVID-19 epidemiological models fit to Navajo Nation regional data.", + "tags": [ + "covid-19", + "epidemiology", + "pybionetgen" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/Miller2022_NavajoNation/supplementary_material_Arizona_Arizona.bngl", + "file": "supplementary_material_Arizona_Arizona.bngl", + "collectionId": "Miller2022_NavajoNation", + "collection": { + "type": "geographic-variants", + "count": 5, + "variant_key": "region", + "variants": [ + { + "id": "supplementary_material_Arizona_Arizona", + "file": "supplementary_material_Arizona_Arizona.bngl" + }, + { + "id": "supplementary_material_Colorado_Colorado", + "file": "supplementary_material_Colorado_Colorado.bngl" + }, + { + "id": "supplementary_material_NavajoNation_NavajoNation", + "file": "supplementary_material_NavajoNation_NavajoNation.bngl" + }, + { + "id": "supplementary_material_NewMexico_NewMexico", + "file": "supplementary_material_NewMexico_NewMexico.bngl" + }, + { + "id": "supplementary_material_Utah_Utah", + "file": "supplementary_material_Utah_Utah.bngl" + } + ] + }, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Miller2025_MEK", + "name": "Miller 2025 - MEK Isoform Models", + "description": "MEK isoform variant models curated for PyBioNetGen.", + "tags": [ + "mek", + "isoforms", + "signaling", + "pybionetgen" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "path": "Published/Miller2025_MEK/MEK_isoform_aMCMC_MEK1_KO.bngl", + "file": "MEK_isoform_aMCMC_MEK1_KO.bngl", + "collectionId": "Miller2025_MEK", + "collection": { + "type": "parameter-fit-variants", + "count": 10, + "variant_key": "isoform", + "variants": [ + { + "id": "MEK_isoform_aMCMC_MEK1_KO", + "file": "MEK_isoform_aMCMC_MEK1_KO.bngl" + }, + { + "id": "MEK_isoform_aMCMC_MEK1_N78G", + "file": "MEK_isoform_aMCMC_MEK1_N78G.bngl" + }, + { + "id": "MEK_isoform_aMCMC_MEK1_T292A", + "file": "MEK_isoform_aMCMC_MEK1_T292A.bngl" + }, + { + "id": "MEK_isoform_aMCMC_MEK1_T292D", + "file": "MEK_isoform_aMCMC_MEK1_T292D.bngl" + }, + { + "id": "MEK_isoform_aMCMC_MEK1_WT", + "file": "MEK_isoform_aMCMC_MEK1_WT.bngl" + }, + { + "id": "MEK_isoform_optimization_DE_MEK1_KO", + "file": "MEK_isoform_optimization_DE_MEK1_KO.bngl" + }, + { + "id": "MEK_isoform_optimization_DE_MEK1_N78G", + "file": "MEK_isoform_optimization_DE_MEK1_N78G.bngl" + }, + { + "id": "MEK_isoform_optimization_DE_MEK1_T292A", + "file": "MEK_isoform_optimization_DE_MEK1_T292A.bngl" + }, + { + "id": "MEK_isoform_optimization_DE_MEK1_T292D", + "file": "MEK_isoform_optimization_DE_MEK1_T292D.bngl" + }, + { + "id": "MEK_isoform_optimization_DE_MEK1_WT", + "file": "MEK_isoform_optimization_DE_MEK1_WT.bngl" + } + ] + }, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Mitra2019_02_egfr_bnf1_InputFiles_egfr", + "name": "InputFiles", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/02-egfr/bnf1/InputFiles/egfr.bngl", + "file": "egfr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "ml_gradient_descent", + "name": "ml gradient descent", + "description": "Gradient Descent Optimizer in BNGL", + "tags": [ + "ml", + "gradient", + "descent", + "posx", + "posy", + "velx", + "vely", + "loss" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/ml/mlgradientdescent/ml_gradient_descent.bngl", + "file": "ml_gradient_descent.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ml_hopfield", + "name": "ml hopfield", + "description": "Model: ml_hopfield.bngl", + "tags": [ + "ml", + "hopfield", + "neuron", + "net1", + "net2", + "net3", + "target1" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/ml/mlhopfield/ml_hopfield.bngl", + "file": "ml_hopfield.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ml_kmeans", + "name": "ml kmeans", + "description": "Model: ml_kmeans.bngl", + "tags": [ + "ml", + "kmeans", + "ax", + "ay", + "bx", + "by" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/ml/mlkmeans/ml_kmeans.bngl", + "file": "ml_kmeans.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ml_q_learning", + "name": "ml q learning", + "description": "Q-Learning Agent in BNGL", + "tags": [ + "ml", + "q", + "learning", + "pos", + "ql", + "qr", + "reward", + "action" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/ml/mlqlearning/ml_q_learning.bngl", + "file": "ml_q_learning.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ml_svm", + "name": "ml svm", + "description": "Model: ml_svm.bngl", + "tags": [ + "ml", + "svm", + "w1", + "w2", + "b", + "db_dt", + "dw1_dt" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/ml/mlsvm/ml_svm.bngl", + "file": "ml_svm.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "model", + "name": "model", + "description": "filename: model.bngl", + "tags": [ + "model", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/model/model.bngl", + "file": "model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "model", + "name": "model", + "description": "A model of IgE receptor signaling", + "tags": [ + "model", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/model_Degranulation_aMCMC/model.bngl", + "file": "model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "model_ground", + "name": "model_ground.bngl", + "description": "filename: model_ground.bngl", + "tags": [ + "x_tot__free", + "k_xoff__free", + "k_xon__free", + "kase__free", + "kdegx__free", + "kdegran__free", + "km_ship1__free", + "km_syk__free", + "km_x__free", + "koff__free", + "kp_ship1__free", + "kp_syk__free", + "kp_x__free", + "kpten__free", + "ksynth1__free", + "pase__free", + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/model_ground.bngl", + "file": "model_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "model_tofit", + "name": "model tofit", + "description": "A model of IgE receptor signaling", + "tags": [ + "model", + "tofit", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/modeltofit/model_tofit.bngl", + "file": "model_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Model_ZAP", + "name": "Model ZAP", + "description": "ZAP-70 recruitment", + "tags": [ + "published", + "immunology", + "nfsim", + "model", + "zap", + "kon", + "a", + "cbl", + "cd16", + "lck", + "ligand", + "zeta", + "dead" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/ModelZAP/Model_ZAP.bngl", + "file": "Model_ZAP.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Motivating_example", + "name": "Motivating_example", + "description": "Signal Transduction with receptor internalization", + "tags": [ + "validation", + "motivating", + "example", + "l", + "r", + "tf", + "dna", + "mrna1", + "mrna2", + "p1", + "p2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/Motivatingexample/Motivating_example.bngl", + "file": "Motivating_example.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Motivating_example_cBNGL", + "name": "Motivating_example_cBNGL", + "description": "Signal transduction with receptor internalization", + "tags": [ + "validation", + "motivating", + "example", + "cbngl", + "l", + "r", + "tf", + "dna", + "mrna1", + "mrna2", + "p1", + "p2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/MotivatingexamplecBNGL/Motivating_example_cBNGL.bngl", + "file": "Motivating_example_cBNGL.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "motor", + "name": "motor", + "description": "Motor protein", + "tags": [ + "validation", + "motor", + "chey", + "kplus", + "kminus" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/motor/motor.bngl", + "file": "motor.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "mt_arithmetic_compiler", + "name": "mt arithmetic compiler", + "description": "Model: mt_arithmetic_compiler.bngl", + "tags": [ + "mt", + "arithmetic", + "compiler", + "node", + "target_add", + "target_mult" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/meta/mtarithmeticcompiler/mt_arithmetic_compiler.bngl", + "file": "mt_arithmetic_compiler.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "mt_bngl_interpreter", + "name": "mt bngl interpreter", + "description": "Model: mt_bngl_interpreter.bngl", + "tags": [ + "mt", + "bngl", + "interpreter", + "rule", + "species", + "exec_s1_s2", + "generate_network", + "simulate" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/meta/mtbnglinterpreter/mt_bngl_interpreter.bngl", + "file": "mt_bngl_interpreter.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "mt_music_sequencer", + "name": "mt music sequencer", + "description": "Music Sequencer / Chord Synthesizer in BNGL", + "tags": [ + "mt", + "music", + "sequencer", + "v1s", + "v1c", + "v2s", + "v2c", + "v3s", + "v3c", + "mix", + "chordphase" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/meta/mtmusicsequencer/mt_music_sequencer.bngl", + "file": "mt_music_sequencer.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "mt_pascal_triangle", + "name": "mt pascal triangle", + "description": "Model: mt_pascal_triangle.bngl", + "tags": [ + "mt", + "pascal", + "triangle", + "node" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/meta/mtpascaltriangle/mt_pascal_triangle.bngl", + "file": "mt_pascal_triangle.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "mt_quine", + "name": "mt quine", + "description": "Model: mt_quine.bngl", + "tags": [ + "mt", + "quine", + "gene", + "protein" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/meta/mtquine/mt_quine.bngl", + "file": "mt_quine.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "mtor-signaling", + "name": "mtor signaling", + "description": "mTOR Signaling Pathway", + "tags": [ + "mtor", + "signaling", + "rheb", + "mtorc1", + "s6k", + "ampk" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/mtorsignaling/mtor-signaling.bngl", + "file": "mtor-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "mtorc2-signaling", + "name": "mtorc2 signaling", + "description": "mTORC2 signaling regulates cell survival and growth via AKT and SGK1.", + "tags": [ + "mtorc2", + "signaling", + "mtor", + "sin1", + "rictor", + "akt", + "sgk1", + "pip3" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/mtorc2signaling/mtorc2-signaling.bngl", + "file": "mtorc2-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Mukhopadhyay_2013", + "name": "Mukhopadhyay 2013", + "description": "FceRI signaling", + "tags": [ + "published", + "immunology", + "mukhopadhyay", + "2013", + "s", + "e", + "f", + "z" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/Mukhopadhyay2013/Mukhopadhyay_2013.bngl", + "file": "Mukhopadhyay_2013.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "mwc", + "name": "mwc", + "description": "Monod-Wyman-Changeux model", + "tags": [ + "validation", + "mwc", + "setoption", + "h", + "ox", + "b" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/mwc/mwc.bngl", + "file": "mwc.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "myogenic-differentiation", + "name": "myogenic differentiation", + "description": "Myogenic Differentiation", + "tags": [ + "myogenic", + "differentiation", + "myod", + "myog", + "mef2" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/myogenicdifferentiation/myogenic-differentiation.bngl", + "file": "myogenic-differentiation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", + "name": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", + "description": "Runtime-only BNGL model migrated from public/models: Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", + "tags": [ + "myrtle", + "beach", + "conway", + "north", + "sc", + "nc" + ], + "category": "other", + "origin": "contributed", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl", + "file": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Nag_2009", + "name": "Nag 2009", + "description": "LAT-Grb2-SOS1 signaling", + "tags": [ + "published", + "nag", + "2009", + "lig", + "lyn", + "syk", + "rec", + "lat", + "grb", + "sos" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Nag2009/Nag_2009.bngl", + "file": "Nag_2009.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "negative-feedback-loop", + "name": "negative feedback loop", + "description": "Negative Feedback Loop", + "tags": [ + "negative", + "feedback", + "loop", + "gene", + "mrna", + "protein" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/negativefeedbackloop/negative-feedback-loop.bngl", + "file": "negative-feedback-loop.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "neurotransmitter-release", + "name": "neurotransmitter release", + "description": "Neurotransmitter Release", + "tags": [ + "neurotransmitter", + "release", + "calcium", + "snare", + "vesicle", + "postsynaptic" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/neurotransmitterrelease/neurotransmitter-release.bngl", + "file": "neurotransmitter-release.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "nfkb", + "name": "nfkb", + "description": "NF-kB signaling pathway", + "tags": [ + "validation", + "nfkb", + "tnfr", + "ikkk", + "tnf", + "ikk", + "ikba", + "a20", + "competitor" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/nfkb/nfkb.bngl", + "file": "nfkb.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "nfkb_illustrating_protocols", + "name": "nfkb_illustrating_protocols", + "description": "NF-kB signaling pathway", + "tags": [ + "validation", + "nfkb", + "illustrating", + "protocols", + "tnfr", + "ikkk", + "tnf", + "ikk", + "ikba", + "a20", + "competitor" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/nfkbillustratingprotocols/nfkb_illustrating_protocols.bngl", + "file": "nfkb_illustrating_protocols.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "nfkb-feedback", + "name": "nfkb feedback", + "description": "TNFalpha-induced NF-kB signaling with IkappaB-alpha feedback.", + "tags": [ + "nfkb", + "feedback", + "ikb", + "ikk", + "a20" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/nfkbfeedback/nfkb-feedback.bngl", + "file": "nfkb-feedback.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "NFmodel", + "name": "NFmodel", + "description": "BioNetGen model: NFmodel", + "tags": [ + "nfmodel", + "ag", + "ab", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/NFmodel/NFmodel.bngl", + "file": "NFmodel.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "nfsim_aggregation_gelation", + "name": "nfsim aggregation gelation", + "description": "Model: nfsim_aggregation_gelation.bngl", + "tags": [ + "nfsim", + "aggregation", + "gelation", + "m" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/nfsim/nfsimaggregationgelation/nfsim_aggregation_gelation.bngl", + "file": "nfsim_aggregation_gelation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "nfsim_coarse_graining", + "name": "nfsim coarse graining", + "description": "Model: nfsim_coarse_graining.bngl", + "tags": [ + "nfsim", + "coarse", + "graining", + "droplet" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/nfsim/nfsimcoarsegraining/nfsim_coarse_graining.bngl", + "file": "nfsim_coarse_graining.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "nfsim_dynamic_compartments", + "name": "nfsim dynamic compartments", + "description": "Model: nfsim_dynamic_compartments.bngl", + "tags": [ + "nfsim", + "dynamic", + "compartments", + "cell", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/nfsim/nfsimdynamiccompartments/nfsim_dynamic_compartments.bngl", + "file": "nfsim_dynamic_compartments.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "nfsim_hybrid_particle_field", + "name": "nfsim hybrid particle field", + "description": "Model: nfsim_hybrid_particle_field.bngl", + "tags": [ + "nfsim", + "hybrid", + "particle", + "field" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/nfsim/nfsimhybridparticlefield/nfsim_hybrid_particle_field.bngl", + "file": "nfsim_hybrid_particle_field.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "nfsim_ring_closure_polymer", + "name": "nfsim ring closure polymer", + "description": "Model: nfsim_ring_closure_polymer.bngl", + "tags": [ + "nfsim", + "ring", + "closure", + "polymer", + "a", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer.bngl", + "file": "nfsim_ring_closure_polymer.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "nn_xor", + "name": "nn xor", + "description": "Model: nn_xor.bngl", + "tags": [ + "nn", + "xor", + "input", + "hidden", + "output", + "target", + "weightih", + "weightho", + "dopamine" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/ml/nnxor/nn_xor.bngl", + "file": "nn_xor.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "no_frees", + "name": "no frees", + "description": "Original values used to generate parabola.exp", + "tags": [ + "no", + "frees", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/nofrees/no_frees.bngl", + "file": "no_frees.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "no_generate_network", + "name": "no generate network", + "description": "Original values used to generate parabola.exp", + "tags": [ + "no", + "generate", + "network", + "counter", + "y", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/nogeneratenetwork/no_generate_network.bngl", + "file": "no_generate_network.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "no_suffix", + "name": "no suffix", + "description": "Original values used to generate parabola.exp", + "tags": [ + "no", + "suffix", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/nosuffix/no_suffix.bngl", + "file": "no_suffix.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "no-cgmp-signaling", + "name": "no cgmp signaling", + "description": "Nitric Oxide (NO) / cGMP signaling pathway.", + "tags": [ + "no", + "cgmp", + "signaling", + "sgc", + "pkg" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/nocgmpsignaling/no-cgmp-signaling.bngl", + "file": "no-cgmp-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Nosbisch_2022", + "name": "Nosbisch 2022", + "description": "RTK-PLCgamma1 signaling", + "tags": [ + "published", + "nosbisch", + "2022", + "rtk", + "plcgamma1", + "generate_network" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Nosbisch2022/Nosbisch_2022.bngl", + "file": "Nosbisch_2022.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "notch", + "name": "Notch", + "description": "Notch signaling", + "tags": [ + "published", + "notch", + "icn", + "ofut1", + "fringe", + "furin", + "dsl", + "csl", + "maml" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "path": "Published/notch/notch.bngl", + "file": "notch.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "notch-delta-lateral-inhibition", + "name": "notch delta lateral inhibition", + "description": "Notch-Delta Lateral Inhibition", + "tags": [ + "notch", + "delta", + "lateral", + "inhibition", + "cellnotch", + "celldelta" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition.bngl", + "file": "notch-delta-lateral-inhibition.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "NYC", + "name": "NYC", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "nyc", + "counter", + "fdcs", + "s", + "sv", + "e", + "a", + "i", + "v" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/VaxAndVariants/NYC/NYC.bngl", + "file": "NYC.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "organelle_transport", + "name": "organelle transport", + "description": "title: organelle_transport.bngl", + "tags": [ + "organelle", + "transport", + "a", + "b", + "c", + "d", + "t1", + "at1", + "ct1", + "t2" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/organelletransport/organelle_transport.bngl", + "file": "organelle_transport.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "organelle_transport_struct", + "name": "organelle transport struct", + "description": "title: organelle_transport_abcd.bngl", + "tags": [ + "organelle", + "transport", + "struct", + "a", + "b", + "t1", + "t2" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/organelletransportstruct/organelle_transport_struct.bngl", + "file": "organelle_transport_struct.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "oxidative-stress-response", + "name": "oxidative stress response", + "description": "Oxidative Stress Response (Keap1-Nrf2 Pathway)", + "tags": [ + "oxidative", + "stress", + "response", + "ros", + "keap1", + "nrf2", + "antioxidant" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl", + "file": "oxidative-stress-response.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "p38-mapk-signaling", + "name": "p38 mapk signaling", + "description": "p38 MAPK stress signaling cascade.", + "tags": [ + "p38", + "mapk", + "signaling", + "mkk3", + "mapkap2", + "v_thermal" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl", + "file": "p38-mapk-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "p53-mdm2-oscillator", + "name": "p53 mdm2 oscillator", + "description": "BioNetGen model: p53 mdm2 oscillator", + "tags": [ + "p53", + "mdm2", + "oscillator", + "generate_network" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl", + "file": "p53-mdm2-oscillator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "parabola", + "name": "parabola", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "parabola", + "counter", + "par", + "line", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/parabola/parabola.bngl", + "file": "parabola.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "parabola", + "name": "parabola", + "description": "Original values used to generate parabola.exp", + "tags": [ + "parabola", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/parabola_demo/parabola.bngl", + "file": "parabola.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "parabola", + "name": "parabola", + "description": "Original values used to generate parabola.exp", + "tags": [ + "parabola", + "counter", + "y", + "generate_network", + "simulate", + "resetconcentrations" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/parabola/parabola.bngl", + "file": "parabola.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "parabola", + "name": "parabola", + "description": "Original values used to generate parabola.exp", + "tags": [ + "parabola", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/parabola_bngl_files/parabola.bngl", + "file": "parabola.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "parabola", + "name": "parabola", + "description": "Original values used to generate parabola.exp", + "tags": [ + "parabola", + "counter", + "y", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola.bngl", + "file": "parabola.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "parabola_ground", + "name": "parabola ground", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "parabola", + "ground", + "counter", + "par", + "line", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/parabolaground/parabola_ground.bngl", + "file": "parabola_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "parabola2", + "name": "parabola2", + "description": "A file for testing behavior with duplicate file names", + "tags": [ + "parabola2", + "counter", + "y", + "generate_network", + "simulate", + "resetconcentrations" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/parabola2/parabola2.bngl", + "file": "parabola2.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ParamsEverywhere", + "name": "ParamsEverywhere", + "description": "An example from a real application", + "tags": [ + "paramseverywhere", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere.bngl", + "file": "ParamsEverywhere.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "parp1-mediated-dna-repair", + "name": "parp1 mediated dna repair", + "description": "PARP1-mediated DNA damage sensing and repair.", + "tags": [ + "parp1", + "mediated", + "dna", + "repair", + "par", + "nad", + "v_parylate" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl", + "file": "parp1-mediated-dna-repair.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Pekalski_2013", + "name": "Pekalski 2013", + "description": "Spontaneous signaling", + "tags": [ + "published", + "pekalski", + "2013", + "tnfr", + "ikk", + "ikkk", + "ikba", + "ikba_mrna", + "a20", + "a20_mrna", + "nfkb" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "path": "Published/Pekalski2013/Pekalski_2013.bngl", + "file": "Pekalski_2013.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "ph_lorenz_attractor", + "name": "ph lorenz attractor", + "description": "Lorenz Attractor in BNGL", + "tags": [ + "ph", + "lorenz", + "attractor", + "lx", + "ly", + "lz", + "x", + "y" + ], + "category": "physics", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "path": "Examples/physics/phlorenzattractor/ph_lorenz_attractor.bngl", + "file": "ph_lorenz_attractor.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ph_nbody_gravity", + "name": "ph nbody gravity", + "description": "Model: ph_nbody_gravity.bngl", + "tags": [ + "ph", + "nbody", + "gravity", + "body", + "r2" + ], + "category": "physics", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "path": "Examples/physics/phnbodygravity/ph_nbody_gravity.bngl", + "file": "ph_nbody_gravity.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ph_schrodinger", + "name": "ph schrodinger", + "description": "Model: ph_schrodinger.bngl", + "tags": [ + "ph", + "schrodinger", + "psi" + ], + "category": "physics", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "path": "Examples/physics/phschrodinger/ph_schrodinger.bngl", + "file": "ph_schrodinger.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ph_wave_equation", + "name": "ph wave equation", + "description": "Model: ph_wave_equation.bngl", + "tags": [ + "ph", + "wave", + "equation", + "node" + ], + "category": "physics", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "path": "Examples/physics/phwaveequation/ph_wave_equation.bngl", + "file": "ph_wave_equation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Phoenix", + "name": "Phoenix", + "description": "- This model is intended to be consistent with the compartmental model", + "tags": [ + "phoenix", + "counter", + "fdcs", + "s", + "sv", + "e", + "a", + "i", + "v" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/VaxAndVariants/Phoenix/Phoenix.bngl", + "file": "Phoenix.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "phosphorelay-chain", + "name": "phosphorelay chain", + "description": "BioNetGen model: phosphorelay chain", + "tags": [ + "phosphorelay", + "chain", + "sensor", + "relay", + "output" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/phosphorelaychain/phosphorelay-chain.bngl", + "file": "phosphorelay-chain.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "platelet-activation", + "name": "platelet activation", + "description": "BioNetGen model: platelet activation", + "tags": [ + "platelet", + "activation", + "adp", + "p2y12", + "integrin", + "thromboxane" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/plateletactivation/platelet-activation.bngl", + "file": "platelet-activation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "polymer", + "name": "polymer", + "description": "Polymerization model", + "tags": [ + "published", + "tutorials", + "nfsim", + "polymer", + "a", + "b", + "c", + "simulate_nf" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "tutorials" + ], + "path": "Tutorials/General/polymer/polymer.bngl", + "file": "polymer.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "polymer_draft", + "name": "polymer draft", + "description": "Polymerization (draft)", + "tags": [ + "published", + "tutorials", + "nfsim", + "polymer", + "draft", + "a", + "b", + "c", + "simulate_nf" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "tutorials" + ], + "path": "Tutorials/General/polymerdraft/polymer_draft.bngl", + "file": "polymer_draft.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "polymer_fixed", + "name": "polymer_fixed", + "description": "Runtime-only BNGL model migrated from public/models: polymer_fixed", + "tags": [ + "polymer", + "fixed" + ], + "category": "other", + "origin": "contributed", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Tutorials/polymerfixed/polymer_fixed.bngl", + "file": "polymer_fixed.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "polynomial", + "name": "polynomial", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "polynomial", + "counter", + "y1", + "y2", + "generate_network", + "simulate", + "setparameter", + "resetconcentrations" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/polynomial/polynomial.bngl", + "file": "polynomial.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "polynomial", + "name": "polynomial", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "polynomial", + "counter", + "y1", + "y2", + "generate_network", + "simulate", + "setparameter", + "resetconcentrations" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/polynomial/polynomial.bngl", + "file": "polynomial.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "polynomial", + "name": "polynomial", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "polynomial", + "counter", + "y1", + "y2", + "generate_network", + "simulate", + "setparameter", + "resetconcentrations" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial.bngl", + "file": "polynomial.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "polynomial_ground", + "name": "polynomial ground", + "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", + "tags": [ + "polynomial", + "ground", + "counter", + "y1", + "y2", + "generate_network", + "simulate", + "setparameter", + "resetconcentrations" + ], + "category": "other", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/polynomialground/polynomial_ground.bngl", + "file": "polynomial_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Posner_1995", + "name": "Posner 1995", + "description": "BLBR rings", + "tags": [ + "published", + "physics", + "posner", + "1995" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "path": "Published/Posner1995/blbr_rings_posner1995.bngl", + "file": "blbr_rings_posner1995.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Posner_2004", + "name": "Posner 2004", + "description": "BLBR cooperativity", + "tags": [ + "published", + "physics", + "posner", + "2004" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "path": "Published/Posner2004/blbr_cooperativity_posner2004.bngl", + "file": "blbr_cooperativity_posner2004.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "predator-prey-dynamics", + "name": "predator prey dynamics", + "description": "BioNetGen model: predator prey dynamics", + "tags": [ + "predator", + "prey", + "dynamics" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl", + "file": "predator-prey-dynamics.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "prion_model", + "name": "ERK_model.bngl", + "description": "filename: ERK_model.bngl", + "tags": [ + "egf", + "erkpp_sos1_fb", + "erkpp_mek_fb", + "erkpp_raf1_fb", + "lambda", + "egfr_tot", + "ras_tot", + "sos_tot", + "rasgap_tot", + "raf_tot", + "mek_tot", + "erk_tot", + "ekar3_tot", + "erktr_tot", + "a1", + "d1", + "b1", + "u1a", + "u1b", + "b2a", + "u2a", + "b2b", + "u2b", + "k2a", + "k2b", + "b3", + "u3", + "k3", + "a2", + "d2", + "p1", + "q1", + "p2", + "q2", + "p3", + "q3", + "p4", + "q4", + "q5", + "p6", + "q6", + "a0_ekar3", + "d0_ekar3", + "a0_erktr", + "d0_erktr", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "path": "Published/Lin2019/prion_model.bngl", + "file": "prion_model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem_quant_model_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem_quant/model_tofit.bngl", + "file": "model_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem16_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem16_3cat/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem16_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem16/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem32_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem32_3cat/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem32_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem32/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem4_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem4_3cat/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem4_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem4/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem64_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem64_3cat/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem64_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem64/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem8_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem8_3cat/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem8_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem8/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "process_actin_treadmilling", + "name": "process actin treadmilling", + "description": "Model: process_actin_treadmilling.bngl", + "tags": [ + "process", + "actin", + "treadmilling", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl", + "file": "process_actin_treadmilling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "process_autophagy_flux", + "name": "process autophagy flux", + "description": "Model: process_autophagy_flux.bngl", + "tags": [ + "process", + "autophagy", + "flux", + "phagophore", + "autophagosome", + "lysosome", + "autolysosome", + "cargo" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/processes/processautophagyflux/process_autophagy_flux.bngl", + "file": "process_autophagy_flux.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "process_cell_adhesion_strength", + "name": "process cell adhesion strength", + "description": "Model: process_cell_adhesion_strength.bngl", + "tags": [ + "process", + "cell", + "adhesion", + "strength", + "c1", + "c2", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl", + "file": "process_cell_adhesion_strength.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "process_kinetic_proofreading_tcr", + "name": "process kinetic proofreading tcr", + "description": "Model: process_kinetic_proofreading_tcr.bngl", + "tags": [ + "process", + "kinetic", + "proofreading", + "tcr", + "l" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl", + "file": "process_kinetic_proofreading_tcr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "process_quorum_sensing_switch", + "name": "process quorum sensing switch", + "description": "Model: process_quorum_sensing_switch.bngl", + "tags": [ + "process", + "quorum", + "sensing", + "switch", + "gene_ai", + "ai", + "r", + "gene_light" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl", + "file": "process_quorum_sensing_switch.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "pt303", + "name": "pt303", + "description": "c = 0.20 /d t_1/2 = 3.5 d (inferred)", + "tags": [ + "pt303", + "counter", + "v", + "lnv", + "s", + "c", + "half_life", + "lnv_tangent" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/HIVdynamics/pt303/pt303.bngl", + "file": "pt303.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "pt403", + "name": "pt403", + "description": "c = 0.23 /d t_1/2 = 3.0 d (inferred)", + "tags": [ + "pt403", + "counter", + "v", + "lnv", + "s", + "c", + "half_life", + "lnv_tangent" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/HIVdynamics/pt403/pt403.bngl", + "file": "pt403.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "pt409", + "name": "pt409", + "description": "c = 0.39 /d t_1/2 = 1.8 d (inferred)", + "tags": [ + "pt409", + "counter", + "v", + "lnv", + "s", + "c", + "half_life", + "lnv_tangent" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/HIVdynamics/pt409/pt409.bngl", + "file": "pt409.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "PyBNF_fitting_setup_190127_CHO_EGFR_forBNF", + "name": "PyBNF-fitting-setup", + "description": "BNGL model: 190127_CHO_EGFR_forBNF", + "tags": [ + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/PyBNF-fitting-setup/190127_CHO_EGFR_forBNF.bngl", + "file": "190127_CHO_EGFR_forBNF.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "quasi_equilibrium", + "name": "quasi equilibrium", + "description": "Quasi-equilibrium approximation", + "tags": [ + "published", + "toy models", + "quasi", + "equilibrium", + "a", + "b", + "c" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials", + "native-tutorials" + ], + "path": "Tutorials/General/quasiequilibrium/quasi_equilibrium.bngl", + "file": "quasi_equilibrium.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "quorum-sensing-circuit", + "name": "quorum sensing circuit", + "description": "BioNetGen model: quorum sensing circuit", + "tags": [ + "quorum", + "sensing", + "circuit", + "autoinducer", + "autoinducer_env", + "gene", + "protein" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl", + "file": "quorum-sensing-circuit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "rab_mon1ccz1_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/rab_mon1ccz1_ox.bngl", + "file": "rab_mon1ccz1_ox.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_mon1ccz1_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/pybnf_files/rab_mon1ccz1_ox.bngl", + "file": "rab_mon1ccz1_ox.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_rab5_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/rab_rab5_ox.bngl", + "file": "rab_rab5_ox.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_rab5_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/pybnf_files/rab_rab5_ox.bngl", + "file": "rab_rab5_ox.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_rab7_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/rab_rab7_ox.bngl", + "file": "rab_rab7_ox.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_rab7_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/pybnf_files/rab_rab7_ox.bngl", + "file": "rab_rab7_ox.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_wt", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/rab_wt.bngl", + "file": "rab_wt.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_wt", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/pybnf_files/rab_wt.bngl", + "file": "rab_wt.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab-gtpase-cycle", + "name": "rab gtpase cycle", + "description": "BioNetGen model: rab gtpase cycle", + "tags": [ + "rab", + "gtpase", + "cycle", + "gef", + "gap", + "effector" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/rabgtpasecycle/rab-gtpase-cycle.bngl", + "file": "rab-gtpase-cycle.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "RAFi", + "name": "RAFi", + "description": "BioNetGen model: RAFi", + "tags": [ + "rafi", + "r", + "i", + "ybar", + "activity" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/RAFi/RAFi.bngl", + "file": "RAFi.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "RAFi_ground", + "name": "RAFi ground", + "description": "BioNetGen model: RAFi ground", + "tags": [ + "rafi", + "ground", + "r", + "i", + "ybar", + "activity" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/RAFiground/RAFi_ground.bngl", + "file": "RAFi_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "rankl-rank-signaling", + "name": "rankl rank signaling", + "description": "RANKL-RANK-OPG signaling in bone remodeling.", + "tags": [ + "rankl", + "rank", + "signaling", + "opg", + "nfat", + "traf6" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/ranklranksignaling/rankl-rank-signaling.bngl", + "file": "rankl-rank-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ras-gef-gap-cycle", + "name": "ras gef gap cycle", + "description": "Ras-GEF-GAP cycle with explicit nucleotide exchange.", + "tags": [ + "ras", + "gef", + "gap", + "cycle", + "sos", + "rasgap", + "v_gef", + "v_gap" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/rasgefgapcycle/ras-gef-gap-cycle.bngl", + "file": "ras-gef-gap-cycle.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "rec_dim", + "name": "rec_dim", + "description": "Ligand-receptor binding", + "tags": [ + "validation", + "rec", + "dim", + "lig", + "writemdl", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/recdim/rec_dim.bngl", + "file": "rec_dim.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "rec_dim_comp", + "name": "rec_dim_comp", + "description": "name dimension volume contained_by", + "tags": [ + "validation", + "rec", + "dim", + "comp", + "kp1", + "kp2", + "lig", + "writemdl", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/recdimcomp/rec_dim_comp.bngl", + "file": "rec_dim_comp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "receptor", + "name": "13-receptor", + "description": "A simple model", + "tags": [ + "ligand_ispresent", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/13-receptor/receptor.bngl", + "file": "receptor.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "receptor", + "name": "receptor", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", + "tags": [ + "receptor", + "l", + "r", + "func" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/receptor/receptor.bngl", + "file": "receptor.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "receptor_nf", + "name": "receptor nf", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", + "tags": [ + "receptor", + "nf", + "l", + "r" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/receptornf/receptor_nf.bngl", + "file": "receptor_nf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "receptor_nf", + "name": "receptor nf", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", + "tags": [ + "receptor", + "nf", + "l", + "r" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/receptornf/receptor_nf.bngl", + "file": "receptor_nf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Repressilator", + "name": "Repressilator", + "description": "Repressilator circuit", + "tags": [ + "published", + "tutorial", + "native", + "repressilator", + "gtetr", + "gci", + "glaci", + "mtetr", + "mci", + "mlaci", + "ptetr", + "pci" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "synbio", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/Repressilator/Repressilator.bngl", + "file": "Repressilator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "repressilator-oscillator", + "name": "repressilator oscillator", + "description": "BioNetGen model: repressilator oscillator", + "tags": [ + "repressilator", + "oscillator", + "genea", + "geneb", + "genec", + "mrna_a", + "mrna_b", + "mrna_c", + "proteina", + "proteinb" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/repressilatoroscillator/repressilator-oscillator.bngl", + "file": "repressilator-oscillator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "retinoic-acid-signaling", + "name": "retinoic acid signaling", + "description": "BioNetGen model: retinoic acid signaling", + "tags": [ + "retinoic", + "acid", + "signaling", + "ra", + "rarrxr", + "corepressor", + "targetgene" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/retinoicacidsignaling/retinoic-acid-signaling.bngl", + "file": "retinoic-acid-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "rho-gtpase-actin-cytoskeleton", + "name": "rho gtpase actin cytoskeleton", + "description": "RhoA-GTPase regulation of the actin cytoskeleton.", + "tags": [ + "rho", + "gtpase", + "actin", + "cytoskeleton", + "rhoa", + "rock", + "limk", + "cofilin" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton.bngl", + "file": "rho-gtpase-actin-cytoskeleton.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Rule_based_egfr_compart", + "name": "Rule based egfr compart", + "description": "Compartmental EGFR model", + "tags": [ + "published", + "rule", + "based", + "egfr", + "compart", + "egf", + "grb2", + "shc", + "generate_network" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "path": "Published/Rulebasedegfrcompart/Rule_based_egfr_compart.bngl", + "file": "Rule_based_egfr_compart.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Rule_based_egfr_tutorial", + "name": "Faeder 2009", + "description": "EGFR signaling", + "tags": [ + "published", + "rule", + "based", + "egfr", + "tutorial", + "egf", + "grb2", + "shc", + "generate_network" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Rulebasedegfrtutorial/Rule_based_egfr_tutorial.bngl", + "file": "Rule_based_egfr_tutorial.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Rule_based_Ran_transport", + "name": "Rule based Ran transport", + "description": "Nuclear Ran transport", + "tags": [ + "published", + "rule", + "based", + "ran", + "transport", + "c", + "rcc1", + "generate_network" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "path": "Published/RulebasedRantransport/Rule_based_Ran_transport.bngl", + "file": "Rule_based_Ran_transport.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Rule_based_Ran_transport_draft", + "name": "Rule based Ran transport draft", + "description": "Ran transport (draft)", + "tags": [ + "published", + "rule", + "based", + "ran", + "transport", + "draft", + "c", + "rcc1", + "generate_network" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "path": "Published/RulebasedRantransportdraft/Rule_based_Ran_transport_draft.bngl", + "file": "Rule_based_Ran_transport_draft.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Scaff-22_ground", + "name": "18-mapk", + "description": "For \"ground truth\" model, use median values such that hierarchy H1 occurs, as shown in Table 3.", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/18-mapk/Scaff-22_ground.bngl", + "file": "Scaff-22_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Scaff-22_tofit", + "name": "18-mapk", + "description": "For \"ground truth\" model, use median values such that hierarchy H1 occurs, as shown in Table 3.", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/18-mapk/Scaff-22_tofit.bngl", + "file": "Scaff-22_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "SHP2_base_model", + "name": "SHP2_base_model", + "description": "Base model of Shp2 regulation", + "tags": [ + "validation", + "shp2", + "base", + "model", + "r", + "s", + "exclude_reactants" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/SHP2basemodel/SHP2_base_model.bngl", + "file": "SHP2_base_model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "shp2-phosphatase-regulation", + "name": "shp2 phosphatase regulation", + "description": "SHP2 phosphatase regulation via autoinhibition and SH2 binding.", + "tags": [ + "shp2", + "phosphatase", + "regulation", + "rtk", + "substrate", + "v_dephos" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation.bngl", + "file": "shp2-phosphatase-regulation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "signal-amplification-cascade", + "name": "signal amplification cascade", + "description": "BioNetGen model: signal amplification cascade", + "tags": [ + "signal", + "amplification", + "cascade", + "ligand", + "receptor", + "effector", + "messenger" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/signalamplificationcascade/signal-amplification-cascade.bngl", + "file": "signal-amplification-cascade.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "simple", + "name": "simple", + "description": "Simple binding model", + "tags": [ + "published", + "tutorials", + "simple", + "s", + "t", + "dnat", + "trash" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "path": "Tutorials/General/simple/simple.bngl", + "file": "simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Simple", + "name": "Simple", + "description": "An example from a real application", + "tags": [ + "simple", + "setoption", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/Simple/Simple.bngl", + "file": "Simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Simple_AddActions", + "name": "Simple AddActions", + "description": "An example from a real application", + "tags": [ + "simple", + "addactions", + "setoption", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/SimpleAddActions/Simple_AddActions.bngl", + "file": "Simple_AddActions.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Simple_Answer", + "name": "Simple Answer", + "description": "An example from a real application", + "tags": [ + "simple", + "answer", + "setoption", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/SimpleAnswer/Simple_Answer.bngl", + "file": "Simple_Answer.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Simple_GenOnly", + "name": "Simple GenOnly", + "description": "An example from a real application", + "tags": [ + "simple", + "genonly", + "setoption", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly.bngl", + "file": "Simple_GenOnly.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "simple_nf_seed", + "name": "simple nf seed", + "description": "BioNetGen model: simple nf seed", + "tags": [ + "simple", + "nf", + "seed", + "a", + "b", + "function1", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/simplenfseed/simple_nf_seed.bngl", + "file": "simple_nf_seed.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "simple_nfsim_test", + "name": "simple_nfsim_test", + "description": "Runtime-only BNGL model migrated from public/models: simple_nfsim_test", + "tags": [ + "simple", + "nfsim", + "test" + ], + "category": "other", + "origin": "contributed", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "path": "Tutorials/simplenfsimtest/simple_nfsim_test.bngl", + "file": "simple_nfsim_test.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Simple_nogen", + "name": "Simple nogen", + "description": "An example from a real application", + "tags": [ + "simple", + "nogen", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/Simplenogen/Simple_nogen.bngl", + "file": "Simple_nogen.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "simple_sbml_import", + "name": "simple_sbml_import", + "description": "SBML import test", + "tags": [ + "validation", + "simple", + "sbml", + "import", + "readfile", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/simplesbmlimport/simple_sbml_import.bngl", + "file": "simple_sbml_import.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "simple_system", + "name": "simple_system", + "description": "Simple binding system", + "tags": [ + "validation", + "simple", + "system", + "x", + "y" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/simplesystem/simple_system.bngl", + "file": "simple_system.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "simple-dimerization", + "name": "simple dimerization", + "description": "BioNetGen model: simple dimerization", + "tags": [ + "simple", + "dimerization", + "a", + "b", + "generate_network", + "simulate" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/simpledimerization/simple-dimerization.bngl", + "file": "simple-dimerization.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "SIR", + "name": "SIR", + "description": "BioNetGen model: SIR", + "tags": [ + "sir", + "saveconcentrations", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/SIR/SIR.bngl", + "file": "SIR.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "sir-epidemic-model", + "name": "sir epidemic model", + "description": "BioNetGen model: sir epidemic model", + "tags": [ + "sir", + "epidemic", + "model", + "human", + "generate_network", + "simulate" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "tutorials", + "test-models" + ], + "path": "Examples/biology/sirepidemicmodel/sir-epidemic-model.bngl", + "file": "sir-epidemic-model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "smad-tgf-beta-signaling", + "name": "smad tgf beta signaling", + "description": "BioNetGen model: smad tgf beta signaling", + "tags": [ + "smad", + "tgf", + "beta", + "signaling", + "tgfb", + "tgfbr", + "smad2", + "smad4" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling.bngl", + "file": "smad-tgf-beta-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "sonic-hedgehog-gradient", + "name": "sonic hedgehog gradient", + "description": "Sonic Hedgehog (Shh) morphogen gradient formation.", + "tags": [ + "sonic", + "hedgehog", + "gradient", + "shh", + "ptc1", + "v_prod" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient.bngl", + "file": "sonic-hedgehog-gradient.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "sp_fourier_synthesizer", + "name": "sp fourier synthesizer", + "description": "Fourier Series Synthesizer in BNGL", + "tags": [ + "sp", + "fourier", + "synthesizer", + "s1", + "s3", + "s5", + "s7", + "s9", + "wave", + "c1" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl", + "file": "sp_fourier_synthesizer.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "sp_image_convolution", + "name": "sp image convolution", + "description": "Image Convolution Filter in BNGL", + "tags": [ + "sp", + "image", + "convolution", + "px", + "ex", + "sink" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/signal-processing/spimageconvolution/sp_image_convolution.bngl", + "file": "sp_image_convolution.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "sp_kalman_filter", + "name": "sp kalman filter", + "description": "Kalman Filter in BNGL", + "tags": [ + "sp", + "kalman", + "filter", + "truex", + "obs", + "estx", + "estv", + "variance", + "innovation" + ], + "category": "computer-science", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/signal-processing/spkalmanfilter/sp_kalman_filter.bngl", + "file": "sp_kalman_filter.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "stat3-mediated-transcription", + "name": "stat3 mediated transcription", + "description": "STAT3-mediated transcription and feedback.", + "tags": [ + "stat3", + "mediated", + "transcription", + "dna", + "pias3", + "mrna" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription.bngl", + "file": "stat3-mediated-transcription.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "stress-response-adaptation", + "name": "stress response adaptation", + "description": "BioNetGen model: stress response adaptation", + "tags": [ + "stress", + "response", + "adaptation", + "sensor", + "adapter", + "enzyme" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/stressresponseadaptation/stress-response-adaptation.bngl", + "file": "stress-response-adaptation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Suderman_2013", + "name": "Suderman 2013", + "description": "Ensemble model translated into BNGL", + "tags": [ + "suderman", + "2013", + "i", + "trash", + "pheromone", + "ste2", + "gpa1", + "ste4", + "sst2", + "ste20" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/Suderman2013/Suderman_2013.bngl", + "file": "Suderman_2013.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "synaptic-plasticity-ltp", + "name": "synaptic plasticity ltp", + "description": "Initial Concentrations", + "tags": [ + "synaptic", + "plasticity", + "ltp", + "glutamate", + "nmda", + "calcium", + "camkii", + "ampar", + "glusource" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp.bngl", + "file": "synaptic-plasticity-ltp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "synbio_band_pass_filter", + "name": "synbio band pass filter", + "description": "Model: synbio_band_pass_filter.bngl", + "tags": [ + "synbio", + "band", + "pass", + "filter", + "i", + "a", + "r", + "out" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter.bngl", + "file": "synbio_band_pass_filter.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "synbio_counter_molecular", + "name": "synbio counter molecular", + "description": "Model: synbio_counter_molecular.bngl", + "tags": [ + "synbio", + "counter", + "molecular", + "state", + "input" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl", + "file": "synbio_counter_molecular.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "synbio_edge_detector", + "name": "synbio edge detector", + "description": "Model: synbio_edge_detector.bngl", + "tags": [ + "synbio", + "edge", + "detector", + "x", + "y", + "z" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl", + "file": "synbio_edge_detector.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "synbio_logic_gates_enzymatic", + "name": "synbio logic gates enzymatic", + "description": "Model: synbio_logic_gates_enzymatic.bngl", + "tags": [ + "synbio", + "logic", + "gates", + "enzymatic", + "i1", + "i2", + "gateand", + "gateor", + "outand", + "outor" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl", + "file": "synbio_logic_gates_enzymatic.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "synbio_oscillator_synchronization", + "name": "synbio oscillator synchronization", + "description": "Model: synbio_oscillator_synchronization.bngl", + "tags": [ + "synbio", + "oscillator", + "synchronization", + "osc1", + "osc2", + "signal" + ], + "category": "synthetic-biology", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl", + "file": "synbio_oscillator_synchronization.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "t-cell-activation", + "name": "t cell activation", + "description": "BioNetGen model: t cell activation", + "tags": [ + "t", + "cell", + "activation", + "tcr", + "antigen", + "cytokine" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/tcellactivation/t-cell-activation.bngl", + "file": "t-cell-activation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "tcr", + "name": "tcr", + "description": "A model of T cell receptor signaling", + "tags": [ + "tcr", + "lig1", + "lig2", + "lig3", + "cd28", + "lck", + "itk", + "zap70" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/tcr/tcr.bngl", + "file": "tcr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "TCR_model", + "name": "ERK_model.bngl", + "description": "filename: ERK_model.bngl", + "tags": [ + "egf", + "erkpp_sos1_fb", + "erkpp_mek_fb", + "erkpp_raf1_fb", + "lambda", + "egfr_tot", + "ras_tot", + "sos_tot", + "rasgap_tot", + "raf_tot", + "mek_tot", + "erk_tot", + "ekar3_tot", + "erktr_tot", + "a1", + "d1", + "b1", + "u1a", + "u1b", + "b2a", + "u2a", + "b2b", + "u2b", + "k2a", + "k2b", + "b3", + "u3", + "k3", + "a2", + "d2", + "p1", + "q1", + "p2", + "q2", + "p3", + "q3", + "p4", + "q4", + "q5", + "p6", + "q6", + "a0_ekar3", + "d0_ekar3", + "a0_erktr", + "d0_erktr", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "path": "Published/Lin2019/TCR_model.bngl", + "file": "TCR_model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "test_ANG_synthesis_simple", + "name": "test_ANG_synthesis_simple", + "description": "Synthesis network test", + "tags": [ + "validation", + "test", + "ang", + "synthesis", + "simple", + "a", + "b", + "c", + "source", + "source2", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testANGsynthesissimple/test_ANG_synthesis_simple.bngl", + "file": "test_ANG_synthesis_simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "test_fixed", + "name": "test_fixed", + "description": "# actions ##", + "tags": [ + "validation", + "test", + "fixed", + "a", + "b", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testfixed/test_fixed.bngl", + "file": "test_fixed.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "test_MM", + "name": "test_MM", + "description": "Kinetic constants", + "tags": [ + "validation", + "test", + "mm", + "e", + "s", + "p", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testMM/test_MM.bngl", + "file": "test_MM.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "test_mratio", + "name": "test_mratio", + "description": "Reaction ratio test", + "tags": [ + "validation", + "test", + "mratio", + "a", + "b", + "c_theory", + "c_upper", + "c_lower" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testmratio/test_mratio.bngl", + "file": "test_mratio.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "test_network_gen", + "name": "test_network_gen", + "description": "fceri model with network generation", + "tags": [ + "validation", + "test", + "network", + "gen", + "lig", + "lyn", + "syk", + "rec" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testnetworkgen/test_network_gen.bngl", + "file": "test_network_gen.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "test_sat", + "name": "test_sat", + "description": "Kinetic constants", + "tags": [ + "validation", + "test", + "sat", + "e", + "s", + "p", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testsat/test_sat.bngl", + "file": "test_sat.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "test_synthesis_cBNGL_simple", + "name": "test_synthesis_cBNGL_simple", + "description": "Compartmental synthesis", + "tags": [ + "validation", + "test", + "synthesis", + "cbngl", + "simple", + "a", + "a2", + "b", + "c", + "source", + "source2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl", + "file": "test_synthesis_cBNGL_simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "test_synthesis_complex", + "name": "test_synthesis_complex", + "description": "Complex synthesis test", + "tags": [ + "validation", + "test", + "synthesis", + "complex", + "a", + "b", + "c", + "receptor", + "source", + "source2" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testsynthesiscomplex/test_synthesis_complex.bngl", + "file": "test_synthesis_complex.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "test_synthesis_complex_0_cBNGL", + "name": "test_synthesis_complex_0_cBNGL", + "description": "volume-surface", + "tags": [ + "validation", + "test", + "synthesis", + "complex", + "0", + "cbngl", + "volume_molecule1", + "volume_molecule2", + "surface_molecule1", + "surface_molecule2", + "volume_molecule3", + "volume_molecule4", + "volume_receptor", + "surface_receptor" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl", + "file": "test_synthesis_complex_0_cBNGL.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "test_synthesis_complex_source_cBNGL", + "name": "test_synthesis_complex_source_cBNGL", + "description": "volume-surface", + "tags": [ + "validation", + "test", + "synthesis", + "complex", + "source", + "cbngl", + "volume_molecule1", + "volume_molecule2", + "surface_molecule1", + "surface_molecule2", + "volume_molecule3", + "volume_molecule4", + "volume_receptor", + "surface_receptor" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl", + "file": "test_synthesis_complex_source_cBNGL.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "test_synthesis_simple", + "name": "test_synthesis_simple", + "description": "Simple synthesis test", + "tags": [ + "validation", + "test", + "synthesis", + "simple", + "a", + "b", + "c", + "source", + "source2", + "generate_network" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testsynthesissimple/test_synthesis_simple.bngl", + "file": "test_synthesis_simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "tlbr", + "name": "tlbr", + "description": "A model of trivalent ligand, bivalent receptor", + "tags": [ + "tlbr", + "l", + "r", + "lambda", + "fl" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/PyBioNetGen/core/tlbr/tlbr.bngl", + "file": "tlbr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "tlbr", + "name": "TLBR Tutorial", + "description": "Ligand binding", + "tags": [ + "published", + "immunology", + "tlbr", + "l", + "r", + "simulate_rm" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/tlbr/tlbr.bngl", + "file": "tlbr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "tlmr", + "name": "tlmr", + "description": "Trivalent ligand monovalent receptor", + "tags": [ + "validation", + "tlmr", + "l", + "r", + "generate_network", + "simulate_ode" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/tlmr/tlmr.bngl", + "file": "tlmr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "tlr3-dsrna-sensing", + "name": "tlr3 dsrna sensing", + "description": "TLR3-mediated dsRNA sensing and TRIF pathway activation.", + "tags": [ + "tlr3", + "dsrna", + "sensing", + "trif", + "irf3", + "sarm" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing.bngl", + "file": "tlr3-dsrna-sensing.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "tnf-induced-apoptosis", + "name": "tnf induced apoptosis", + "description": "BioNetGen model: tnf induced apoptosis", + "tags": [ + "tnf", + "induced", + "apoptosis", + "tnfr", + "caspase8", + "bid", + "caspase3" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis.bngl", + "file": "tnf-induced-apoptosis.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "toggle", + "name": "Toggle", + "description": "Toggle switch", + "tags": [ + "published", + "tutorial", + "native", + "toggle", + "x", + "y", + "generate_network", + "writemfile", + "setconcentration" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "synbio", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/toggle/toggle.bngl", + "file": "toggle.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "toy-jim", + "name": "toy-jim", + "description": "The model consists of a monovalent extracellular ligand,", + "tags": [ + "validation", + "toy", + "jim", + "l", + "r", + "a", + "k", + "null" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/toyjim/toy-jim.bngl", + "file": "toy-jim.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "toy1", + "name": "toy1", + "description": "Basic signaling toy", + "tags": [ + "published", + "tutorials", + "toy1", + "l", + "r", + "a", + "generate_network", + "writesbml", + "simulate_ode" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "path": "Tutorials/General/toy1/toy1.bngl", + "file": "toy1.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "toy2", + "name": "toy2", + "description": "Enzymatic reaction toy", + "tags": [ + "published", + "tutorials", + "toy2", + "l", + "r", + "a", + "k" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "path": "Tutorials/General/toy2/toy2.bngl", + "file": "toy2.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "translateSBML", + "name": "translateSBML", + "description": "title: translateSBML.bngl", + "tags": [ + "translatesbml", + "generate_network", + "simulate" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorial" + ], + "path": "Tutorials/NativeTutorials/translateSBML/translateSBML.bngl", + "file": "translateSBML.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Tricky", + "name": "Tricky", + "description": "An example from a real application", + "tags": [ + "tricky", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/Tricky/Tricky.bngl", + "file": "Tricky.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "TrickyUS", + "name": "TrickyUS", + "description": "An example from a real application", + "tags": [ + "trickyus", + "ag", + "r", + "h" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/TrickyUS/TrickyUS.bngl", + "file": "TrickyUS.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "trivial", + "name": "trivial", + "description": "A trivial model file for testing MCMC distributions.", + "tags": [ + "trivial", + "q", + "r", + "output", + "generate_network", + "simulate" + ], + "category": "validation", + "origin": "test-case", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/trivial/trivial.bngl", + "file": "trivial.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "two-component-system", + "name": "two component system", + "description": "BioNetGen model: two component system", + "tags": [ + "two", + "component", + "system", + "kinase", + "regulator", + "target" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/twocomponentsystem/two-component-system.bngl", + "file": "two-component-system.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "univ_synth", + "name": "univ_synth", + "description": "example of universal synthesis", + "tags": [ + "validation", + "univ", + "synth", + "a", + "b", + "c", + "generate_network", + "simulate_ode" + ], + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/univsynth/univ_synth.bngl", + "file": "univ_synth.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "vegf-angiogenesis", + "name": "vegf angiogenesis", + "description": "VEGF-mediated signaling in angiogenesis.", + "tags": [ + "vegf", + "angiogenesis", + "vegfr2", + "vegfr1", + "erk", + "endothelial" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/vegfangiogenesis/vegf-angiogenesis.bngl", + "file": "vegf-angiogenesis.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "vilar_2002", + "name": "Vilar 2002", + "description": "Genetic oscillator", + "tags": [ + "published", + "vilar", + "2002", + "dna", + "a", + "r" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "path": "Published/vilar2002/vilar_2002.bngl", + "file": "vilar_2002.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "vilar_2002b", + "name": "Vilar 2002b", + "description": "Gene oscillator", + "tags": [ + "published", + "vilar", + "2002b", + "dna", + "a", + "r" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "path": "Published/vilar2002b/vilar_2002b.bngl", + "file": "vilar_2002b.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "vilar_2002c", + "name": "Vilar 2002c", + "description": "Gene oscillator", + "tags": [ + "published", + "vilar", + "2002c", + "dna", + "a", + "r" + ], + "category": "regulation", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "path": "Published/vilar2002c/vilar_2002c.bngl", + "file": "vilar_2002c.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "viral-sensing-innate-immunity", + "name": "viral sensing innate immunity", + "description": "BioNetGen model: viral sensing innate immunity", + "tags": [ + "viral", + "sensing", + "innate", + "immunity", + "viralrna", + "rigi", + "mavs", + "irf3", + "ifnb" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity.bngl", + "file": "viral-sensing-innate-immunity.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "visualize", + "name": "Visualize", + "description": "Visualization toy", + "tags": [ + "published", + "tutorial", + "native", + "visualize", + "x", + "a1", + "a2", + "b" + ], + "category": "tutorial", + "origin": "tutorial", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/visualize/visualize.bngl", + "file": "visualize.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "wacky_alchemy_stone", + "name": "wacky alchemy stone", + "description": "Model: wacky_alchemy_stone.bngl", + "tags": [ + "wacky", + "alchemy", + "stone", + "lead", + "gold" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/wacky/wackyalchemystone/wacky_alchemy_stone.bngl", + "file": "wacky_alchemy_stone.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "wacky_black_hole", + "name": "wacky black hole", + "description": "Model: wacky_black_hole.bngl", + "tags": [ + "wacky", + "black", + "hole", + "m", + "bh", + "k_accrete", + "k_evap" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/wacky/wackyblackhole/wacky_black_hole.bngl", + "file": "wacky_black_hole.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "wacky_bouncing_ball", + "name": "wacky bouncing ball", + "description": "Model: wacky_bouncing_ball.bngl", + "tags": [ + "wacky", + "bouncing", + "ball", + "height", + "velocity" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "path": "Examples/wacky/wackybouncingball/wacky_bouncing_ball.bngl", + "file": "wacky_bouncing_ball.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "wacky_traffic_jam_asep", + "name": "wacky traffic jam asep", + "description": "Model: wacky_traffic_jam_asep.bngl", + "tags": [ + "wacky", + "traffic", + "jam", + "asep", + "site", + "car", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "path": "Examples/wacky/wackytrafficjamasep/wacky_traffic_jam_asep.bngl", + "file": "wacky_traffic_jam_asep.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "wacky_zombie_infection", + "name": "wacky zombie infection", + "description": "Model: wacky_zombie_infection.bngl", + "tags": [ + "wacky", + "zombie", + "infection", + "human" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "path": "Examples/wacky/wackyzombieinfection/wacky_zombie_infection.bngl", + "file": "wacky_zombie_infection.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "wnt", + "name": "Wnt Signaling", + "description": "Wnt signaling", + "tags": [ + "published", + "wnt", + "dsh", + "axc", + "frz", + "lrp5", + "bcat" + ], + "category": "regulation", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "path": "Published/wnt/wnt.bngl", + "file": "wnt.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "wnt-beta-catenin-signaling", + "name": "wnt beta catenin signaling", + "description": "Wnt/Beta-Catenin signaling (Canonical pathway).", + "tags": [ + "wnt", + "beta", + "catenin", + "signaling", + "frizzled", + "dvl", + "dest_complex", + "betacatenin", + "tcf" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling.bngl", + "file": "wnt-beta-catenin-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "wound-healing-pdgf-signaling", + "name": "wound healing pdgf signaling", + "description": "BioNetGen model: wound healing pdgf signaling", + "tags": [ + "wound", + "healing", + "pdgf", + "signaling", + "pdgfr", + "stat3", + "fibroblast" + ], + "category": "signaling", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling.bngl", + "file": "wound-healing-pdgf-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Yang_2008", + "name": "Yang 2008", + "description": "TLBR yang 2008", + "tags": [ + "published", + "physics", + "yang", + "2008" + ], + "category": "physics", + "origin": "published", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "path": "Published/Yang2008/tlbr_yang2008.bngl", + "file": "tlbr_yang2008.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Zhang_2021", + "name": "Zhang 2021", + "description": "CAR-T signaling", + "tags": [ + "published", + "zhang", + "2021", + "tie2", + "tie1", + "ang1_4", + "ang2_2", + "ang2_3", + "ang2_4", + "veptp", + "pten" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental" + ], + "path": "Published/Zhang2021/Zhang_2021.bngl", + "file": "Zhang_2021.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Zhang_2023", + "name": "Zhang 2023", + "description": "VEGF signaling", + "tags": [ + "published", + "zhang", + "2023", + "vegf", + "vegfr2", + "vegfr1", + "nrp1", + "pi", + "plcgamma", + "dag", + "ip3_cyto" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental" + ], + "path": "Published/Zhang2023/Zhang_2023.bngl", + "file": "Zhang_2023.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + } +] \ No newline at end of file diff --git a/manifest.json b/manifest.json index da96b57..fe5e655 100644 --- a/manifest.json +++ b/manifest.json @@ -1,10 +1,970 @@ [ + { + "id": "03_fcerig_fceri_gamma2", + "name": "03-fcerig", + "description": "Added molecule type definition block so that the", + "tags": [ + "immunology" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/03-fcerig/fceri_gamma2.bngl", + "file": "fceri_gamma2.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "04_egfrnf_egfr_nf", + "name": "example2_starting_point.bngl", + "description": "Filename: example2_starting_point.bngl", + "tags": [ + "f", + "lt_nm", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "molecules" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/04-egfrnf/egfr_nf.bngl", + "file": "egfr_nf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "06_degranulation_model_tofit", + "name": "of IgE receptor signaling", + "description": "A model of IgE receptor signaling", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/06-degranulation/model_tofit.bngl", + "file": "model_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "07_egg_egg", + "name": "07-egg", + "description": "BNGL model: egg", + "tags": [ + "a0", + "a1", + "a2", + "b1", + "b2", + "c0", + "c1", + "c2", + "d1", + "d2", + "period", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/07-egg/egg.bngl", + "file": "egg.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "10_egfr_egfr_ode", + "name": "example1.bngl", + "description": "Filename: example1.bngl", + "tags": [ + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/10-egfr/egfr_ode.bngl", + "file": "egfr_ode.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "11_TLBR_tlbr", + "name": "11-TLBR", + "description": "BNGL model: tlbr", + "tags": [ + "alpha", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/11-TLBR/tlbr.bngl", + "file": "tlbr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "12_TCR_tcr", + "name": "of T cell receptor signaling", + "description": "A model of T cell receptor signaling", + "tags": [ + "immunology" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/12-TCR/tcr.bngl", + "file": "tcr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "14_receptor_nf_receptor_nf", + "name": "of ligand/receptor binding and receptor phosphorylation.", + "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", + "tags": [ + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/14-receptor-nf/receptor_nf.bngl", + "file": "receptor_nf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "15_igf1r_IGF1R_fit_all", + "name": "15-igf1r", + "description": "Author: William S. Hlavacek", + "tags": [ + "dilution", + "a1_permpers", + "a2_permpers", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/15-igf1r/IGF1R_fit_all.bngl", + "file": "IGF1R_fit_all.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "19_raf_constraint_RAFi", + "name": "19-raf-constraint", + "description": "BNGL model: RAFi", + "tags": [ + "k1", + "k2", + "k3", + "k5", + "kf1", + "kf2", + "kf3", + "kf4", + "kf5", + "kf6", + "rtot", + "ifree", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/19-raf-constraint/RAFi.bngl", + "file": "RAFi.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_CHO_EGFR_best-fit", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_CHO_EGFR_best-fit.bngl", + "file": "190127_CHO_EGFR_best-fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_CHO_EGFR_Epigen", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_CHO_EGFR_Epigen.bngl", + "file": "190127_CHO_EGFR_Epigen.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_CHO_EGFR_sensitivity", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_CHO_EGFR_sensitivity.bngl", + "file": "190127_CHO_EGFR_sensitivity.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_CHO_HA_EGFR_L858R", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_CHO_HA_EGFR_L858R.bngl", + "file": "190127_CHO_HA_EGFR_L858R.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_HeLa", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_HeLa.bngl", + "file": "190127_HeLa.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_HMEC", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_HMEC.bngl", + "file": "190127_HMEC.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "190127_MCF10A", + "name": "Salazar-Cavazos2019", + "description": "BNGL model: 190127_CHO_EGFR_best-fit", + "tags": [ + "grb2_total__free", + "shc1_total__free", + "kdephosy1068__free", + "kdephosyn__free", + "ratio_kpkd_y1068__free", + "ratio_kpkd_yn__free", + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/190127_MCF10A.bngl", + "file": "190127_MCF10A.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "20_raf_constraint4_RAFi", + "name": "20-raf-constraint4", + "description": "BNGL model: RAFi", + "tags": [ + "k1", + "k2", + "k3", + "k5", + "kf1", + "kf2", + "kf3", + "kf4", + "kf5", + "kf6", + "rtot", + "ifree", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/20-raf-constraint4/RAFi.bngl", + "file": "RAFi.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "24_jnk_JNKmodel_180724_bnf", + "name": "24-jnk", + "description": "BNGL model: JNKmodel_180724_bnf", + "tags": [ + "scale_t", + "ani", + "k3_zakbyu1", + "k1_u1tozak", + "d3_zak", + "d1_zak", + "k3_mkk4byzak", + "k1_zaktomkk4", + "d3_mkk4", + "d1_mkk4", + "k3_mkk7byzak", + "k1_zaktomkk7", + "f3_mkk7byzak", + "d3_mkk7", + "d1_mkk7", + "k3_jnkbymkk4", + "k1_mkk4tojnk", + "k3_jnkbymkk7", + "k1_mkk7tojnk", + "f3_jnkbymkk7", + "d3_jnk", + "d1_jnk", + "k3_mkk7byjnk", + "k1_jnktomkk7", + "inh_jnk", + "d3_mkk7byjnkpt", + "d1_jnkpttomkk7", + "f1_zaktomkk7p", + "k1_zaktojnk", + "k3_mkk4byakt", + "k1_akttomkk4", + "k3_mkk7byakt", + "k1_akttomkk7", + "d3_mkk4byaktpt", + "d1_aktpttomkk4", + "d3_mkk7byaktpt", + "d1_aktpttomkk7", + "scale_ppmkk4", + "scale_ppmkk7", + "scale_ppjnk", + "pakt", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/24-jnk/JNKmodel_180724_bnf.bngl", + "file": "JNKmodel_180724_bnf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "26_tcr_sens_tcr_sens_tofit", + "name": "for the Manz/Groves 2011 data", + "description": "Modification of Mukhopadhyay/Dushek 2013 model for the Manz/Groves 2011 data", + "tags": [ + "immunology" + ], + "category": "immunology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/26-tcr-sens/tcr_sens_tofit.bngl", + "file": "tcr_sens_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "31_elephant_elephant", + "name": "31-elephant", + "description": "BNGL model: elephant", + "tags": [ + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10", + "a11", + "a12", + "a13", + "a14", + "a15", + "a16", + "a17", + "a18", + "a19", + "a20", + "b1", + "b2", + "b3", + "b4", + "b5", + "b6", + "b7", + "b8", + "b9", + "b10", + "b11", + "b12", + "b13", + "b14", + "b15", + "b16", + "b17", + "b18", + "b19", + "b20", + "c0", + "c1", + "c2", + "c3", + "c4", + "c5", + "c6", + "c7", + "c8", + "c9", + "c10", + "c11", + "c12", + "c13", + "c14", + "c15", + "c16", + "c17", + "c18", + "c19", + "c20", + "d1", + "d2", + "d3", + "d4", + "d5", + "d6", + "d7", + "d8", + "d9", + "d10", + "d11", + "d12", + "d13", + "d14", + "d15", + "d16", + "d17", + "d18", + "d19", + "d20", + "tmax", + "t", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/31-elephant/elephant.bngl", + "file": "elephant.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, { "id": "AB", "name": "AB", "description": "BioNetGen model: AB", - "path": "Tutorials/NativeTutorials/AB/AB.bngl", - "file": "AB.bngl", "tags": [ "ab", "a", @@ -12,34 +972,59 @@ "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/AB/AB.bngl", + "file": "AB.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "ABC", "name": "ABC", "description": "BioNetGen model: ABC", - "path": "Tutorials/NativeTutorials/ABC/ABC.bngl", - "file": "ABC.bngl", "tags": [ "abc", "a", "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABC/ABC.bngl", + "file": "ABC.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "ABC_scan", "name": "ABC scan", "description": "BioNetGen model: ABC scan", - "path": "Tutorials/NativeTutorials/ABCscan/ABC_scan.bngl", - "file": "ABC_scan.bngl", "tags": [ "abc", "scan", @@ -48,17 +1033,29 @@ "parameter_scan" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABCscan/ABC_scan.bngl", + "file": "ABC_scan.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ABC_ssa", "name": "ABC ssa", "description": "BioNetGen model: ABC ssa", - "path": "Tutorials/NativeTutorials/ABCssa/ABC_ssa.bngl", - "file": "ABC_ssa.bngl", "tags": [ "abc", "ssa", @@ -66,35 +1063,29 @@ "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null - }, - { - "id": "Abilene_TX_Abilene_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - Abilene_TX_Abilene_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Abilene_TX_Abilene_TX.bngl", - "file": "Abilene_TX_Abilene_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "native-tutorials" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Tutorials/NativeTutorials/ABCssa/ABC_ssa.bngl", + "file": "ABC_ssa.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ABp", "name": "ABp", "description": "title: ABp.bngl", - "path": "Tutorials/NativeTutorials/ABp/ABp.bngl", - "file": "ABp.bngl", "tags": [ "abp", "a", @@ -102,17 +1093,30 @@ "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABp/ABp.bngl", + "file": "ABp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "ABp_approx", "name": "ABp approx", "description": "title: ABp.bngl", - "path": "Tutorials/NativeTutorials/ABpapprox/ABp_approx.bngl", - "file": "ABp_approx.bngl", "tags": [ "abp", "approx", @@ -122,17 +1126,29 @@ "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ABpapprox/ABp_approx.bngl", + "file": "ABp_approx.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "actions_syntax", "name": "actions syntax", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/actionssyntax/actions_syntax.bngl", - "file": "actions_syntax.bngl", "tags": [ "actions", "syntax", @@ -142,35 +1158,134 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null - }, - { - "id": "Akron_OH_Akron_OH", - "name": "Mallela 2022 - COVID-19 MSA Models - Akron_OH_Akron_OH", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Akron_OH_Akron_OH.bngl", - "file": "Akron_OH_Akron_OH.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/actionssyntax/actions_syntax.bngl", + "file": "actions_syntax.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "after_bunching", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/after_bunching.bngl", + "file": "after_bunching.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "after_decoupling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/after_decoupling.bngl", + "file": "after_decoupling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "after_scaling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/after_scaling.bngl", + "file": "after_scaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "akt-signaling", "name": "akt signaling", "description": "Signaling rates", - "path": "Contributed/BNGPlayground_Examples/biology/aktsignaling/akt-signaling.bngl", - "file": "akt-signaling.bngl", "tags": [ "akt", "signaling", @@ -182,17 +1297,29 @@ "s6k" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/aktsignaling/akt-signaling.bngl", + "file": "akt-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Alabama", "name": "Alabama", "description": "reporting period (1 d)", - "path": "Published/Mallela2022/Alabama/Alabama.bngl", - "file": "Alabama.bngl", "tags": [ "alabama", "fdcs", @@ -205,145 +1332,62 @@ "e5" ], "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/Mallela2022/Alabama/Alabama.bngl", + "file": "Alabama.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Albany_GA_Albany_GA", - "name": "Mallela 2022 - COVID-19 MSA Models - Albany_GA_Albany_GA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Albany_GA_Albany_GA.bngl", - "file": "Albany_GA_Albany_GA.bngl", + "id": "allosteric-activation", + "name": "allosteric activation", + "description": "Binding constants", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "allosteric", + "activation", + "enzyme", + "substrate", + "activator", + "product" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Albany-Schenectady-Troy_NY_Albany-Schenectady-Troy_NY", - "name": "Mallela 2022 - COVID-19 MSA Models - Albany-Schenectady-Troy_NY_Albany-Schenectady-Troy_NY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Albany-Schenectady-Troy_NY_Albany-Schenectady-Troy_NY.bngl", - "file": "Albany-Schenectady-Troy_NY_Albany-Schenectady-Troy_NY.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Albuquerque_NM_Albuquerque_NM", - "name": "Mallela 2022 - COVID-19 MSA Models - Albuquerque_NM_Albuquerque_NM", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Albuquerque_NM_Albuquerque_NM.bngl", - "file": "Albuquerque_NM_Albuquerque_NM.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Alexandria_LA_Alexandria_LA", - "name": "Mallela 2022 - COVID-19 MSA Models - Alexandria_LA_Alexandria_LA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Alexandria_LA_Alexandria_LA.bngl", - "file": "Alexandria_LA_Alexandria_LA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Allentown-Bethlehem-Easton_PA-NJ_Allentown-Bethlehem-Easton_PA-NJ", - "name": "Mallela 2022 - COVID-19 MSA Models - Allentown-Bethlehem-Easton_PA-NJ_Allentown-Bethlehem-Easton_PA-NJ", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Allentown-Bethlehem-Easton_PA-NJ_Allentown-Bethlehem-Easton_PA-NJ.bngl", - "file": "Allentown-Bethlehem-Easton_PA-NJ_Allentown-Bethlehem-Easton_PA-NJ.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "allosteric-activation", - "name": "allosteric activation", - "description": "Binding constants", - "path": "Contributed/BNGPlayground_Examples/biology/allostericactivation/allosteric-activation.bngl", + "path": "Examples/biology/allostericactivation/allosteric-activation.bngl", "file": "allosteric-activation.bngl", - "tags": [ - "allosteric", - "activation", - "enzyme", - "substrate", - "activator", - "product" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "ai-generated", - "visible": false, - "collectionId": null - }, - { - "id": "Amarillo_TX_Amarillo_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - Amarillo_TX_Amarillo_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Amarillo_TX_Amarillo_TX.bngl", - "file": "Amarillo_TX_Amarillo_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ampk-signaling", "name": "ampk signaling", "description": "AMPK signaling: The cellular energy sensor.", - "path": "Contributed/BNGPlayground_Examples/biology/ampksignaling/ampk-signaling.bngl", - "file": "ampk-signaling.bngl", "tags": [ "ampk", "signaling", @@ -354,17 +1398,30 @@ "crtc" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/ampksignaling/ampk-signaling.bngl", + "file": "ampk-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "An_2009", "name": "An 2009", "description": "TLR4 signaling", - "path": "Published/An2009/An_2009.bngl", - "file": "An_2009.bngl", "tags": [ "published", "immunology", @@ -380,53 +1437,29 @@ "irak1" ], "category": "immunology", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null - }, - { - "id": "Anchorage_AK_Anchorage_AK", - "name": "Mallela 2022 - COVID-19 MSA Models - Anchorage_AK_Anchorage_AK", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Anchorage_AK_Anchorage_AK.bngl", - "file": "Anchorage_AK_Anchorage_AK.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Ann_Arbor_MI_Ann_Arbor_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Ann_Arbor_MI_Ann_Arbor_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Ann_Arbor_MI_Ann_Arbor_MI.bngl", - "file": "Ann_Arbor_MI_Ann_Arbor_MI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/An2009/An_2009.bngl", + "file": "An_2009.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "apoptosis-cascade", "name": "apoptosis cascade", "description": "Apoptosis cascade: Integrated extrinsic and intrinsic death signaling.", - "path": "Contributed/BNGPlayground_Examples/biology/apoptosiscascade/apoptosis-cascade.bngl", - "file": "apoptosis-cascade.bngl", "tags": [ "apoptosis", "cascade", @@ -440,161 +1473,30 @@ "smac" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Appleton_WI_Appleton_WI", - "name": "Mallela 2022 - COVID-19 MSA Models - Appleton_WI_Appleton_WI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Appleton_WI_Appleton_WI.bngl", - "file": "Appleton_WI_Appleton_WI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Asheville_NC_Asheville_NC", - "name": "Mallela 2022 - COVID-19 MSA Models - Asheville_NC_Asheville_NC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Asheville_NC_Asheville_NC.bngl", - "file": "Asheville_NC_Asheville_NC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Athens-Clarke_County_GA_Athens-Clarke_County_GA", - "name": "Mallela 2022 - COVID-19 MSA Models - Athens-Clarke_County_GA_Athens-Clarke_County_GA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Athens-Clarke_County_GA_Athens-Clarke_County_GA.bngl", - "file": "Athens-Clarke_County_GA_Athens-Clarke_County_GA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Atlanta-Sandy_Springs-Alpharetta_GA_Atlanta-Sandy_Springs-Alpharetta_GA", - "name": "Mallela 2022 - COVID-19 MSA Models - Atlanta-Sandy_Springs-Alpharetta_GA_Atlanta-Sandy_Springs-Alpharetta_GA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Atlanta-Sandy_Springs-Alpharetta_GA_Atlanta-Sandy_Springs-Alpharetta_GA.bngl", - "file": "Atlanta-Sandy_Springs-Alpharetta_GA_Atlanta-Sandy_Springs-Alpharetta_GA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Atlantic_City-Hammonton_NJ_Atlantic_City-Hammonton_NJ", - "name": "Mallela 2022 - COVID-19 MSA Models - Atlantic_City-Hammonton_NJ_Atlantic_City-Hammonton_NJ", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Atlantic_City-Hammonton_NJ_Atlantic_City-Hammonton_NJ.bngl", - "file": "Atlantic_City-Hammonton_NJ_Atlantic_City-Hammonton_NJ.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Auburn-Opelika_AL_Auburn-Opelika_AL", - "name": "Mallela 2022 - COVID-19 MSA Models - Auburn-Opelika_AL_Auburn-Opelika_AL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Auburn-Opelika_AL_Auburn-Opelika_AL.bngl", - "file": "Auburn-Opelika_AL_Auburn-Opelika_AL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Augusta-Richmond_County_GA-SC_Augusta-Richmond_County_GA-SC", - "name": "Mallela 2022 - COVID-19 MSA Models - Augusta-Richmond_County_GA-SC_Augusta-Richmond_County_GA-SC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Augusta-Richmond_County_GA-SC_Augusta-Richmond_County_GA-SC.bngl", - "file": "Augusta-Richmond_County_GA-SC_Augusta-Richmond_County_GA-SC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Austin-Round_Rock_TX_Austin-Round_Rock_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - Austin-Round_Rock_TX_Austin-Round_Rock_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Austin-Round_Rock_TX_Austin-Round_Rock_TX.bngl", - "file": "Austin-Round_Rock_TX_Austin-Round_Rock_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/apoptosiscascade/apoptosis-cascade.bngl", + "file": "apoptosis-cascade.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "auto-activation-loop", "name": "auto activation loop", "description": "Auto-activation loop: A positive feedback circuit.", - "path": "Contributed/BNGPlayground_Examples/biology/autoactivationloop/auto-activation-loop.bngl", - "file": "auto-activation-loop.bngl", "tags": [ "auto", "activation", @@ -605,17 +1507,30 @@ "rbp" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/autoactivationloop/auto-activation-loop.bngl", + "file": "auto-activation-loop.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "autophagy-regulation", "name": "autophagy regulation", "description": "Autophagy regulation: mTOR and AMPK competition on the ULK1 switch.", - "path": "Contributed/BNGPlayground_Examples/biology/autophagyregulation/autophagy-regulation.bngl", - "file": "autophagy-regulation.bngl", "tags": [ "autophagy", "regulation", @@ -626,17 +1541,30 @@ "p62" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/autophagyregulation/autophagy-regulation.bngl", + "file": "autophagy-regulation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "BAB", "name": "BAB", "description": "Simple binding model with a bivalent A molecule that has two identical sites", - "path": "Tutorials/NativeTutorials/BAB/BAB.bngl", - "file": "BAB.bngl", "tags": [ "bab", "a", @@ -644,17 +1572,29 @@ "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/BAB/BAB.bngl", + "file": "BAB.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "BAB_coop", "name": "BAB coop", "description": "Simple binding model with a bivalent A molecule that has two identical sites", - "path": "Tutorials/NativeTutorials/BABcoop/BAB_coop.bngl", - "file": "BAB_coop.bngl", "tags": [ "bab", "coop", @@ -663,17 +1603,29 @@ "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/BABcoop/BAB_coop.bngl", + "file": "BAB_coop.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "BAB_scan", "name": "BAB scan", "description": "Simple binding model with a bivalent A molecule that has two identical sites", - "path": "Tutorials/NativeTutorials/BABscan/BAB_scan.bngl", - "file": "BAB_scan.bngl", "tags": [ "bab", "scan", @@ -683,91 +1635,61 @@ "parameter_scan" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/BABscan/BAB_scan.bngl", + "file": "BAB_scan.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Bakersfield_CA_Bakersfield_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Bakersfield_CA_Bakersfield_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Bakersfield_CA_Bakersfield_CA.bngl", - "file": "Bakersfield_CA_Bakersfield_CA.bngl", + "id": "Barua_2007", + "name": "Barua 2007", + "description": "Model from Haugh (2006)", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "published", + "barua", + "2007", + "version", + "r", + "s" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "signaling", "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Barua2007/Barua_2007.bngl", + "file": "Barua_2007.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "Baltimore-Columbia-Towson_MD_Baltimore-Columbia-Towson_MD", - "name": "Mallela 2022 - COVID-19 MSA Models - Baltimore-Columbia-Towson_MD_Baltimore-Columbia-Towson_MD", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Baltimore-Columbia-Towson_MD_Baltimore-Columbia-Towson_MD.bngl", - "file": "Baltimore-Columbia-Towson_MD_Baltimore-Columbia-Towson_MD.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Barnstable_Town_MA_Barnstable_Town_MA", - "name": "Mallela 2022 - COVID-19 MSA Models - Barnstable_Town_MA_Barnstable_Town_MA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Barnstable_Town_MA_Barnstable_Town_MA.bngl", - "file": "Barnstable_Town_MA_Barnstable_Town_MA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Barua_2007", - "name": "Barua 2007", - "description": "Model from Haugh (2006)", - "path": "Published/Barua2007/Barua_2007.bngl", - "file": "Barua_2007.bngl", - "tags": [ - "published", - "barua", - "2007", - "version", - "r", - "s" - ], - "category": "signaling", - "bng2_compatible": false, - "origin": "published", - "visible": true, - "collectionId": null - }, - { - "id": "Barua_2009", - "name": "Barua 2009", - "description": "JAK2-SH2B signaling", - "path": "Published/Barua2009/Barua_2009.bngl", - "file": "Barua_2009.bngl", + "id": "Barua_2009", + "name": "Barua 2009", + "description": "JAK2-SH2B signaling", "tags": [ "published", "barua", @@ -776,17 +1698,29 @@ "j" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Barua2009/Barua_2009.bngl", + "file": "Barua_2009.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Barua_2013", "name": "Barua 2013", "description": "Beta-catenin destruction", - "path": "Published/Barua2013/Barua_2013.bngl", - "file": "Barua_2013.bngl", "tags": [ "published", "barua", @@ -798,17 +1732,27 @@ "ck1a" ], "category": "regulation", - "bng2_compatible": false, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Barua2013/Barua_2013.bngl", + "file": "Barua_2013.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "BaruaBCR_2012", "name": "Barua 2012", "description": "BCR signaling", - "path": "Published/BaruaBCR2012/BaruaBCR_2012.bngl", - "file": "BaruaBCR_2012.bngl", "tags": [ "published", "immunology", @@ -822,17 +1766,29 @@ "syk" ], "category": "immunology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/BaruaBCR2012/BaruaBCR_2012.bngl", + "file": "BaruaBCR_2012.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "BaruaFceRI_2012", "name": "BaruaFceRI 2012", "description": "FcεRI signaling", - "path": "Published/BaruaFceRI2012/BaruaFceRI_2012.bngl", - "file": "BaruaFceRI_2012.bngl", "tags": [ "published", "immunology", @@ -848,71 +1804,29 @@ "syk" ], "category": "immunology", - "bng2_compatible": false, - "origin": "published", - "visible": false, - "collectionId": null - }, - { - "id": "Baton_Rouge_LA_Baton_Rouge_LA", - "name": "Mallela 2022 - COVID-19 MSA Models - Baton_Rouge_LA_Baton_Rouge_LA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Baton_Rouge_LA_Baton_Rouge_LA.bngl", - "file": "Baton_Rouge_LA_Baton_Rouge_LA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Battle_Creek_MI_Battle_Creek_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Battle_Creek_MI_Battle_Creek_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Battle_Creek_MI_Battle_Creek_MI.bngl", - "file": "Battle_Creek_MI_Battle_Creek_MI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Bay_City_MI_Bay_City_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Bay_City_MI_Bay_City_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Bay_City_MI_Bay_City_MI.bngl", - "file": "Bay_City_MI_Bay_City_MI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/BaruaFceRI2012/BaruaFceRI_2012.bngl", + "file": "BaruaFceRI_2012.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "bcr-signaling", "name": "bcr signaling", "description": "BCR signaling: The B-cell antigen receptor cascade.", - "path": "Contributed/BNGPlayground_Examples/biology/bcrsignaling/bcr-signaling.bngl", - "file": "bcr-signaling.bngl", "tags": [ "bcr", "signaling", @@ -924,71 +1838,135 @@ "calcium" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Beantown_m11", - "name": "Mallela 2021 - COVID-19 City Models - Beantown_m11", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/Beantown_m11.bngl", - "file": "Beantown_m11.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, + "path": "Examples/biology/bcrsignaling/bcr-signaling.bngl", + "file": "bcr-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "before_bunching", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" + ], + "category": "other", "origin": "published", "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "Beaumont-Port_Arthur_TX_Beaumont-Port_Arthur_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - Beaumont-Port_Arthur_TX_Beaumont-Port_Arthur_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Beaumont-Port_Arthur_TX_Beaumont-Port_Arthur_TX.bngl", - "file": "Beaumont-Port_Arthur_TX_Beaumont-Port_Arthur_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/before_bunching.bngl", + "file": "before_bunching.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "before_decoupling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "other", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Bellingham_WA_Bellingham_WA", - "name": "Mallela 2022 - COVID-19 MSA Models - Bellingham_WA_Bellingham_WA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Bellingham_WA_Bellingham_WA.bngl", - "file": "Bellingham_WA_Bellingham_WA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/before_decoupling.bngl", + "file": "before_decoupling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "before_scaling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "other", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/before_scaling.bngl", + "file": "before_scaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "beta-adrenergic-response", "name": "beta adrenergic response", "description": "Beta-adrenergic signaling: GPCR pathway and desensitization.", - "path": "Contributed/BNGPlayground_Examples/biology/betaadrenergicresponse/beta-adrenergic-response.bngl", - "file": "beta-adrenergic-response.bngl", "tags": [ "beta", "adrenergic", @@ -1001,89 +1979,30 @@ "camp" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "BigApple_m1", - "name": "Mallela 2021 - COVID-19 City Models - BigApple_m1", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/BigApple_m1.bngl", - "file": "BigApple_m1.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "BigD_m4", - "name": "Mallela 2021 - COVID-19 City Models - BigD_m4", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/BigD_m4.bngl", - "file": "BigD_m4.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "Binghamton_NY_Binghamton_NY", - "name": "Mallela 2022 - COVID-19 MSA Models - Binghamton_NY_Binghamton_NY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Binghamton_NY_Binghamton_NY.bngl", - "file": "Binghamton_NY_Binghamton_NY.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Birmingham-Hoover_AL_Birmingham-Hoover_AL", - "name": "Mallela 2022 - COVID-19 MSA Models - Birmingham-Hoover_AL_Birmingham-Hoover_AL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Birmingham-Hoover_AL_Birmingham-Hoover_AL.bngl", - "file": "Birmingham-Hoover_AL_Birmingham-Hoover_AL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/biology/betaadrenergicresponse/beta-adrenergic-response.bngl", + "file": "beta-adrenergic-response.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "birth-death", "name": "Birth-Death", "description": "Stochastic process", - "path": "Tutorials/NativeTutorials/birthdeath/birth-death.bngl", - "file": "birth-death.bngl", "tags": [ "published", "tutorial", @@ -1096,17 +2015,30 @@ "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/birthdeath/birth-death.bngl", + "file": "birth-death.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "bistable-toggle-switch", "name": "bistable toggle switch", "description": "Genetic Toggle Switch: Mutual repression circuit.", - "path": "Contributed/BNGPlayground_Examples/biology/bistabletoggleswitch/bistable-toggle-switch.bngl", - "file": "bistable-toggle-switch.bngl", "tags": [ "bistable", "toggle", @@ -1119,17 +2051,29 @@ "ind_r" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/bistabletoggleswitch/bistable-toggle-switch.bngl", + "file": "bistable-toggle-switch.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "BLBR", "name": "BLBR", "description": "title: BLBR.bngl", - "path": "Tutorials/NativeTutorials/BLBR/BLBR.bngl", - "file": "BLBR.bngl", "tags": [ "blbr", "setoption", @@ -1138,17 +2082,30 @@ "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode", + "nf" + ] + }, + "gallery": [ + "tutorial" + ], + "path": "Tutorials/NativeTutorials/BLBR/BLBR.bngl", + "file": "BLBR.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Blinov_2006", "name": "Blinov 2006", "description": "Phosphotyrosine signaling", - "path": "Published/Blinov2006/Blinov_2006.bngl", - "file": "Blinov_2006.bngl", "tags": [ "published", "blinov", @@ -1160,17 +2117,29 @@ "sos" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "path": "Published/Blinov2006/Blinov_2006.bngl", + "file": "Blinov_2006.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Blinov_egfr", "name": "Blinov egfr", "description": "EGFR signaling model", - "path": "Published/Blinovegfr/Blinov_egfr.bngl", - "file": "Blinov_egfr.bngl", "tags": [ "published", "nfsim", @@ -1182,17 +2151,29 @@ "simulate_nf" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Blinovegfr/Blinov_egfr.bngl", + "file": "Blinov_egfr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Blinov_ran", "name": "Blinov ran", "description": "Ran GTPase cycle", - "path": "Published/Blinovran/Blinov_ran.bngl", - "file": "Blinov_ran.bngl", "tags": [ "published", "nfsim", @@ -1203,17 +2184,29 @@ "simulate_nf" ], "category": "regulation", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "cell-cycle" + ], + "path": "Published/Blinovran/Blinov_ran.bngl", + "file": "Blinov_ran.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "blood-coagulation-thrombin", "name": "blood coagulation thrombin", "description": "Blood coagulation: Thrombin burst and feedback propagation.", - "path": "Contributed/BNGPlayground_Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin.bngl", - "file": "blood-coagulation-thrombin.bngl", "tags": [ "blood", "coagulation", @@ -1226,53 +2219,30 @@ "at" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Bloomington_IN_Bloomington_IN", - "name": "Mallela 2022 - COVID-19 MSA Models - Bloomington_IN_Bloomington_IN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Bloomington_IN_Bloomington_IN.bngl", - "file": "Bloomington_IN_Bloomington_IN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Bloomsburg-Berwick_PA_Bloomsburg-Berwick_PA", - "name": "Mallela 2022 - COVID-19 MSA Models - Bloomsburg-Berwick_PA_Bloomsburg-Berwick_PA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Bloomsburg-Berwick_PA_Bloomsburg-Berwick_PA.bngl", - "file": "Bloomsburg-Berwick_PA_Bloomsburg-Berwick_PA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/biology/bloodcoagulationthrombin/blood-coagulation-thrombin.bngl", + "file": "blood-coagulation-thrombin.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "bmp-signaling", "name": "bmp signaling", "description": "BMP-Smad signaling: Developmental gradient relay.", - "path": "Contributed/BNGPlayground_Examples/biology/bmpsignaling/bmp-signaling.bngl", - "file": "bmp-signaling.bngl", "tags": [ "bmp", "signaling", @@ -1284,17 +2254,30 @@ "smad6" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/bmpsignaling/bmp-signaling.bngl", + "file": "bmp-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "bng_error", "name": "bng error", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/bngerror/bng_error.bngl", - "file": "bng_error.bngl", "tags": [ "bng", "error", @@ -1304,217 +2287,62 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/bngerror/bng_error.bngl", + "file": "bng_error.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Boise_City_ID_Boise_City_ID", - "name": "Mallela 2022 - COVID-19 MSA Models - Boise_City_ID_Boise_City_ID", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Boise_City_ID_Boise_City_ID.bngl", - "file": "Boise_City_ID_Boise_City_ID.bngl", + "id": "brusselator-oscillator", + "name": "brusselator oscillator", + "description": "The Brusselator: Auto-catalytic chemical oscillator.", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "brusselator", + "oscillator", + "a", + "b", + "x", + "y" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Boston-Cambridge-Newton_MA-NH_Boston-Cambridge-Newton_MA-NH", - "name": "Mallela 2022 - COVID-19 MSA Models - Boston-Cambridge-Newton_MA-NH_Boston-Cambridge-Newton_MA-NH", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Boston-Cambridge-Newton_MA-NH_Boston-Cambridge-Newton_MA-NH.bngl", - "file": "Boston-Cambridge-Newton_MA-NH_Boston-Cambridge-Newton_MA-NH.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Boulder_CO_Boulder_CO", - "name": "Mallela 2022 - COVID-19 MSA Models - Boulder_CO_Boulder_CO", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Boulder_CO_Boulder_CO.bngl", - "file": "Boulder_CO_Boulder_CO.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Bowling_Green_KY_Bowling_Green_KY", - "name": "Mallela 2022 - COVID-19 MSA Models - Bowling_Green_KY_Bowling_Green_KY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Bowling_Green_KY_Bowling_Green_KY.bngl", - "file": "Bowling_Green_KY_Bowling_Green_KY.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Bridgeport-Stamford-Norwalk_CT_Bridgeport-Stamford-Norwalk_CT", - "name": "Mallela 2022 - COVID-19 MSA Models - Bridgeport-Stamford-Norwalk_CT_Bridgeport-Stamford-Norwalk_CT", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Bridgeport-Stamford-Norwalk_CT_Bridgeport-Stamford-Norwalk_CT.bngl", - "file": "Bridgeport-Stamford-Norwalk_CT_Bridgeport-Stamford-Norwalk_CT.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "BrotherlyLove_m8", - "name": "Mallela 2021 - COVID-19 City Models - BrotherlyLove_m8", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/BrotherlyLove_m8.bngl", - "file": "BrotherlyLove_m8.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "Brownsville-Harlingen_TX_Brownsville-Harlingen_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - Brownsville-Harlingen_TX_Brownsville-Harlingen_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Brownsville-Harlingen_TX_Brownsville-Harlingen_TX.bngl", - "file": "Brownsville-Harlingen_TX_Brownsville-Harlingen_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "brusselator-oscillator", - "name": "brusselator oscillator", - "description": "The Brusselator: Auto-catalytic chemical oscillator.", - "path": "Contributed/BNGPlayground_Examples/biology/brusselatoroscillator/brusselator-oscillator.bngl", - "file": "brusselator-oscillator.bngl", - "tags": [ - "brusselator", - "oscillator", - "a", - "b", - "x", - "y" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "ai-generated", - "visible": false, - "collectionId": null - }, - { - "id": "Buffalo-Niagara_Falls_NY_Buffalo-Niagara_Falls_NY", - "name": "Mallela 2022 - COVID-19 MSA Models - Buffalo-Niagara_Falls_NY_Buffalo-Niagara_Falls_NY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Buffalo-Niagara_Falls_NY_Buffalo-Niagara_Falls_NY.bngl", - "file": "Buffalo-Niagara_Falls_NY_Buffalo-Niagara_Falls_NY.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Burlington_NC_Burlington_NC", - "name": "Mallela 2022 - COVID-19 MSA Models - Burlington_NC_Burlington_NC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Burlington_NC_Burlington_NC.bngl", - "file": "Burlington_NC_Burlington_NC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Burlington-South_Burlington_VT_Burlington-South_Burlington_VT", - "name": "Mallela 2022 - COVID-19 MSA Models - Burlington-South_Burlington_VT_Burlington-South_Burlington_VT", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Burlington-South_Burlington_VT_Burlington-South_Burlington_VT.bngl", - "file": "Burlington-South_Burlington_VT_Burlington-South_Burlington_VT.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "path": "Examples/biology/brusselatoroscillator/brusselator-oscillator.bngl", + "file": "brusselator-oscillator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "calcineurin-nfat-pathway", "name": "calcineurin nfat pathway", "description": "NFAT Signaling: Calcium-dependent nuclear translocation.", - "path": "Contributed/BNGPlayground_Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway.bngl", - "file": "calcineurin-nfat-pathway.bngl", "tags": [ "calcineurin", "nfat", @@ -1525,17 +2353,30 @@ "rcan1" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/calcineurinnfatpathway/calcineurin-nfat-pathway.bngl", + "file": "calcineurin-nfat-pathway.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "calcium-spike-signaling", "name": "calcium spike signaling", "description": "Calcium spikes: Oscillations driven by IP3R and CICR feedback.", - "path": "Contributed/BNGPlayground_Examples/biology/calciumspikesignaling/calcium-spike-signaling.bngl", - "file": "calcium-spike-signaling.bngl", "tags": [ "calcium", "spike", @@ -1546,35 +2387,30 @@ "stim1" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "California-Lexington_Park_MD_California-Lexington_Park_MD", - "name": "Mallela 2022 - COVID-19 MSA Models - California-Lexington_Park_MD_California-Lexington_Park_MD", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/California-Lexington_Park_MD_California-Lexington_Park_MD.bngl", - "file": "California-Lexington_Park_MD_California-Lexington_Park_MD.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/biology/calciumspikesignaling/calcium-spike-signaling.bngl", + "file": "calcium-spike-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "CaMKII_holo", "name": "Ordyan 2020: CaMKII holo", "description": "CaMKII holo", - "path": "Published/Ordyan2020/CaMKIIholo/CaMKII_holo.bngl", - "file": "CaMKII_holo.bngl", "tags": [ "published", "neuroscience", @@ -1587,35 +2423,27 @@ "time_counter" ], "category": "signaling", - "bng2_compatible": false, - "origin": "published", - "visible": false, - "collectionId": null - }, - { - "id": "Canton-Massillon_OH_Canton-Massillon_OH", - "name": "Mallela 2022 - COVID-19 MSA Models - Canton-Massillon_OH_Canton-Massillon_OH", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Canton-Massillon_OH_Canton-Massillon_OH.bngl", - "file": "Canton-Massillon_OH_Canton-Massillon_OH.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Ordyan2020/CaMKIIholo/CaMKII_holo.bngl", + "file": "CaMKII_holo.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "CaOscillate_Func", "name": "CaOscillate_Func", "description": "Calcium oscillations (func)", - "path": "Contributed/BNGPlayground_Validation/CaOscillateFunc/CaOscillate_Func.bngl", - "file": "CaOscillate_Func.bngl", "tags": [ "validation", "caoscillate", @@ -1626,17 +2454,28 @@ "ca" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "path": "Tutorials/CaOscillateFunc/CaOscillate_Func.bngl", + "file": "CaOscillate_Func.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "CaOscillate_Sat", "name": "CaOscillate_Sat", "description": "Calcium oscillations (sat)", - "path": "Contributed/BNGPlayground_Validation/CaOscillateSat/CaOscillate_Sat.bngl", - "file": "CaOscillate_Sat.bngl", "tags": [ "validation", "caoscillate", @@ -1647,53 +2486,30 @@ "ca" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null - }, - { - "id": "Cape_Coral-Fort_Myers_FL_Cape_Coral-Fort_Myers_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Cape_Coral-Fort_Myers_FL_Cape_Coral-Fort_Myers_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Cape_Coral-Fort_Myers_FL_Cape_Coral-Fort_Myers_FL.bngl", - "file": "Cape_Coral-Fort_Myers_FL_Cape_Coral-Fort_Myers_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Carbondale-Marion_IL_Carbondale-Marion_IL", - "name": "Mallela 2022 - COVID-19 MSA Models - Carbondale-Marion_IL_Carbondale-Marion_IL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Carbondale-Marion_IL_Carbondale-Marion_IL.bngl", - "file": "Carbondale-Marion_IL_Carbondale-Marion_IL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/CaOscillateSat/CaOscillate_Sat.bngl", + "file": "CaOscillate_Sat.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "caspase-activation-loop", "name": "caspase activation loop", "description": "Caspase activation loop: The executioner feedback system.", - "path": "Contributed/BNGPlayground_Examples/biology/caspaseactivationloop/caspase-activation-loop.bngl", - "file": "caspase-activation-loop.bngl", "tags": [ "caspase", "activation", @@ -1705,17 +2521,30 @@ "flip" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/caspaseactivationloop/caspase-activation-loop.bngl", + "file": "caspase-activation-loop.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "catalysis", "name": "catalysis", "description": "Catalysis in energy BNG", - "path": "Contributed/BNGPlayground_Validation/catalysis/catalysis.bngl", - "file": "catalysis.bngl", "tags": [ "validation", "catalysis", @@ -1728,17 +2557,29 @@ "adp" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/catalysis/catalysis.bngl", + "file": "catalysis.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "cBNGL_simple", "name": "cBNGL simple", "description": "A simplified signal transduction model including the following processes:", - "path": "Tutorials/NativeTutorials/cBNGLsimple/cBNGL_simple.bngl", - "file": "cBNGL_simple.bngl", "tags": [ "cbngl", "simple", @@ -1750,17 +2591,29 @@ "p" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/cBNGLsimple/cBNGL_simple.bngl", + "file": "cBNGL_simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "cd40-signaling", "name": "cd40 signaling", "description": "CD40 Signaling: B-cell activation and TRAF-mediated relay.", - "path": "Contributed/BNGPlayground_Examples/biology/cd40signaling/cd40-signaling.bngl", - "file": "cd40-signaling.bngl", "tags": [ "cd40", "signaling", @@ -1772,35 +2625,30 @@ "relb" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Cedar_Rapids_IA_Cedar_Rapids_IA", - "name": "Mallela 2022 - COVID-19 MSA Models - Cedar_Rapids_IA_Cedar_Rapids_IA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Cedar_Rapids_IA_Cedar_Rapids_IA.bngl", - "file": "Cedar_Rapids_IA_Cedar_Rapids_IA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/biology/cd40signaling/cd40-signaling.bngl", + "file": "cd40-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "cell-cycle-checkpoint", "name": "cell cycle checkpoint", "description": "Cell cycle checkpoint: Mitotic entry switch (CDK1).", - "path": "Contributed/BNGPlayground_Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint.bngl", - "file": "cell-cycle-checkpoint.bngl", "tags": [ "cell", "cycle", @@ -1813,164 +2661,98 @@ "p21" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/cellcyclecheckpoint/cell-cycle-checkpoint.bngl", + "file": "cell-cycle-checkpoint.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Chambersburg-Waynesboro_PA_Chambersburg-Waynesboro_PA", - "name": "Mallela 2022 - COVID-19 MSA Models - Chambersburg-Waynesboro_PA_Chambersburg-Waynesboro_PA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Chambersburg-Waynesboro_PA_Chambersburg-Waynesboro_PA.bngl", - "file": "Chambersburg-Waynesboro_PA_Chambersburg-Waynesboro_PA.bngl", + "id": "Chattaraj_2021", + "name": "Chattaraj 2021", + "description": "NFkB oscillations", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "published", + "chattaraj", + "2021", + "nephrin", + "nck", + "nwasp", + "writexml" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "signaling", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Champaign-Urbana_IL_Champaign-Urbana_IL", - "name": "Mallela 2022 - COVID-19 MSA Models - Champaign-Urbana_IL_Champaign-Urbana_IL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Champaign-Urbana_IL_Champaign-Urbana_IL.bngl", - "file": "Champaign-Urbana_IL_Champaign-Urbana_IL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Charleston_WV_Charleston_WV", - "name": "Mallela 2022 - COVID-19 MSA Models - Charleston_WV_Charleston_WV", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Charleston_WV_Charleston_WV.bngl", - "file": "Charleston_WV_Charleston_WV.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "path": "Published/Chattaraj2021/Chattaraj_2021.bngl", + "file": "Chattaraj_2021.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "check_scaling", + "name": "Hlavacek2018Restructuration", + "description": "BNGL model: after_bunching", + "tags": [ + "na", + "vecf", + "egftot", + "egfrtot", + "kd", + "kr", + "kpx", + "kmx", + "kp", + "kdp", + "molecules" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "other", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Restructuration/check_scaling.bngl", + "file": "check_scaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "Charleston-North_Charleston_SC_Charleston-North_Charleston_SC", - "name": "Mallela 2022 - COVID-19 MSA Models - Charleston-North_Charleston_SC_Charleston-North_Charleston_SC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Charleston-North_Charleston_SC_Charleston-North_Charleston_SC.bngl", - "file": "Charleston-North_Charleston_SC_Charleston-North_Charleston_SC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Charlotte-Concord-Gastonia_NC-SC_Charlotte-Concord-Gastonia_NC-SC", - "name": "Mallela 2022 - COVID-19 MSA Models - Charlotte-Concord-Gastonia_NC-SC_Charlotte-Concord-Gastonia_NC-SC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Charlotte-Concord-Gastonia_NC-SC_Charlotte-Concord-Gastonia_NC-SC.bngl", - "file": "Charlotte-Concord-Gastonia_NC-SC_Charlotte-Concord-Gastonia_NC-SC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Charlottesville_VA_Charlottesville_VA", - "name": "Mallela 2022 - COVID-19 MSA Models - Charlottesville_VA_Charlottesville_VA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Charlottesville_VA_Charlottesville_VA.bngl", - "file": "Charlottesville_VA_Charlottesville_VA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Chattanooga_TN-GA_Chattanooga_TN-GA", - "name": "Mallela 2022 - COVID-19 MSA Models - Chattanooga_TN-GA_Chattanooga_TN-GA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Chattanooga_TN-GA_Chattanooga_TN-GA.bngl", - "file": "Chattanooga_TN-GA_Chattanooga_TN-GA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Chattaraj_2021", - "name": "Chattaraj 2021", - "description": "NFkB oscillations", - "path": "Published/Chattaraj2021/Chattaraj_2021.bngl", - "file": "Chattaraj_2021.bngl", - "tags": [ - "published", - "chattaraj", - "2021", - "nephrin", - "nck", - "nwasp", - "writexml" - ], - "category": "signaling", - "bng2_compatible": false, - "origin": "published", - "visible": false, - "collectionId": null - }, - { - "id": "checkpoint-kinase-signaling", - "name": "checkpoint kinase signaling", - "description": "DNA Checkpoint: ATM/ATR mediated damage sensing.", - "path": "Contributed/BNGPlayground_Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling.bngl", - "file": "checkpoint-kinase-signaling.bngl", + "id": "checkpoint-kinase-signaling", + "name": "checkpoint kinase signaling", + "description": "DNA Checkpoint: ATM/ATR mediated damage sensing.", "tags": [ "checkpoint", "kinase", @@ -1984,17 +2766,30 @@ "cdc25" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/checkpointkinasesignaling/checkpoint-kinase-signaling.bngl", + "file": "checkpoint-kinase-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Cheemalavagu_JAK_STAT", "name": "Cheemalavagu 2024", "description": "JAK-STAT signaling", - "path": "Published/CheemalavaguJAKSTAT/Cheemalavagu_JAK_STAT.bngl", - "file": "Cheemalavagu_JAK_STAT.bngl", "tags": [ "published", "literature", @@ -2012,17 +2807,29 @@ "jak2" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/CheemalavaguJAKSTAT/Cheemalavagu_JAK_STAT.bngl", + "file": "Cheemalavagu_JAK_STAT.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "chemistry", "name": "chemistry", "description": "Basic chemical reactions", - "path": "Tutorials/General/chemistry/chemistry.bngl", - "file": "chemistry.bngl", "tags": [ "published", "tutorials", @@ -2034,17 +2841,29 @@ "e" ], "category": "tutorial", - "bng2_compatible": false, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "path": "Tutorials/General/chemistry/chemistry.bngl", + "file": "chemistry.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "chemotaxis-signal-transduction", "name": "chemotaxis signal transduction", "description": "Bacterial Chemotaxis: Adaptation through methylation.", - "path": "Contributed/BNGPlayground_Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction.bngl", - "file": "chemotaxis-signal-transduction.bngl", "tags": [ "chemotaxis", "signal", @@ -2057,35 +2876,29 @@ "motor" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Chicago-Naperville-Elgin_IL-IN-WI_Chicago-Naperville-Elgin_IL-IN-WI", - "name": "Mallela 2022 - COVID-19 MSA Models - Chicago-Naperville-Elgin_IL-IN-WI_Chicago-Naperville-Elgin_IL-IN-WI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Chicago-Naperville-Elgin_IL-IN-WI_Chicago-Naperville-Elgin_IL-IN-WI.bngl", - "file": "Chicago-Naperville-Elgin_IL-IN-WI_Chicago-Naperville-Elgin_IL-IN-WI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/chemotaxissignaltransduction/chemotaxis-signal-transduction.bngl", + "file": "chemotaxis-signal-transduction.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Chylek_library", "name": "Chylek library", "description": "Created by BioNetGen 2.2.6", - "path": "Tutorials/NativeTutorials/Chyleklibrary/Chylek_library.bngl", - "file": "Chylek_library.bngl", "tags": [ "chylek", "library", @@ -2099,17 +2912,29 @@ "pag1" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/Chyleklibrary/Chylek_library.bngl", + "file": "Chylek_library.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ChylekFceRI_2014", "name": "Chylek 2014 (FceRI)", "description": "FceRI signaling", - "path": "Published/ChylekFceRI2014/ChylekFceRI_2014.bngl", - "file": "ChylekFceRI_2014.bngl", "tags": [ "published", "immunology", @@ -2125,17 +2950,29 @@ "lat" ], "category": "immunology", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/ChylekFceRI2014/ChylekFceRI_2014.bngl", + "file": "ChylekFceRI_2014.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ChylekTCR_2014", "name": "Chylek 2014 (TCR)", "description": "TCR signaling", - "path": "Published/ChylekTCR2014/ChylekTCR_2014.bngl", - "file": "ChylekTCR_2014.bngl", "tags": [ "published", "immunology", @@ -2151,35 +2988,29 @@ "zap70" ], "category": "immunology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null - }, - { - "id": "Cincinnati_OH-KY-IN_Cincinnati_OH-KY-IN", - "name": "Mallela 2022 - COVID-19 MSA Models - Cincinnati_OH-KY-IN_Cincinnati_OH-KY-IN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Cincinnati_OH-KY-IN_Cincinnati_OH-KY-IN.bngl", - "file": "Cincinnati_OH-KY-IN_Cincinnati_OH-KY-IN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/ChylekTCR2014/ChylekTCR_2014.bngl", + "file": "ChylekTCR_2014.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "circadian-oscillator", "name": "circadian oscillator", "description": "title: Vilar Circadian Oscillator Model", - "path": "Contributed/BNGPlayground_Examples/biology/circadianoscillator/circadian-oscillator.bngl", - "file": "circadian-oscillator.bngl", "tags": [ "circadian", "oscillator", @@ -2191,17 +3022,29 @@ "mrna_r" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/circadianoscillator/circadian-oscillator.bngl", + "file": "circadian-oscillator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "CircadianOscillator", "name": "CircadianOscillator", "description": "Circadian rhythm", - "path": "Tutorials/NativeTutorials/CircadianOscillator/CircadianOscillator.bngl", - "file": "CircadianOscillator.bngl", "tags": [ "published", "tutorial", @@ -2215,53 +3058,30 @@ "mrna_r" ], "category": "tutorial", - "bng2_compatible": false, "origin": "tutorial", "visible": false, - "collectionId": null - }, - { - "id": "Clarksville_TN-KY_Clarksville_TN-KY", - "name": "Mallela 2022 - COVID-19 MSA Models - Clarksville_TN-KY_Clarksville_TN-KY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Clarksville_TN-KY_Clarksville_TN-KY.bngl", - "file": "Clarksville_TN-KY_Clarksville_TN-KY.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Cleveland-Elyria_OH_Cleveland-Elyria_OH", - "name": "Mallela 2022 - COVID-19 MSA Models - Cleveland-Elyria_OH_Cleveland-Elyria_OH", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Cleveland-Elyria_OH_Cleveland-Elyria_OH.bngl", - "file": "Cleveland-Elyria_OH_Cleveland-Elyria_OH.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "cell-cycle", + "native-tutorials" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Tutorials/NativeTutorials/CircadianOscillator/CircadianOscillator.bngl", + "file": "CircadianOscillator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "clock-bmal1-gene-circuit", "name": "clock bmal1 gene circuit", "description": "BMAL1-CLOCK: The master activator of the circadian circuit.", - "path": "Contributed/BNGPlayground_Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit.bngl", - "file": "clock-bmal1-gene-circuit.bngl", "tags": [ "clock", "bmal1", @@ -2272,125 +3092,30 @@ "dna" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "College_Station-Bryan_TX_College_Station-Bryan_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - College_Station-Bryan_TX_College_Station-Bryan_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/College_Station-Bryan_TX_College_Station-Bryan_TX.bngl", - "file": "College_Station-Bryan_TX_College_Station-Bryan_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Colorado_Springs_CO_Colorado_Springs_CO", - "name": "Mallela 2022 - COVID-19 MSA Models - Colorado_Springs_CO_Colorado_Springs_CO", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Colorado_Springs_CO_Colorado_Springs_CO.bngl", - "file": "Colorado_Springs_CO_Colorado_Springs_CO.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Columbia_SC_Columbia_SC", - "name": "Mallela 2022 - COVID-19 MSA Models - Columbia_SC_Columbia_SC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Columbia_SC_Columbia_SC.bngl", - "file": "Columbia_SC_Columbia_SC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Columbus_GA-AL_Columbus_GA-AL", - "name": "Mallela 2022 - COVID-19 MSA Models - Columbus_GA-AL_Columbus_GA-AL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Columbus_GA-AL_Columbus_GA-AL.bngl", - "file": "Columbus_GA-AL_Columbus_GA-AL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Columbus_IN_Columbus_IN", - "name": "Mallela 2022 - COVID-19 MSA Models - Columbus_IN_Columbus_IN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Columbus_IN_Columbus_IN.bngl", - "file": "Columbus_IN_Columbus_IN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Columbus_OH_Columbus_OH", - "name": "Mallela 2022 - COVID-19 MSA Models - Columbus_OH_Columbus_OH", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Columbus_OH_Columbus_OH.bngl", - "file": "Columbus_OH_Columbus_OH.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/clockbmal1genecircuit/clock-bmal1-gene-circuit.bngl", + "file": "clock-bmal1-gene-circuit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "compartment_endocytosis", "name": "compartment endocytosis", "description": "Model: compartment_endocytosis.bngl", - "path": "Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl", - "file": "compartment_endocytosis.bngl", "tags": [ "compartment", "endocytosis", @@ -2399,17 +3124,29 @@ "t" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/compartments/compartmentendocytosis/compartment_endocytosis.bngl", + "file": "compartment_endocytosis.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "compartment_membrane_bound", "name": "compartment membrane bound", "description": "Model: compartment_membrane_bound.bngl", - "path": "Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl", - "file": "compartment_membrane_bound.bngl", "tags": [ "compartment", "membrane", @@ -2420,17 +3157,29 @@ "simulate" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/compartments/compartmentmembranebound/compartment_membrane_bound.bngl", + "file": "compartment_membrane_bound.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "compartment_nested_transport", "name": "compartment nested transport", "description": "Model: compartment_nested_transport.bngl", - "path": "Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl", - "file": "compartment_nested_transport.bngl", "tags": [ "compartment", "nested", @@ -2440,17 +3189,29 @@ "simulate" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/compartments/compartmentnestedtransport/compartment_nested_transport.bngl", + "file": "compartment_nested_transport.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "compartment_nuclear_transport", "name": "compartment nuclear transport", "description": "Model: compartment_nuclear_transport.bngl", - "path": "Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl", - "file": "compartment_nuclear_transport.bngl", "tags": [ "compartment", "nuclear", @@ -2460,17 +3221,29 @@ "simulate" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/compartments/compartmentnucleartransport/compartment_nuclear_transport.bngl", + "file": "compartment_nuclear_transport.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "compartment_organelle_exchange", "name": "compartment organelle exchange", "description": "Model: compartment_organelle_exchange.bngl", - "path": "Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl", - "file": "compartment_organelle_exchange.bngl", "tags": [ "compartment", "organelle", @@ -2480,17 +3253,29 @@ "simulate" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/compartments/compartmentorganelleexchange/compartment_organelle_exchange.bngl", + "file": "compartment_organelle_exchange.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "competitive-enzyme-inhibition", "name": "competitive enzyme inhibition", "description": "Competitive inhibition: Inhibitor (I) and Substrate (S) compete for the same", - "path": "Contributed/BNGPlayground_Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition.bngl", - "file": "competitive-enzyme-inhibition.bngl", "tags": [ "competitive", "enzyme", @@ -2501,17 +3286,30 @@ "product" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/competitiveenzymeinhibition/competitive-enzyme-inhibition.bngl", + "file": "competitive-enzyme-inhibition.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "complement-activation-cascade", "name": "complement activation cascade", "description": "Complement System: Pathogen opsonization and the Alternative Pathway.", - "path": "Contributed/BNGPlayground_Examples/biology/complementactivationcascade/complement-activation-cascade.bngl", - "file": "complement-activation-cascade.bngl", "tags": [ "complement", "activation", @@ -2523,17 +3321,30 @@ "surf" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/complementactivationcascade/complement-activation-cascade.bngl", + "file": "complement-activation-cascade.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ComplexDegradation", "name": "ComplexDegradation", "description": "Degradation model", - "path": "Tutorials/NativeTutorials/ComplexDegradation/ComplexDegradation.bngl", - "file": "ComplexDegradation.bngl", "tags": [ "published", "tutorial", @@ -2545,17 +3356,29 @@ "generate_network" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/ComplexDegradation/ComplexDegradation.bngl", + "file": "ComplexDegradation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "contact-inhibition-hippo-yap", "name": "contact inhibition hippo yap", "description": "Hippo Pathway: Contact inhibition and YAP regulation.", - "path": "Contributed/BNGPlayground_Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl", - "file": "contact-inhibition-hippo-yap.bngl", "tags": [ "contact", "inhibition", @@ -2566,17 +3389,29 @@ "tead" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/contactinhibitionhippoyap/contact-inhibition-hippo-yap.bngl", + "file": "contact-inhibition-hippo-yap.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "continue", "name": "continue", "description": "Test trajectory continuation", - "path": "Contributed/BNGPlayground_Validation/continue/continue.bngl", - "file": "continue.bngl", "tags": [ "validation", "continue", @@ -2586,17 +3421,29 @@ "trash" ], "category": "validation", - "bng2_compatible": false, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/continue/continue.bngl", + "file": "continue.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "cooperative-binding", "name": "cooperative binding", "description": "Cooperative binding: The binding of the first ligand molecule increases", - "path": "Contributed/BNGPlayground_Examples/biology/cooperativebinding/cooperative-binding.bngl", - "file": "cooperative-binding.bngl", "tags": [ "cooperative", "binding", @@ -2605,35 +3452,29 @@ "competitor" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/cooperativebinding/cooperative-binding.bngl", + "file": "cooperative-binding.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Corpus_Christi_TX_Corpus_Christi_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - Corpus_Christi_TX_Corpus_Christi_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Corpus_Christi_TX_Corpus_Christi_TX.bngl", - "file": "Corpus_Christi_TX_Corpus_Christi_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Creamer_2012", - "name": "Creamer 2012", - "description": "Initial values", - "path": "Tutorials/NativeTutorials/Creamer2012/Creamer_2012.bngl", - "file": "Creamer_2012.bngl", + "id": "Creamer_2012", + "name": "Creamer 2012", + "description": "Initial values", "tags": [ "creamer", "2012", @@ -2647,35 +3488,29 @@ "grb2" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null - }, - { - "id": "Crestview-Fort_Walton_Beach-Destin_FL_Crestview-Fort_Walton_Beach-Destin_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Crestview-Fort_Walton_Beach-Destin_FL_Crestview-Fort_Walton_Beach-Destin_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Crestview-Fort_Walton_Beach-Destin_FL_Crestview-Fort_Walton_Beach-Destin_FL.bngl", - "file": "Crestview-Fort_Walton_Beach-Destin_FL_Crestview-Fort_Walton_Beach-Destin_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Tutorials/NativeTutorials/Creamer2012/Creamer_2012.bngl", + "file": "Creamer_2012.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "cs_diffie_hellman", "name": "cs diffie hellman", "description": "Model: cs_diffie_hellman.bngl", - "path": "Contributed/BNGPlayground_Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl", - "file": "cs_diffie_hellman.bngl", "tags": [ "cs", "diffie", @@ -2686,17 +3521,30 @@ "dsharedb_dt" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/cs/csdiffiehellman/cs_diffie_hellman.bngl", + "file": "cs_diffie_hellman.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "cs_hash_function", "name": "cs hash function", "description": "Cryptographic Hash Function in BNGL", - "path": "Contributed/BNGPlayground_Examples/cs/cshashfunction/cs_hash_function.bngl", - "file": "cs_hash_function.bngl", "tags": [ "cs", "hash", @@ -2711,17 +3559,30 @@ "h3" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/cs/cshashfunction/cs_hash_function.bngl", + "file": "cs_hash_function.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "cs_huffman", "name": "cs huffman", "description": "Model: cs_huffman.bngl", - "path": "Contributed/BNGPlayground_Examples/cs/cshuffman/cs_huffman.bngl", - "file": "cs_huffman.bngl", "tags": [ "cs", "huffman", @@ -2731,17 +3592,30 @@ "simulate" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/cs/cshuffman/cs_huffman.bngl", + "file": "cs_huffman.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "cs_monte_carlo_pi", "name": "cs monte carlo pi", "description": "Model: cs_monte_carlo_pi.bngl", - "path": "Contributed/BNGPlayground_Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl", - "file": "cs_monte_carlo_pi.bngl", "tags": [ "cs", "monte", @@ -2753,17 +3627,30 @@ "simulate" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/cs/csmontecarlopi/cs_monte_carlo_pi.bngl", + "file": "cs_monte_carlo_pi.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "cs_pagerank", "name": "cs pagerank", "description": "Model: cs_pagerank.bngl", - "path": "Contributed/BNGPlayground_Examples/cs/cspagerank/cs_pagerank.bngl", - "file": "cs_pagerank.bngl", "tags": [ "cs", "pagerank", @@ -2771,17 +3658,30 @@ "page" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/cs/cspagerank/cs_pagerank.bngl", + "file": "cs_pagerank.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "cs_pid_controller", "name": "cs pid controller", "description": "PID Controller in BNGL", - "path": "Contributed/BNGPlayground_Examples/cs/cspidcontroller/cs_pid_controller.bngl", - "file": "cs_pid_controller.bngl", "tags": [ "cs", "pid", @@ -2793,17 +3693,30 @@ "disturbance" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/cs/cspidcontroller/cs_pid_controller.bngl", + "file": "cs_pid_controller.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "cs_regex_nfa", "name": "cs regex nfa", "description": "Model: cs_regex_nfa.bngl", - "path": "Contributed/BNGPlayground_Examples/cs/csregexnfa/cs_regex_nfa.bngl", - "file": "cs_regex_nfa.bngl", "tags": [ "cs", "regex", @@ -2815,35 +3728,30 @@ "setparameter" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Cumberland_MD-WV_Cumberland_MD-WV", - "name": "Mallela 2022 - COVID-19 MSA Models - Cumberland_MD-WV_Cumberland_MD-WV", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Cumberland_MD-WV_Cumberland_MD-WV.bngl", - "file": "Cumberland_MD-WV_Cumberland_MD-WV.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "cs", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/cs/csregexnfa/cs_regex_nfa.bngl", + "file": "cs_regex_nfa.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Dallas", "name": "Dallas", "description": "- This model is intended to be consistent with the compartmental model", - "path": "Published/VaxAndVariants/Dallas/Dallas.bngl", - "file": "Dallas.bngl", "tags": [ "dallas", "counter", @@ -2856,125 +3764,29 @@ "v" ], "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": null - }, - { - "id": "Dallas-Fort_Worth-Arlington_TX_Dallas-Fort_Worth-Arlington_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - Dallas-Fort_Worth-Arlington_TX_Dallas-Fort_Worth-Arlington_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Dallas-Fort_Worth-Arlington_TX_Dallas-Fort_Worth-Arlington_TX.bngl", - "file": "Dallas-Fort_Worth-Arlington_TX_Dallas-Fort_Worth-Arlington_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Dalton_GA_Dalton_GA", - "name": "Mallela 2022 - COVID-19 MSA Models - Dalton_GA_Dalton_GA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Dalton_GA_Dalton_GA.bngl", - "file": "Dalton_GA_Dalton_GA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Daphne-Fairhope-Foley_AL_Daphne-Fairhope-Foley_AL", - "name": "Mallela 2022 - COVID-19 MSA Models - Daphne-Fairhope-Foley_AL_Daphne-Fairhope-Foley_AL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Daphne-Fairhope-Foley_AL_Daphne-Fairhope-Foley_AL.bngl", - "file": "Daphne-Fairhope-Foley_AL_Daphne-Fairhope-Foley_AL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Davenport-Moline-Rock_Island_IA-IL_Davenport-Moline-Rock_Island_IA-IL", - "name": "Mallela 2022 - COVID-19 MSA Models - Davenport-Moline-Rock_Island_IA-IL_Davenport-Moline-Rock_Island_IA-IL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Davenport-Moline-Rock_Island_IA-IL_Davenport-Moline-Rock_Island_IA-IL.bngl", - "file": "Davenport-Moline-Rock_Island_IA-IL_Davenport-Moline-Rock_Island_IA-IL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Dayton_OH_Dayton_OH", - "name": "Mallela 2022 - COVID-19 MSA Models - Dayton_OH_Dayton_OH", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Dayton_OH_Dayton_OH.bngl", - "file": "Dayton_OH_Dayton_OH.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "DC_m6", - "name": "Mallela 2021 - COVID-19 City Models - DC_m6", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/DC_m6.bngl", - "file": "DC_m6.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_Cities" + "path": "Published/VaxAndVariants/Dallas/Dallas.bngl", + "file": "Dallas.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "degranulation_model", "name": "PyBNG: Degranulation model", "description": "Degranulation model", - "path": "PyBioNetGen/core/degranulationmodel/degranulation_model.bngl", - "file": "degranulation_model.bngl", "tags": [ "published", "pybng", @@ -2989,35 +3801,29 @@ "h" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null - }, - { - "id": "Deltona-Daytona_Beach-Ormond_Beach_FL_Deltona-Daytona_Beach-Ormond_Beach_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Deltona-Daytona_Beach-Ormond_Beach_FL_Deltona-Daytona_Beach-Ormond_Beach_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Deltona-Daytona_Beach-Ormond_Beach_FL_Deltona-Daytona_Beach-Ormond_Beach_FL.bngl", - "file": "Deltona-Daytona_Beach-Ormond_Beach_FL_Deltona-Daytona_Beach-Ormond_Beach_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/PyBioNetGen/core/degranulationmodel/degranulation_model.bngl", + "file": "degranulation_model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Dembo_1978", "name": "Dembo 1978", "description": "BLBR dembo 1978", - "path": "Published/Dembo1978/blbr_dembo1978.bngl", - "file": "blbr_dembo1978.bngl", "tags": [ "published", "physics", @@ -3025,89 +3831,29 @@ "1978" ], "category": "physics", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null - }, - { - "id": "Denver-Aurora-Lakewood_CO_Denver-Aurora-Lakewood_CO", - "name": "Mallela 2022 - COVID-19 MSA Models - Denver-Aurora-Lakewood_CO_Denver-Aurora-Lakewood_CO", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Denver-Aurora-Lakewood_CO_Denver-Aurora-Lakewood_CO.bngl", - "file": "Denver-Aurora-Lakewood_CO_Denver-Aurora-Lakewood_CO.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Des_Moines-West_Des_Moines_IA_Des_Moines-West_Des_Moines_IA", - "name": "Mallela 2022 - COVID-19 MSA Models - Des_Moines-West_Des_Moines_IA_Des_Moines-West_Des_Moines_IA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Des_Moines-West_Des_Moines_IA_Des_Moines-West_Des_Moines_IA.bngl", - "file": "Des_Moines-West_Des_Moines_IA_Des_Moines-West_Des_Moines_IA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Detroit_Warren_Dearborn_MI_Detroit_Warren_Dearborn_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Detroit_Warren_Dearborn_MI_Detroit_Warren_Dearborn_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Detroit_Warren_Dearborn_MI_Detroit_Warren_Dearborn_MI.bngl", - "file": "Detroit_Warren_Dearborn_MI_Detroit_Warren_Dearborn_MI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Detroit-Warren-Dearborn_MI_Detroit-Warren-Dearborn_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Detroit-Warren-Dearborn_MI_Detroit-Warren-Dearborn_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Detroit-Warren-Dearborn_MI_Detroit-Warren-Dearborn_MI.bngl", - "file": "Detroit-Warren-Dearborn_MI_Detroit-Warren-Dearborn_MI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/Dembo1978/blbr_dembo1978.bngl", + "file": "blbr_dembo1978.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "dna-damage-repair", "name": "dna damage repair", "description": "DNA damage sensing and repair pathway (ATM-CHK2-p53 axis)", - "path": "Contributed/BNGPlayground_Examples/biology/dnadamagerepair/dna-damage-repair.bngl", - "file": "dna-damage-repair.bngl", "tags": [ "dna", "damage", @@ -3118,17 +3864,30 @@ "repaircomplex" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/dnadamagerepair/dna-damage-repair.bngl", + "file": "dna-damage-repair.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "dna-methylation-dynamics", "name": "dna methylation dynamics", "description": "DNA Methylation: Maintenance and de novo dynamics.", - "path": "Contributed/BNGPlayground_Examples/biology/dnamethylationdynamics/dna-methylation-dynamics.bngl", - "file": "dna-methylation-dynamics.bngl", "tags": [ "dna", "methylation", @@ -3140,17 +3899,29 @@ "v_erase" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/dnamethylationdynamics/dna-methylation-dynamics.bngl", + "file": "dna-methylation-dynamics.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Dolan_2015", - "name": "Dolan 2015 - Dolan_2015", + "name": "Dolan 2015", "description": "Insulin signaling", - "path": "Published/Dolan2015/Dolan_2015.bngl", - "file": "Dolan_2015.bngl", "tags": [ "published", "literature", @@ -3167,17 +3938,29 @@ "p53" ], "category": "other", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": "Dolan_2015" + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism" + ], + "path": "Published/Dolan2015/Dolan_2015.bngl", + "file": "Dolan_2015.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Dolan2015", - "name": "Dolan 2015 - Dolan2015", + "name": "Dolan 2015", "description": "Insulin signaling", - "path": "Published/Dolan2015/Dolan2015.bngl", - "file": "Dolan2015.bngl", "tags": [ "published", "literature", @@ -3194,53 +3977,29 @@ "p53" ], "category": "other", - "bng2_compatible": false, - "origin": "published", - "visible": false, - "collectionId": "Dolan_2015" - }, - { - "id": "Dothan_AL_Dothan_AL", - "name": "Mallela 2022 - COVID-19 MSA Models - Dothan_AL_Dothan_AL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Dothan_AL_Dothan_AL.bngl", - "file": "Dothan_AL_Dothan_AL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Dover_DE_Dover_DE", - "name": "Mallela 2022 - COVID-19 MSA Models - Dover_DE_Dover_DE", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Dover_DE_Dover_DE.bngl", - "file": "Dover_DE_Dover_DE.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/Dolan2015/Dolan2015.bngl", + "file": "Dolan2015.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "dr5-apoptosis-signaling", "name": "dr5 apoptosis signaling", "description": "DR5 (TRAIL) Signaling: Extrinsic apoptosis and DISC formation.", - "path": "Contributed/BNGPlayground_Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling.bngl", - "file": "dr5-apoptosis-signaling.bngl", "tags": [ "dr5", "apoptosis", @@ -3252,17 +4011,30 @@ "death_signal" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/dr5apoptosissignaling/dr5-apoptosis-signaling.bngl", + "file": "dr5-apoptosis-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Dreisigmeyer_2008", "name": "Dreisigmeyer 2008", "description": "Lac operon", - "path": "Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl", - "file": "lac_operon_dreisigmeyer2008.bngl", "tags": [ "published", "gene-expression", @@ -3270,17 +4042,29 @@ "2008" ], "category": "gene-expression", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "gene-expression" + ], + "path": "Published/Dreisigmeyer2008/lac_operon_dreisigmeyer2008.bngl", + "file": "lac_operon_dreisigmeyer2008.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "dual-site-phosphorylation", "name": "dual site phosphorylation", "description": "Dual-site phosphorylation: Requires two sequential modifications for activity.", - "path": "Contributed/BNGPlayground_Examples/biology/dualsitephosphorylation/dual-site-phosphorylation.bngl", - "file": "dual-site-phosphorylation.bngl", "tags": [ "dual", "site", @@ -3290,53 +4074,29 @@ "substrate" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/dualsitephosphorylation/dual-site-phosphorylation.bngl", + "file": "dual-site-phosphorylation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Dubuque_IA_Dubuque_IA", - "name": "Mallela 2022 - COVID-19 MSA Models - Dubuque_IA_Dubuque_IA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Dubuque_IA_Dubuque_IA.bngl", - "file": "Dubuque_IA_Dubuque_IA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Durham-Chapel_Hill_NC_Durham-Chapel_Hill_NC", - "name": "Mallela 2022 - COVID-19 MSA Models - Durham-Chapel_Hill_NC_Durham-Chapel_Hill_NC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Durham-Chapel_Hill_NC_Durham-Chapel_Hill_NC.bngl", - "file": "Durham-Chapel_Hill_NC_Durham-Chapel_Hill_NC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Dushek_2011", - "name": "Dushek 2011", - "description": "TCR signaling", - "path": "Published/Dushek2011/Dushek_2011.bngl", - "file": "Dushek_2011.bngl", + "id": "Dushek_2011", + "name": "Dushek 2011", + "description": "TCR signaling", "tags": [ "published", "dushek", @@ -3344,17 +4104,29 @@ "s" ], "category": "signaling", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/Dushek2011/Dushek_2011.bngl", + "file": "Dushek_2011.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Dushek_2014", "name": "Dushek 2014", "description": "TCR signaling dynamics", - "path": "Published/Dushek2014/Dushek_2014.bngl", - "file": "Dushek_2014.bngl", "tags": [ "published", "dushek", @@ -3364,17 +4136,29 @@ "b" ], "category": "signaling", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/Dushek2014/Dushek_2014.bngl", + "file": "Dushek_2014.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "e2f-rb-cell-cycle-switch", "name": "e2f rb cell cycle switch", "description": "E2F/Rb Switch: The G1/S transition gate.", - "path": "Contributed/BNGPlayground_Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch.bngl", - "file": "e2f-rb-cell-cycle-switch.bngl", "tags": [ "e2f", "rb", @@ -3387,35 +4171,30 @@ "p27" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "East_Stroudsburg_PA_East_Stroudsburg_PA", - "name": "Mallela 2022 - COVID-19 MSA Models - East_Stroudsburg_PA_East_Stroudsburg_PA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/East_Stroudsburg_PA_East_Stroudsburg_PA.bngl", - "file": "East_Stroudsburg_PA_East_Stroudsburg_PA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/e2frbcellcycleswitch/e2f-rb-cell-cycle-switch.bngl", + "file": "e2f-rb-cell-cycle-switch.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "eco_coevolution_host_parasite", "name": "eco coevolution host parasite", "description": "Model: eco_coevolution_host_parasite.bngl", - "path": "Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl", - "file": "eco_coevolution_host_parasite.bngl", "tags": [ "eco", "coevolution", @@ -3423,17 +4202,30 @@ "parasite" ], "category": "ecology", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "path": "Examples/ecology/ecocoevolutionhostparasite/eco_coevolution_host_parasite.bngl", + "file": "eco_coevolution_host_parasite.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "eco_food_web_chaos_3sp", "name": "eco food web chaos 3sp", "description": "Model: eco_food_web_chaos_3sp.bngl", - "path": "Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl", - "file": "eco_food_web_chaos_3sp.bngl", "tags": [ "eco", "food", @@ -3447,17 +4239,30 @@ "k_eat_c" ], "category": "ecology", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "path": "Examples/ecology/ecofoodwebchaos3sp/eco_food_web_chaos_3sp.bngl", + "file": "eco_food_web_chaos_3sp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "eco_lotka_volterra_grid", "name": "eco lotka volterra grid", "description": "Model: eco_lotka_volterra_grid.bngl", - "path": "Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl", - "file": "eco_lotka_volterra_grid.bngl", "tags": [ "eco", "lotka", @@ -3467,17 +4272,30 @@ "pred" ], "category": "ecology", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "path": "Examples/ecology/ecolotkavolterragrid/eco_lotka_volterra_grid.bngl", + "file": "eco_lotka_volterra_grid.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "eco_mutualism_obligate", "name": "eco mutualism obligate", "description": "Model: eco_mutualism_obligate.bngl", - "path": "Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl", - "file": "eco_mutualism_obligate.bngl", "tags": [ "eco", "mutualism", @@ -3486,17 +4304,30 @@ "b" ], "category": "ecology", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "path": "Examples/ecology/ecomutualismobligate/eco_mutualism_obligate.bngl", + "file": "eco_mutualism_obligate.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "eco_rock_paper_scissors_spatial", "name": "eco rock paper scissors spatial", "description": "Model: eco_rock_paper_scissors_spatial.bngl", - "path": "Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl", - "file": "eco_rock_paper_scissors_spatial.bngl", "tags": [ "eco", "rock", @@ -3507,17 +4338,80 @@ "generate_network" ], "category": "ecology", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "path": "Examples/ecology/ecorockpaperscissorsspatial/eco_rock_paper_scissors_spatial.bngl", + "file": "eco_rock_paper_scissors_spatial.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "egfr", + "name": "02-egfr", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/02-egfr/egfr.bngl", + "file": "egfr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "egfr", + "name": "17-egfr-ssa", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/17-egfr-ssa/egfr.bngl", + "file": "egfr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "egfr", "name": "egfr", "description": "Blinov et al. 2006. Biosystems, 83:136", - "path": "PyBioNetGen/core/egfr/egfr.bngl", - "file": "egfr.bngl", "tags": [ "egfr", "egf", @@ -3526,17 +4420,79 @@ "sos" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/egfr/egfr.bngl", + "file": "egfr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "egfr_ground", + "name": "02-egfr", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/02-egfr/egfr_ground.bngl", + "file": "egfr_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "egfr_ground", + "name": "17-egfr-ssa", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/17-egfr-ssa/egfr_ground.bngl", + "file": "egfr_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "egfr_ground", "name": "egfr ground", "description": "Blinov et al. 2006. Biosystems, 83:136", - "path": "PyBioNetGen/core/egfrground/egfr_ground.bngl", - "file": "egfr_ground.bngl", "tags": [ "egfr", "ground", @@ -3546,17 +4502,29 @@ "sos" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/egfrground/egfr_ground.bngl", + "file": "egfr_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "egfr_net", "name": "egfr_net", "description": "check detailed balanced", - "path": "Contributed/BNGPlayground_Validation/egfrnet/egfr_net.bngl", - "file": "egfr_net.bngl", "tags": [ "validation", "egfr", @@ -3567,17 +4535,29 @@ "sos" ], "category": "validation", - "bng2_compatible": false, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/egfrnet/egfr_net.bngl", + "file": "egfr_net.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "egfr_net_red", "name": "egfr_net_red", "description": "Reduced state-space version of EGFR_NET.BNGL with equivalent ODE dynamics", - "path": "Contributed/BNGPlayground_Validation/egfrnetred/egfr_net_red.bngl", - "file": "egfr_net_red.bngl", "tags": [ "validation", "egfr", @@ -3592,17 +4572,29 @@ "sos" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/egfrnetred/egfr_net_red.bngl", + "file": "egfr_net_red.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "egfr_nf", "name": "egfr nf", "description": "Filename: example2_starting_point.bngl", - "path": "PyBioNetGen/core/egfrnf/egfr_nf.bngl", - "file": "egfr_nf.bngl", "tags": [ "egfr", "nf", @@ -3612,17 +4604,29 @@ "pre2_time" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/egfrnf/egfr_nf.bngl", + "file": "egfr_nf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "egfr_ode", "name": "egfr ode", "description": "Filename: example1.bngl", - "path": "PyBioNetGen/core/egfrode/egfr_ode.bngl", - "file": "egfr_ode.bngl", "tags": [ "egfr", "ode", @@ -3632,17 +4636,29 @@ "pre3_dose" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/PyBioNetGen/core/egfrode/egfr_ode.bngl", + "file": "egfr_ode.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "egfr_ode", "name": "PyBNG: EGFR ODE", "description": "EGFR ODE", - "path": "PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode.bngl", - "file": "egfr_ode.bngl", "tags": [ "published", "pybng", @@ -3654,17 +4670,29 @@ "pre3_dose" ], "category": "other", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/PyBioNetGen/core/egfrode_published-models_PyBNG/egfr_ode.bngl", + "file": "egfr_ode.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "egfr_path", "name": "egfr_path", "description": "The primary focus of the model developed by Kholodenko", - "path": "Contributed/BNGPlayground_Validation/egfrpath/egfr_path.bngl", - "file": "egfr_path.bngl", "tags": [ "validation", "egfr", @@ -3674,17 +4702,29 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/egfrpath/egfr_path.bngl", + "file": "egfr_path.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "egfr_simple", "name": "egfr simple", "description": "This is a demo model of EGFR signaling.", - "path": "Tutorials/NativeTutorials/egfrsimple/egfr_simple.bngl", - "file": "egfr_simple.bngl", "tags": [ "egfr", "simple", @@ -3693,17 +4733,29 @@ "sos1" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/egfrsimple/egfr_simple.bngl", + "file": "egfr_simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "egfr-signaling-pathway", "name": "egfr signaling pathway", "description": "Enhanced EGFR Signaling: Combinatorial complexity with multiple phosphorylation sites.", - "path": "Contributed/BNGPlayground_Examples/biology/egfrsignalingpathway/egfr-signaling-pathway.bngl", - "file": "egfr-signaling-pathway.bngl", "tags": [ "egfr", "signaling", @@ -3713,17 +4765,30 @@ "shc" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/egfrsignalingpathway/egfr-signaling-pathway.bngl", + "file": "egfr-signaling-pathway.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "egg", "name": "egg", "description": "BioNetGen model: egg", - "path": "PyBioNetGen/tests/egg/egg.bngl", - "file": "egg.bngl", "tags": [ "egg", "x", @@ -3732,17 +4797,29 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/egg/egg.bngl", + "file": "egg.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "eif2a-stress-response", "name": "eif2a stress response", "description": "Integrated Stress Response: eIF2alpha and the translational gate.", - "path": "Contributed/BNGPlayground_Examples/biology/eif2astressresponse/eif2a-stress-response.bngl", - "file": "eif2a-stress-response.bngl", "tags": [ "eif2a", "stress", @@ -3752,89 +4829,251 @@ "gadd34" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "El_Centro_CA_El_Centro_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - El_Centro_CA_El_Centro_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/El_Centro_CA_El_Centro_CA.bngl", - "file": "El_Centro_CA_El_Centro_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "El_Paso_TX_El_Paso_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - El_Paso_TX_El_Paso_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/El_Paso_TX_El_Paso_TX.bngl", - "file": "El_Paso_TX_El_Paso_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/eif2astressresponse/eif2a-stress-response.bngl", + "file": "eif2a-stress-response.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Elkhart-Goshen_IN_Elkhart-Goshen_IN", - "name": "Mallela 2022 - COVID-19 MSA Models - Elkhart-Goshen_IN_Elkhart-Goshen_IN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Elkhart-Goshen_IN_Elkhart-Goshen_IN.bngl", - "file": "Elkhart-Goshen_IN_Elkhart-Goshen_IN.bngl", + "id": "elephant_EFA", + "name": "Hlavacek2018Elephant", + "description": "BNGL model: elephant_EFA", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10", + "a11", + "a12", + "a13", + "a14", + "a15", + "a16", + "a17", + "a18", + "a19", + "a20", + "b0", + "b1", + "b2", + "b3", + "b4", + "b5", + "b6", + "b7", + "b8", + "b9", + "b10", + "b11", + "b12", + "b13", + "b14", + "b15", + "b16", + "b17", + "b18", + "b19", + "b20", + "c0", + "c1", + "c2", + "c3", + "c4", + "c5", + "c6", + "c7", + "c8", + "c9", + "c10", + "c11", + "c12", + "c13", + "c14", + "c15", + "c16", + "c17", + "c18", + "c19", + "c20", + "d0", + "d1", + "d2", + "d3", + "d4", + "d5", + "d6", + "d7", + "d8", + "d9", + "d10", + "d11", + "d12", + "d13", + "d14", + "d15", + "d16", + "d17", + "d18", + "d19", + "d20", + "period", + "t", + "species" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "other", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Elephant/elephant_EFA.bngl", + "file": "elephant_EFA.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "EmeraldCity_m15", - "name": "Mallela 2021 - COVID-19 City Models - EmeraldCity_m15", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/EmeraldCity_m15.bngl", - "file": "EmeraldCity_m15.bngl", + "id": "elephant_fit", + "name": "Hlavacek2018Elephant", + "description": "BNGL model: elephant_EFA", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "a0", + "a1", + "a2", + "a3", + "a4", + "a5", + "a6", + "a7", + "a8", + "a9", + "a10", + "a11", + "a12", + "a13", + "a14", + "a15", + "a16", + "a17", + "a18", + "a19", + "a20", + "b0", + "b1", + "b2", + "b3", + "b4", + "b5", + "b6", + "b7", + "b8", + "b9", + "b10", + "b11", + "b12", + "b13", + "b14", + "b15", + "b16", + "b17", + "b18", + "b19", + "b20", + "c0", + "c1", + "c2", + "c3", + "c4", + "c5", + "c6", + "c7", + "c8", + "c9", + "c10", + "c11", + "c12", + "c13", + "c14", + "c15", + "c16", + "c17", + "c18", + "c19", + "c20", + "d0", + "d1", + "d2", + "d3", + "d4", + "d5", + "d6", + "d7", + "d8", + "d9", + "d10", + "d11", + "d12", + "d13", + "d14", + "d15", + "d16", + "d17", + "d18", + "d19", + "d20", + "period", + "t", + "species" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "other", "origin": "published", "visible": false, - "collectionId": "Mallela2021_Cities" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Elephant/elephant_fit.bngl", + "file": "elephant_fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "endosomal-sorting-rab", "name": "endosomal sorting rab", "description": "Endosomal Sorting: Rab GTPase conversion and effector recruitment.", - "path": "Contributed/BNGPlayground_Examples/biology/endosomalsortingrab/endosomal-sorting-rab.bngl", - "file": "endosomal-sorting-rab.bngl", "tags": [ "endosomal", "sorting", @@ -3846,17 +5085,29 @@ "v_gap_drive" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/endosomalsortingrab/endosomal-sorting-rab.bngl", + "file": "endosomal-sorting-rab.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "energy_allostery_mwc", "name": "energy allostery mwc", "description": "Model: energy_allostery_mwc.bngl", - "path": "Contributed/BNGPlayground_Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl", - "file": "energy_allostery_mwc.bngl", "tags": [ "energy", "allostery", @@ -3865,17 +5116,29 @@ "l" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/energy/energyallosterymwc/energy_allostery_mwc.bngl", + "file": "energy_allostery_mwc.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "energy_catalysis_mm", "name": "energy catalysis mm", "description": "Model: energy_catalysis_mm.bngl", - "path": "Contributed/BNGPlayground_Examples/energy/energycatalysismm/energy_catalysis_mm.bngl", - "file": "energy_catalysis_mm.bngl", "tags": [ "energy", "catalysis", @@ -3885,17 +5148,29 @@ "p" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/energy/energycatalysismm/energy_catalysis_mm.bngl", + "file": "energy_catalysis_mm.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "energy_cooperativity_adh", "name": "energy cooperativity adh", "description": "Model: energy_cooperativity_adh.bngl", - "path": "Contributed/BNGPlayground_Examples/energy/energycooperativityadh/energy_cooperativity_adh.bngl", - "file": "energy_cooperativity_adh.bngl", "tags": [ "energy", "cooperativity", @@ -3904,17 +5179,29 @@ "l" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/energy/energycooperativityadh/energy_cooperativity_adh.bngl", + "file": "energy_cooperativity_adh.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "energy_example1", "name": "energy_example1", "description": "Illustration of energy modeling approach w/ a simple protein scaffold model", - "path": "Contributed/BNGPlayground_Validation/energyexample1/energy_example1.bngl", - "file": "energy_example1.bngl", "tags": [ "validation", "energy", @@ -3927,17 +5214,29 @@ "c" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/energyexample1/energy_example1.bngl", + "file": "energy_example1.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "energy_linear_chain", "name": "energy linear chain", "description": "Model: energy_linear_chain.bngl", - "path": "Contributed/BNGPlayground_Examples/energy/energylinearchain/energy_linear_chain.bngl", - "file": "energy_linear_chain.bngl", "tags": [ "energy", "linear", @@ -3946,17 +5245,29 @@ "generate_network" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/energy/energylinearchain/energy_linear_chain.bngl", + "file": "energy_linear_chain.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "energy_transport_pump", "name": "energy transport pump", "description": "Model: energy_transport_pump.bngl", - "path": "Contributed/BNGPlayground_Examples/energy/energytransportpump/energy_transport_pump.bngl", - "file": "energy_transport_pump.bngl", "tags": [ "energy", "transport", @@ -3968,17 +5279,54 @@ "t" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/energy/energytransportpump/energy_transport_pump.bngl", + "file": "energy_transport_pump.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ensemble_tofit", + "name": "translated into BNGL", + "description": "Ensemble model translated into BNGL", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/28-mapk/ensemble_tofit.bngl", + "file": "ensemble_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "er-stress-response", "name": "er stress response", "description": "Rate Constants", - "path": "Contributed/BNGPlayground_Examples/biology/erstressresponse/er-stress-response.bngl", - "file": "er-stress-response.bngl", "tags": [ "er", "stress", @@ -3989,17 +5337,29 @@ "chaperone" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/erstressresponse/er-stress-response.bngl", + "file": "er-stress-response.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Erdem_2021", "name": "Erdem 2021", "description": "InsR/IGF1R signaling", - "path": "Published/Erdem2021/Erdem_2021.bngl", - "file": "Erdem_2021.bngl", "tags": [ "published", "erdem", @@ -4014,17 +5374,100 @@ "raf" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism" + ], + "path": "Published/Erdem2021/Erdem_2021.bngl", + "file": "Erdem_2021.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "ERK_model", + "name": "ERK_model.bngl", + "description": "filename: ERK_model.bngl", + "tags": [ + "egf", + "erkpp_sos1_fb", + "erkpp_mek_fb", + "erkpp_raf1_fb", + "lambda", + "egfr_tot", + "ras_tot", + "sos_tot", + "rasgap_tot", + "raf_tot", + "mek_tot", + "erk_tot", + "ekar3_tot", + "erktr_tot", + "a1", + "d1", + "b1", + "u1a", + "u1b", + "b2a", + "u2a", + "b2b", + "u2b", + "k2a", + "k2b", + "b3", + "u3", + "k3", + "a2", + "d2", + "p1", + "q1", + "p2", + "q2", + "p3", + "q3", + "p4", + "q4", + "q5", + "p6", + "q6", + "a0_ekar3", + "d0_ekar3", + "a0_erktr", + "d0_erktr", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "path": "Published/Lin2019/ERK_model.bngl", + "file": "ERK_model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "erk-nuclear-translocation", "name": "erk nuclear translocation", "description": "ERK Translocation: Spatial signaling and transcriptional assembly.", - "path": "Contributed/BNGPlayground_Examples/biology/erknucleartranslocation/erk-nuclear-translocation.bngl", - "file": "erk-nuclear-translocation.bngl", "tags": [ "erk", "nuclear", @@ -4035,17 +5478,29 @@ "transcription_signal" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/erknucleartranslocation/erk-nuclear-translocation.bngl", + "file": "erk-nuclear-translocation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ErrNoFrees", "name": "ErrNoFrees", "description": "An example from a real application", - "path": "PyBioNetGen/tests/ErrNoFrees/ErrNoFrees.bngl", - "file": "ErrNoFrees.bngl", "tags": [ "errnofrees", "ag", @@ -4053,35 +5508,61 @@ "h" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/ErrNoFrees/ErrNoFrees.bngl", + "file": "ErrNoFrees.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "Evansville_IN-KY_Evansville_IN-KY", - "name": "Mallela 2022 - COVID-19 MSA Models - Evansville_IN-KY_Evansville_IN-KY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Evansville_IN-KY_Evansville_IN-KY.bngl", - "file": "Evansville_IN-KY_Evansville_IN-KY.bngl", + "id": "example1", + "name": "example1", + "description": "Filename: example1.bngl", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "example1", + "egf", + "egfr", + "pre1_dose", + "pre2_time", + "pre3_dose" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "other", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/example1/example1.bngl", + "file": "example1.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "example1", "name": "example1", "description": "Example file for BNG2 tutorial.", - "path": "Contributed/BNGPlayground_Validation/example1/example1.bngl", - "file": "example1.bngl", "tags": [ "validation", "example1", @@ -4090,37 +5571,255 @@ "simulate_ode" ], "category": "validation", - "bng2_compatible": false, "origin": "test-case", "visible": true, - "collectionId": null - }, - { - "id": "example1", - "name": "example1", - "description": "Filename: example1.bngl", - "path": "PyBioNetGen/core/example1/example1.bngl", + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/example1/example1.bngl", + "file": "example1.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example1_BNFfiles_example1", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example1_BNFfiles/example1.bngl", "file": "example1.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example1_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example1_fit.bngl", + "file": "example1_fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example2_BNFfiles_example2", + "name": "example2_starting_point.bngl", + "description": "Filename: example2_starting_point.bngl", "tags": [ - "example1", - "egf", - "egfr", - "pre1_dose", - "pre2_time", - "pre3_dose" + "f", + "lt_nm", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example2_BNFfiles/example2.bngl", + "file": "example2.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example2_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example2_fit.bngl", + "file": "example2_fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "example2_starting_point", "name": "example2 starting point", "description": "Filename: example2_starting_point.bngl", - "path": "PyBioNetGen/core/example2startingpoint/example2_starting_point.bngl", - "file": "example2_starting_point.bngl", "tags": [ "example2", "starting", @@ -4132,17 +5831,471 @@ "pre2_time" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/example2startingpoint/example2_starting_point.bngl", + "file": "example2_starting_point.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "example3_BNFfiles_example3", + "name": "example3 BNFfiles", + "description": "BNGL model: example3", + "tags": [ + "alpha", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example3_BNFfiles/example3.bngl", + "file": "example3.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example3_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example3_fit.bngl", + "file": "example3_fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example4_BNFfiles_example4", + "name": "in BNGL. For a description of BNGL, see:", + "description": "Supplementary File A in File S1", + "tags": [ + "other" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example4_BNFfiles/example4.bngl", + "file": "example4.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example4_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example4_fit.bngl", + "file": "example4_fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example5_BNFfiles_example5", + "name": "example5 BNFfiles", + "description": "A simple model", + "tags": [ + "ligand_ispresent", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example5_BNFfiles/example5.bngl", + "file": "example5.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example5_fit", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example5_fit.bngl", + "file": "example5_fit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example5_ground_truth", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example5_ground_truth.bngl", + "file": "example5_ground_truth.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example5_starting_point", + "name": "13-receptor", + "description": "A simple model", + "tags": [ + "ligand_ispresent", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/13-receptor/example5_starting_point.bngl", + "file": "example5_starting_point.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example6_BNFfiles_example6", + "name": "example6 BNFfiles", + "description": "A simple model", + "tags": [ + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example6_BNFfiles/example6.bngl", + "file": "example6.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "example6_ground_truth", + "name": "example1_starting_point.bngl", + "description": "Filename: example1_starting_point.bngl", + "tags": [ + "chi_r__free__", + "k_c__free__", + "k_o__free__", + "kaf__free__", + "kar__free__", + "alpha1_pre__free__", + "alpha2_pre__free__", + "alpha3_pre__free__", + "alpha4_pre__free__", + "lt", + "rt", + "k11", + "k11r", + "k21", + "k21r", + "k22", + "k22r", + "l20", + "l20r", + "l21r", + "l22r", + "k_o", + "k_c", + "kaf", + "kar", + "kp", + "kdp", + "chi_r", + "avg1", + "avg2", + "avg3", + "avg4", + "alpha1", + "alpha2", + "alpha3", + "alpha4", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Thomas2016/example6_ground_truth.bngl", + "file": "example6_ground_truth.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "extra_CaMKII_Holo", "name": "Ordyan 2020: extra CaMKII holo", "description": "Extra CaMKII holo (supplement)", - "path": "Published/Ordyan2020/extraCaMKIIHolo/extra_CaMKII_Holo.bngl", - "file": "extra_CaMKII_Holo.bngl", "tags": [ "published", "neuroscience", @@ -4159,17 +6312,29 @@ "t8" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "path": "Published/Ordyan2020/extraCaMKIIHolo/extra_CaMKII_Holo.bngl", + "file": "extra_CaMKII_Holo.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Faeder_2003", - "name": "Faeder 2003 - Faeder_2003", + "name": "Faeder 2003", "description": "FceRI signaling", - "path": "Published/Faeder2003/Faeder_2003.bngl", - "file": "Faeder_2003.bngl", "tags": [ "published", "immunology", @@ -4181,89 +6346,29 @@ "rec" ], "category": "immunology", - "bng2_compatible": false, "origin": "published", "visible": true, - "collectionId": "Faeder_2003" - }, - { - "id": "Fargo_ND-MN_Fargo_ND-MN", - "name": "Mallela 2022 - COVID-19 MSA Models - Fargo_ND-MN_Fargo_ND-MN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Fargo_ND-MN_Fargo_ND-MN.bngl", - "file": "Fargo_ND-MN_Fargo_ND-MN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Farmington_NM_Farmington_NM", - "name": "Mallela 2022 - COVID-19 MSA Models - Farmington_NM_Farmington_NM", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Farmington_NM_Farmington_NM.bngl", - "file": "Farmington_NM_Farmington_NM.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Fayetteville_NC_Fayetteville_NC", - "name": "Mallela 2022 - COVID-19 MSA Models - Fayetteville_NC_Fayetteville_NC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Fayetteville_NC_Fayetteville_NC.bngl", - "file": "Fayetteville_NC_Fayetteville_NC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Fayetteville-Springdale-Rogers_AR_Fayetteville-Springdale-Rogers_AR", - "name": "Mallela 2022 - COVID-19 MSA Models - Fayetteville-Springdale-Rogers_AR_Fayetteville-Springdale-Rogers_AR", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Fayetteville-Springdale-Rogers_AR_Fayetteville-Springdale-Rogers_AR.bngl", - "file": "Fayetteville-Springdale-Rogers_AR_Fayetteville-Springdale-Rogers_AR.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/Faeder2003/Faeder_2003.bngl", + "file": "Faeder_2003.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "fceri_fyn", "name": "FceRI Fyn", "description": "FceRI signaling", - "path": "Published/fcerifyn/fceri_fyn.bngl", - "file": "fceri_fyn.bngl", "tags": [ "published", "immunology", @@ -4275,17 +6380,29 @@ "rec" ], "category": "immunology", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/fcerifyn/fceri_fyn.bngl", + "file": "fceri_fyn.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "fceri_gamma2", "name": "fceri gamma2", "description": "BioNetGen model: fceri gamma2", - "path": "PyBioNetGen/core/fcerigamma2/fceri_gamma2.bngl", - "file": "fceri_gamma2.bngl", "tags": [ "fceri", "gamma2", @@ -4295,17 +6412,29 @@ "rec" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/fcerigamma2/fceri_gamma2.bngl", + "file": "fceri_gamma2.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "fceri_gamma2_ground_truth", "name": "fceri gamma2 ground truth", "description": "BioNetGen model: fceri gamma2 ground truth", - "path": "PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth.bngl", - "file": "fceri_gamma2_ground_truth.bngl", "tags": [ "fceri", "gamma2", @@ -4317,17 +6446,29 @@ "rec" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/fcerigamma2groundtruth/fceri_gamma2_ground_truth.bngl", + "file": "fceri_gamma2_ground_truth.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "fceri_ji", - "name": "Faeder 2003 - fceri_ji", + "name": "Faeder 2003", "description": "FceRI signaling", - "path": "Published/Faeder2003/fceri_ji.bngl", - "file": "fceri_ji.bngl", "tags": [ "published", "immunology", @@ -4339,17 +6480,29 @@ "rec" ], "category": "immunology", - "bng2_compatible": false, "origin": "published", "visible": true, - "collectionId": "Faeder_2003" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/Faeder2003/fceri_ji.bngl", + "file": "fceri_ji.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "FceRI_ji", "name": "FceRI ji", "description": "title: FceRI_ji.bngl", - "path": "Tutorials/NativeTutorials/FceRIji/FceRI_ji.bngl", - "file": "FceRI_ji.bngl", "tags": [ "fceri", "ji", @@ -4359,17 +6512,29 @@ "rec" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/FceRIji/FceRI_ji.bngl", + "file": "FceRI_ji.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "fceri_ji_comp", "name": "fceri_ji_comp", "description": "Ligand-receptor binding", - "path": "Contributed/BNGPlayground_Validation/fcerijicomp/fceri_ji_comp.bngl", - "file": "fceri_ji_comp.bngl", "tags": [ "validation", "fceri", @@ -4381,17 +6546,29 @@ "rec" ], "category": "validation", - "bng2_compatible": false, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/fcerijicomp/fceri_ji_comp.bngl", + "file": "fceri_ji_comp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "FceRI_viz", "name": "FceRI Viz", "description": "FcεRI (viz)", - "path": "Tutorials/NativeTutorials/FceRIviz/FceRI_viz.bngl", - "file": "FceRI_viz.bngl", "tags": [ "published", "tutorial", @@ -4408,17 +6585,29 @@ "sykp" ], "category": "tutorial", - "bng2_compatible": false, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/FceRIviz/FceRI_viz.bngl", + "file": "FceRI_viz.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "feature_functional_rates_volume", "name": "feature functional rates volume", "description": "Model: feature_functional_rates_volume.bngl", - "path": "Contributed/BNGPlayground_Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume.bngl", - "file": "feature_functional_rates_volume.bngl", "tags": [ "feature", "functional", @@ -4429,17 +6618,29 @@ "c" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/feature-demos/featurefunctionalratesvolume/feature_functional_rates_volume.bngl", + "file": "feature_functional_rates_volume.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "feature_global_functions_scan", "name": "feature global functions scan", "description": "Model: feature_global_functions_scan.bngl", - "path": "Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl", - "file": "feature_global_functions_scan.bngl", "tags": [ "feature", "global", @@ -4450,17 +6651,29 @@ "stimulus" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/feature-demos/featureglobalfunctionsscan/feature_global_functions_scan.bngl", + "file": "feature_global_functions_scan.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "feature_local_functions_explicit", "name": "feature local functions explicit", "description": "Model: feature_local_functions_explicit.bngl", - "path": "Contributed/BNGPlayground_Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit.bngl", - "file": "feature_local_functions_explicit.bngl", "tags": [ "feature", "local", @@ -4473,17 +6686,29 @@ "ratelaw" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/feature-demos/featurelocalfunctionsexplicit/feature_local_functions_explicit.bngl", + "file": "feature_local_functions_explicit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "feature_symmetry_factors_cyclic", "name": "feature symmetry factors cyclic", "description": "Model: feature_symmetry_factors_cyclic.bngl", - "path": "Contributed/BNGPlayground_Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic.bngl", - "file": "feature_symmetry_factors_cyclic.bngl", "tags": [ "feature", "symmetry", @@ -4494,17 +6719,29 @@ "simulate" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/feature-demos/featuresymmetryfactorscyclic/feature_symmetry_factors_cyclic.bngl", + "file": "feature_symmetry_factors_cyclic.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "feature_synthesis_degradation_ss", "name": "feature synthesis degradation ss", "description": "Model: feature_synthesis_degradation_ss.bngl", - "path": "Contributed/BNGPlayground_Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss.bngl", - "file": "feature_synthesis_degradation_ss.bngl", "tags": [ "feature", "synthesis", @@ -4515,17 +6752,29 @@ "simulate" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/feature-demos/featuresynthesisdegradationss/feature_synthesis_degradation_ss.bngl", + "file": "feature_synthesis_degradation_ss.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "fgf-signaling-pathway", "name": "fgf signaling pathway", "description": "FGF Signaling: FGFR dimerization and FRS2-Ras/PI3K relay.", - "path": "Contributed/BNGPlayground_Examples/biology/fgfsignalingpathway/fgf-signaling-pathway.bngl", - "file": "fgf-signaling-pathway.bngl", "tags": [ "fgf", "signaling", @@ -4537,293 +6786,156 @@ "internalized_rec" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/fgfsignalingpathway/fgf-signaling-pathway.bngl", + "file": "fgf-signaling-pathway.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Flagstaff_AZ_Flagstaff_AZ", - "name": "Mallela 2022 - COVID-19 MSA Models - Flagstaff_AZ_Flagstaff_AZ", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Flagstaff_AZ_Flagstaff_AZ.bngl", - "file": "Flagstaff_AZ_Flagstaff_AZ.bngl", + "id": "free_missing", + "name": "free missing", + "description": "Original values used to generate parabola.exp", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "free", + "missing", + "counter", + "y", + "generate_network", + "simulate" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/freemissing/free_missing.bngl", + "file": "free_missing.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Flint_MI_Flint_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Flint_MI_Flint_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Flint_MI_Flint_MI.bngl", - "file": "Flint_MI_Flint_MI.bngl", + "id": "Gardner_2000", + "name": "Gardner 2000", + "description": "Genetic toggle switch", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "published", + "synthetic-biology", + "gardner", + "2000" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "synthetic-biology", "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synthetic-biology" + ], + "path": "Published/Gardner2000/genetic_switch_gardner2000.bngl", + "file": "genetic_switch_gardner2000.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "Florence_SC_Florence_SC", - "name": "Mallela 2022 - COVID-19 MSA Models - Florence_SC_Florence_SC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Florence_SC_Florence_SC.bngl", - "file": "Florence_SC_Florence_SC.bngl", + "id": "gas6-axl-signaling", + "name": "gas6 axl signaling", + "description": "GAS6/AXL Signaling: AKT activation and SOCS feedback.", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "gas6", + "axl", + "signaling", + "pi3k", + "akt", + "socs", + "survival_burst" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/gas6axlsignaling/gas6-axl-signaling.bngl", + "file": "gas6-axl-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Florence-Muscle_Shoals_AL_Florence-Muscle_Shoals_AL", - "name": "Mallela 2022 - COVID-19 MSA Models - Florence-Muscle_Shoals_AL_Florence-Muscle_Shoals_AL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Florence-Muscle_Shoals_AL_Florence-Muscle_Shoals_AL.bngl", - "file": "Florence-Muscle_Shoals_AL_Florence-Muscle_Shoals_AL.bngl", + "id": "gene-expression-toggle", + "name": "gene expression toggle", + "description": "Kinetic Parameters", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "gene", + "expression", + "toggle", + "mrna", + "protein" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Fort_Collins_CO_Fort_Collins_CO", - "name": "Mallela 2022 - COVID-19 MSA Models - Fort_Collins_CO_Fort_Collins_CO", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Fort_Collins_CO_Fort_Collins_CO.bngl", - "file": "Fort_Collins_CO_Fort_Collins_CO.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Fort_Wayne_IN_Fort_Wayne_IN", - "name": "Mallela 2022 - COVID-19 MSA Models - Fort_Wayne_IN_Fort_Wayne_IN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Fort_Wayne_IN_Fort_Wayne_IN.bngl", - "file": "Fort_Wayne_IN_Fort_Wayne_IN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "free_missing", - "name": "free missing", - "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/freemissing/free_missing.bngl", - "file": "free_missing.bngl", - "tags": [ - "free", - "missing", - "counter", - "y", - "generate_network", - "simulate" - ], - "category": "validation", - "bng2_compatible": true, - "origin": "test-case", - "visible": false, - "collectionId": null - }, - { - "id": "Fresno_CA_Fresno_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Fresno_CA_Fresno_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Fresno_CA_Fresno_CA.bngl", - "file": "Fresno_CA_Fresno_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Frisco_m12", - "name": "Mallela 2021 - COVID-19 City Models - Frisco_m12", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/Frisco_m12.bngl", - "file": "Frisco_m12.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "Gadsden_AL_Gadsden_AL", - "name": "Mallela 2022 - COVID-19 MSA Models - Gadsden_AL_Gadsden_AL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Gadsden_AL_Gadsden_AL.bngl", - "file": "Gadsden_AL_Gadsden_AL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Gainesville_FL_Gainesville_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Gainesville_FL_Gainesville_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Gainesville_FL_Gainesville_FL.bngl", - "file": "Gainesville_FL_Gainesville_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Gainesville_GA_Gainesville_GA", - "name": "Mallela 2022 - COVID-19 MSA Models - Gainesville_GA_Gainesville_GA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Gainesville_GA_Gainesville_GA.bngl", - "file": "Gainesville_GA_Gainesville_GA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Gardner_2000", - "name": "Gardner 2000", - "description": "Genetic toggle switch", - "path": "Published/Gardner2000/genetic_switch_gardner2000.bngl", - "file": "genetic_switch_gardner2000.bngl", - "tags": [ - "published", - "synthetic-biology", - "gardner", - "2000" - ], - "category": "synthetic-biology", - "bng2_compatible": true, - "origin": "published", - "visible": true, - "collectionId": null - }, - { - "id": "gas6-axl-signaling", - "name": "gas6 axl signaling", - "description": "GAS6/AXL Signaling: AKT activation and SOCS feedback.", - "path": "Contributed/BNGPlayground_Examples/biology/gas6axlsignaling/gas6-axl-signaling.bngl", - "file": "gas6-axl-signaling.bngl", - "tags": [ - "gas6", - "axl", - "signaling", - "pi3k", - "akt", - "socs", - "survival_burst" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "ai-generated", - "visible": false, - "collectionId": null - }, - { - "id": "gene-expression-toggle", - "name": "gene expression toggle", - "description": "Kinetic Parameters", - "path": "Contributed/BNGPlayground_Examples/biology/geneexpressiontoggle/gene-expression-toggle.bngl", + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/geneexpressiontoggle/gene-expression-toggle.bngl", "file": "gene-expression-toggle.bngl", - "tags": [ - "gene", - "expression", - "toggle", - "mrna", - "protein" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "ai-generated", - "visible": false, - "collectionId": null + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "genetic_bistability_energy", "name": "genetic bistability energy", "description": "Model: genetic_bistability_energy.bngl", - "path": "Contributed/BNGPlayground_Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy.bngl", - "file": "genetic_bistability_energy.bngl", "tags": [ "genetic", "bistability", @@ -4834,17 +6946,29 @@ "protb" ], "category": "gene-expression", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/genetics/geneticbistabilityenergy/genetic_bistability_energy.bngl", + "file": "genetic_bistability_energy.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "genetic_dna_replication_stochastic", "name": "genetic dna replication stochastic", "description": "Model: genetic_dna_replication_stochastic.bngl", - "path": "Contributed/BNGPlayground_Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic.bngl", - "file": "genetic_dna_replication_stochastic.bngl", "tags": [ "genetic", "dna", @@ -4855,17 +6979,29 @@ "generate_network" ], "category": "gene-expression", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/genetics/geneticdnareplicationstochastic/genetic_dna_replication_stochastic.bngl", + "file": "genetic_dna_replication_stochastic.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "genetic_goodwin_oscillator", "name": "genetic goodwin oscillator", "description": "Model: genetic_goodwin_oscillator.bngl", - "path": "Contributed/BNGPlayground_Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator.bngl", - "file": "genetic_goodwin_oscillator.bngl", "tags": [ "genetic", "goodwin", @@ -4876,17 +7012,29 @@ "repressor" ], "category": "gene-expression", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/genetics/geneticgoodwinoscillator/genetic_goodwin_oscillator.bngl", + "file": "genetic_goodwin_oscillator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "genetic_translation_kinetics", "name": "genetic translation kinetics", "description": "Model: genetic_translation_kinetics.bngl", - "path": "Contributed/BNGPlayground_Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics.bngl", - "file": "genetic_translation_kinetics.bngl", "tags": [ "genetic", "translation", @@ -4896,17 +7044,29 @@ "protein" ], "category": "gene-expression", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/genetics/genetictranslationkinetics/genetic_translation_kinetics.bngl", + "file": "genetic_translation_kinetics.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "genetic_turing_pattern_1d", "name": "genetic turing pattern 1d", "description": "Model: genetic_turing_pattern_1d.bngl", - "path": "Contributed/BNGPlayground_Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d.bngl", - "file": "genetic_turing_pattern_1d.bngl", "tags": [ "genetic", "turing", @@ -4916,52 +7076,59 @@ "b" ], "category": "gene-expression", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/genetics/geneticturingpattern1d/genetic_turing_pattern_1d.bngl", + "file": "genetic_turing_pattern_1d.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "GK", "name": "GK", "description": "title: GK.bngl", - "path": "Tutorials/NativeTutorials/GK/GK.bngl", - "file": "GK.bngl", "tags": [ "gk", "b", "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null - }, - { - "id": "Glens_Falls_NY_Glens_Falls_NY", - "name": "Mallela 2022 - COVID-19 MSA Models - Glens_Falls_NY_Glens_Falls_NY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Glens_Falls_NY_Glens_Falls_NY.bngl", - "file": "Glens_Falls_NY_Glens_Falls_NY.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "native-tutorials" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Tutorials/NativeTutorials/GK/GK.bngl", + "file": "GK.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "glioblastoma-egfrviii-signaling", "name": "glioblastoma egfrviii signaling", "description": "EGFRvIII in Glioblastoma: Constitutive AKT drive and escape from decay.", - "path": "Contributed/BNGPlayground_Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling.bngl", - "file": "glioblastoma-egfrviii-signaling.bngl", "tags": [ "glioblastoma", "egfrviii", @@ -4972,17 +7139,30 @@ "v_viii_act" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/glioblastomaegfrviiisignaling/glioblastoma-egfrviii-signaling.bngl", + "file": "glioblastoma-egfrviii-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "glycolysis-branch-point", "name": "glycolysis branch point", "description": "BioNetGen model: glycolysis branch point", - "path": "Contributed/BNGPlayground_Examples/biology/glycolysisbranchpoint/glycolysis-branch-point.bngl", - "file": "glycolysis-branch-point.bngl", "tags": [ "glycolysis", "branch", @@ -4992,17 +7172,30 @@ "biomass" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/glycolysisbranchpoint/glycolysis-branch-point.bngl", + "file": "glycolysis-branch-point.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "gm_game_of_life", "name": "gm game of life", "description": "Model: gm_game_of_life.bngl", - "path": "Contributed/BNGPlayground_Examples/generative/gmgameoflife/gm_game_of_life.bngl", - "file": "gm_game_of_life.bngl", "tags": [ "gm", "game", @@ -5011,17 +7204,29 @@ "cell" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/generative/gmgameoflife/gm_game_of_life.bngl", + "file": "gm_game_of_life.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "gm_ray_marcher", "name": "gm ray marcher", "description": "Ray Marching Renderer in BNGL", - "path": "Contributed/BNGPlayground_Examples/generative/gmraymarcher/gm_ray_marcher.bngl", - "file": "gm_ray_marcher.bngl", "tags": [ "gm", "ray", @@ -5036,35 +7241,29 @@ "speed0" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Goldsboro_NC_Goldsboro_NC", - "name": "Mallela 2022 - COVID-19 MSA Models - Goldsboro_NC_Goldsboro_NC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Goldsboro_NC_Goldsboro_NC.bngl", - "file": "Goldsboro_NC_Goldsboro_NC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/generative/gmraymarcher/gm_ray_marcher.bngl", + "file": "gm_ray_marcher.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Goldstein_1980", "name": "Goldstein 1980", "description": "BLBR heterogeneity", - "path": "Published/Goldstein1980/blbr_heterogeneity_goldstein1980.bngl", - "file": "blbr_heterogeneity_goldstein1980.bngl", "tags": [ "published", "physics", @@ -5072,17 +7271,29 @@ "1980" ], "category": "physics", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "path": "Published/Goldstein1980/blbr_heterogeneity_goldstein1980.bngl", + "file": "blbr_heterogeneity_goldstein1980.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "gpcr-desensitization-arrestin", "name": "gpcr desensitization arrestin", "description": "GPCR Desensitization: Arrestin-mediated spatial sequestration.", - "path": "Contributed/BNGPlayground_Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin.bngl", - "file": "gpcr-desensitization-arrestin.bngl", "tags": [ "gpcr", "desensitization", @@ -5091,348 +7302,98 @@ "gprotein" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/gpcrdesensitizationarrestin/gpcr-desensitization-arrestin.bngl", + "file": "gpcr-desensitization-arrestin.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Grand_Forks_ND-MN_Grand_Forks_ND-MN", - "name": "Mallela 2022 - COVID-19 MSA Models - Grand_Forks_ND-MN_Grand_Forks_ND-MN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Grand_Forks_ND-MN_Grand_Forks_ND-MN.bngl", - "file": "Grand_Forks_ND-MN_Grand_Forks_ND-MN.bngl", + "id": "Harmon_2017", + "name": "Harmon 2017", + "description": "Antigen pulses", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "published", + "immunology", + "harmon", + "2017" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "immunology", "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/Harmon2017/antigen_pulses_harmon2017.bngl", + "file": "antigen_pulses_harmon2017.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "Grand_Island_NE_Grand_Island_NE", - "name": "Mallela 2022 - COVID-19 MSA Models - Grand_Island_NE_Grand_Island_NE", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Grand_Island_NE_Grand_Island_NE.bngl", - "file": "Grand_Island_NE_Grand_Island_NE.bngl", + "id": "Hat_2016", + "name": "Hat 2016", + "description": "Nuclear transport", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "published", + "hat", + "2016", + "dna_dsb", + "atm", + "siah1", + "hipk2", + "wip1", + "gene_wip1", + "mrna_wip1", + "p53" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "regulation", "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "visible": true, + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "cell-cycle", + "multistage" + ], + "path": "Published/Hat2016/Hat_2016.bngl", + "file": "Hat_2016.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "Grand_Rapids-Kentwood_MI_Grand_Rapids-Kentwood_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Grand_Rapids-Kentwood_MI_Grand_Rapids-Kentwood_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Grand_Rapids-Kentwood_MI_Grand_Rapids-Kentwood_MI.bngl", - "file": "Grand_Rapids-Kentwood_MI_Grand_Rapids-Kentwood_MI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Greeley_CO_Greeley_CO", - "name": "Mallela 2022 - COVID-19 MSA Models - Greeley_CO_Greeley_CO", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Greeley_CO_Greeley_CO.bngl", - "file": "Greeley_CO_Greeley_CO.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Green_Bay_WI_Green_Bay_WI", - "name": "Mallela 2022 - COVID-19 MSA Models - Green_Bay_WI_Green_Bay_WI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Green_Bay_WI_Green_Bay_WI.bngl", - "file": "Green_Bay_WI_Green_Bay_WI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Greensboro-High_Point_NC_Greensboro-High_Point_NC", - "name": "Mallela 2022 - COVID-19 MSA Models - Greensboro-High_Point_NC_Greensboro-High_Point_NC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Greensboro-High_Point_NC_Greensboro-High_Point_NC.bngl", - "file": "Greensboro-High_Point_NC_Greensboro-High_Point_NC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Greenville_NC_Greenville_NC", - "name": "Mallela 2022 - COVID-19 MSA Models - Greenville_NC_Greenville_NC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Greenville_NC_Greenville_NC.bngl", - "file": "Greenville_NC_Greenville_NC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Greenville-Anderson_SC_Greenville-Anderson_SC", - "name": "Mallela 2022 - COVID-19 MSA Models - Greenville-Anderson_SC_Greenville-Anderson_SC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Greenville-Anderson_SC_Greenville-Anderson_SC.bngl", - "file": "Greenville-Anderson_SC_Greenville-Anderson_SC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Gulfport-Biloxi_MS_Gulfport-Biloxi_MS", - "name": "Mallela 2022 - COVID-19 MSA Models - Gulfport-Biloxi_MS_Gulfport-Biloxi_MS", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Gulfport-Biloxi_MS_Gulfport-Biloxi_MS.bngl", - "file": "Gulfport-Biloxi_MS_Gulfport-Biloxi_MS.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Hagerstown-Martinsburg_MD-WV_Hagerstown-Martinsburg_MD-WV", - "name": "Mallela 2022 - COVID-19 MSA Models - Hagerstown-Martinsburg_MD-WV_Hagerstown-Martinsburg_MD-WV", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Hagerstown-Martinsburg_MD-WV_Hagerstown-Martinsburg_MD-WV.bngl", - "file": "Hagerstown-Martinsburg_MD-WV_Hagerstown-Martinsburg_MD-WV.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Hammond_LA_Hammond_LA", - "name": "Mallela 2022 - COVID-19 MSA Models - Hammond_LA_Hammond_LA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Hammond_LA_Hammond_LA.bngl", - "file": "Hammond_LA_Hammond_LA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Hanford-Corcoran_CA_Hanford-Corcoran_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Hanford-Corcoran_CA_Hanford-Corcoran_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Hanford-Corcoran_CA_Hanford-Corcoran_CA.bngl", - "file": "Hanford-Corcoran_CA_Hanford-Corcoran_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Harmon_2017", - "name": "Harmon 2017", - "description": "Antigen pulses", - "path": "Published/Harmon2017/antigen_pulses_harmon2017.bngl", - "file": "antigen_pulses_harmon2017.bngl", - "tags": [ - "published", - "immunology", - "harmon", - "2017" - ], - "category": "immunology", - "bng2_compatible": true, - "origin": "published", - "visible": true, - "collectionId": null - }, - { - "id": "Harrisburg-Carlisle_PA_Harrisburg-Carlisle_PA", - "name": "Mallela 2022 - COVID-19 MSA Models - Harrisburg-Carlisle_PA_Harrisburg-Carlisle_PA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Harrisburg-Carlisle_PA_Harrisburg-Carlisle_PA.bngl", - "file": "Harrisburg-Carlisle_PA_Harrisburg-Carlisle_PA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Harrisonburg_VA_Harrisonburg_VA", - "name": "Mallela 2022 - COVID-19 MSA Models - Harrisonburg_VA_Harrisonburg_VA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Harrisonburg_VA_Harrisonburg_VA.bngl", - "file": "Harrisonburg_VA_Harrisonburg_VA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Hartford-East_Hartford-Middletown_CT_Hartford-East_Hartford-Middletown_CT", - "name": "Mallela 2022 - COVID-19 MSA Models - Hartford-East_Hartford-Middletown_CT_Hartford-East_Hartford-Middletown_CT", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Hartford-East_Hartford-Middletown_CT_Hartford-East_Hartford-Middletown_CT.bngl", - "file": "Hartford-East_Hartford-Middletown_CT_Hartford-East_Hartford-Middletown_CT.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Hat_2016", - "name": "Hat 2016", - "description": "Nuclear transport", - "path": "Published/Hat2016/Hat_2016.bngl", - "file": "Hat_2016.bngl", - "tags": [ - "published", - "hat", - "2016", - "dna_dsb", - "atm", - "siah1", - "hipk2", - "wip1", - "gene_wip1", - "mrna_wip1", - "p53" - ], - "category": "regulation", - "bng2_compatible": false, - "origin": "published", - "visible": true, - "collectionId": null - }, - { - "id": "Hattiesburg_MS_Hattiesburg_MS", - "name": "Mallela 2022 - COVID-19 MSA Models - Hattiesburg_MS_Hattiesburg_MS", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Hattiesburg_MS_Hattiesburg_MS.bngl", - "file": "Hattiesburg_MS_Hattiesburg_MS.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Haugh2b", - "name": "Haugh2b", - "description": "R(KD,Y1~U,Y2~U) 1.00", - "path": "Contributed/BNGPlayground_Validation/Haugh2b/Haugh2b.bngl", - "file": "Haugh2b.bngl", + "id": "Haugh2b", + "name": "Haugh2b", + "description": "R(KD,Y1~U,Y2~U) 1.00", "tags": [ "validation", "haugh2b", @@ -5443,17 +7404,29 @@ "include_reactants" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/Haugh2b/Haugh2b.bngl", + "file": "Haugh2b.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "hedgehog-signaling-pathway", "name": "hedgehog signaling pathway", "description": "Hedgehog (Hh) Signaling: Ciliary translocation and Gli processing.", - "path": "Contributed/BNGPlayground_Examples/biology/hedgehogsignalingpathway/hedgehog-signaling-pathway.bngl", - "file": "hedgehog-signaling-pathway.bngl", "tags": [ "hedgehog", "signaling", @@ -5465,17 +7438,30 @@ "sufu" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/hedgehogsignalingpathway/hedgehog-signaling-pathway.bngl", + "file": "hedgehog-signaling-pathway.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "heise", "name": "heise", "description": "Validate state inheritance in a symmetric context", - "path": "Contributed/BNGPlayground_Validation/heise/heise.bngl", - "file": "heise.bngl", "tags": [ "validation", "heise", @@ -5486,17 +7472,29 @@ "setparameter" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/heise/heise.bngl", + "file": "heise.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "hematopoietic-growth-factor", "name": "hematopoietic growth factor", "description": "Kinetic Parameters", - "path": "Contributed/BNGPlayground_Examples/biology/hematopoieticgrowthfactor/hematopoietic-growth-factor.bngl", - "file": "hematopoietic-growth-factor.bngl", "tags": [ "hematopoietic", "growth", @@ -5507,35 +7505,29 @@ "stat5" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Hickory-Lenoir-Morganton_NC_Hickory-Lenoir-Morganton_NC", - "name": "Mallela 2022 - COVID-19 MSA Models - Hickory-Lenoir-Morganton_NC_Hickory-Lenoir-Morganton_NC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Hickory-Lenoir-Morganton_NC_Hickory-Lenoir-Morganton_NC.bngl", - "file": "Hickory-Lenoir-Morganton_NC_Hickory-Lenoir-Morganton_NC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/hematopoieticgrowthfactor/hematopoietic-growth-factor.bngl", + "file": "hematopoietic-growth-factor.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "hif1a_degradation_loop", "name": "hif1a degradation loop", "description": "HIF-1alpha Oxygen Sensing: Hydroxylation and VHL-mediated decay.", - "path": "Contributed/BNGPlayground_Examples/biology/hif1adegradationloop/hif1a_degradation_loop.bngl", - "file": "hif1a_degradation_loop.bngl", "tags": [ "hif1a", "degradation", @@ -5545,35 +7537,29 @@ "v_hydrox" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Hilton_Head_Island-Bluffton-Beaufort_SC_Hilton_Head_Island-Bluffton-Beaufort_SC", - "name": "Mallela 2022 - COVID-19 MSA Models - Hilton_Head_Island-Bluffton-Beaufort_SC_Hilton_Head_Island-Bluffton-Beaufort_SC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Hilton_Head_Island-Bluffton-Beaufort_SC_Hilton_Head_Island-Bluffton-Beaufort_SC.bngl", - "file": "Hilton_Head_Island-Bluffton-Beaufort_SC_Hilton_Head_Island-Bluffton-Beaufort_SC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/hif1adegradationloop/hif1a_degradation_loop.bngl", + "file": "hif1a_degradation_loop.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Hlavacek_1999", "name": "Hlavacek 1999", "description": "Steric effects", - "path": "Published/Hlavacek1999/steric_effects_hlavacek1999.bngl", - "file": "steric_effects_hlavacek1999.bngl", "tags": [ "published", "physics", @@ -5581,17 +7567,29 @@ "1999" ], "category": "physics", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "path": "Published/Hlavacek1999/steric_effects_hlavacek1999.bngl", + "file": "steric_effects_hlavacek1999.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Hlavacek_2001", "name": "Hlavacek 2001", "description": "Kinetic proofreading", - "path": "Published/Hlavacek2001/kinetic_proofreading_hlavacek2001.bngl", - "file": "kinetic_proofreading_hlavacek2001.bngl", "tags": [ "published", "physics", @@ -5599,53 +7597,76 @@ "2001" ], "category": "physics", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null - }, - { - "id": "Hotlanta_m9", - "name": "Mallela 2021 - COVID-19 City Models - Hotlanta_m9", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/Hotlanta_m9.bngl", - "file": "Hotlanta_m9.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "Houma-Thibodaux_LA_Houma-Thibodaux_LA", - "name": "Mallela 2022 - COVID-19 MSA Models - Houma-Thibodaux_LA_Houma-Thibodaux_LA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Houma-Thibodaux_LA_Houma-Thibodaux_LA.bngl", - "file": "Houma-Thibodaux_LA_Houma-Thibodaux_LA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "path": "Published/Hlavacek2001/kinetic_proofreading_hlavacek2001.bngl", + "file": "kinetic_proofreading_hlavacek2001.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "Hlavacek2018Egg_egg", + "name": "Hlavacek2018Egg", + "description": "End of permute change log", + "tags": [ + "a0__free", + "a1__free", + "a2__free", + "b1__free", + "b2__free", + "c0__free", + "c1__free", + "c2__free", + "d1__free", + "d2__free", + "a0", + "a1", + "a2", + "b1", + "b2", + "c0", + "c1", + "c2", + "d1", + "d2", + "period", + "t", + "species" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "other", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Hlavacek2018Egg/egg.bngl", + "file": "egg.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Houston", "name": "Houston", "description": "- This model is intended to be consistent with the compartmental model", - "path": "Published/VaxAndVariants/Houston/Houston.bngl", - "file": "Houston.bngl", "tags": [ "houston", "counter", @@ -5658,89 +7679,29 @@ "v" ], "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": null - }, - { - "id": "Houston-The_Woodlands-Sugar_Land_TX_Houston-The_Woodlands-Sugar_Land_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - Houston-The_Woodlands-Sugar_Land_TX_Houston-The_Woodlands-Sugar_Land_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Houston-The_Woodlands-Sugar_Land_TX_Houston-The_Woodlands-Sugar_Land_TX.bngl", - "file": "Houston-The_Woodlands-Sugar_Land_TX_Houston-The_Woodlands-Sugar_Land_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "HTown_m5", - "name": "Mallela 2021 - COVID-19 City Models - HTown_m5", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/HTown_m5.bngl", - "file": "HTown_m5.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "Huntington-Ashland_WV-KY-OH_Huntington-Ashland_WV-KY-OH", - "name": "Mallela 2022 - COVID-19 MSA Models - Huntington-Ashland_WV-KY-OH_Huntington-Ashland_WV-KY-OH", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Huntington-Ashland_WV-KY-OH_Huntington-Ashland_WV-KY-OH.bngl", - "file": "Huntington-Ashland_WV-KY-OH_Huntington-Ashland_WV-KY-OH.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Huntsville_AL_Huntsville_AL", - "name": "Mallela 2022 - COVID-19 MSA Models - Huntsville_AL_Huntsville_AL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Huntsville_AL_Huntsville_AL.bngl", - "file": "Huntsville_AL_Huntsville_AL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/VaxAndVariants/Houston/Houston.bngl", + "file": "Houston.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "hypoxia-response-signaling", "name": "hypoxia response signaling", "description": "Rate Constants", - "path": "Contributed/BNGPlayground_Examples/biology/hypoxiaresponsesignaling/hypoxia-response-signaling.bngl", - "file": "hypoxia-response-signaling.bngl", "tags": [ "hypoxia", "response", @@ -5750,17 +7711,30 @@ "vegf" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/hypoxiaresponsesignaling/hypoxia-response-signaling.bngl", + "file": "hypoxia-response-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "IGF1R_Model_receptor_activation_bnf", "name": "IGF1R Model receptor activation bnf", "description": "Author: William S. Hlavacek", - "path": "PyBioNetGen/core/IGF1RModelreceptoractivationbnf/IGF1R_Model_receptor_activation_bnf.bngl", - "file": "IGF1R_Model_receptor_activation_bnf.bngl", "tags": [ "igf1r", "model", @@ -5770,17 +7744,29 @@ "igf1" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/IGF1RModelreceptoractivationbnf/IGF1R_Model_receptor_activation_bnf.bngl", + "file": "IGF1R_Model_receptor_activation_bnf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "il1b-signaling", "name": "il1b signaling", "description": "IL-1beta Signaling: MyD88/IRAK assembly and NF-kB translocation.", - "path": "Contributed/BNGPlayground_Examples/biology/il1bsignaling/il1b-signaling.bngl", - "file": "il1b-signaling.bngl", "tags": [ "il1b", "signaling", @@ -5790,17 +7776,29 @@ "nfkb" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/il1bsignaling/il1b-signaling.bngl", + "file": "il1b-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "il6-jak-stat-pathway", "name": "il6 jak stat pathway", "description": "IL-6 Signaling: gp130 hexamerization and pSTAT3 import.", - "path": "Contributed/BNGPlayground_Examples/biology/il6jakstatpathway/il6-jak-stat-pathway.bngl", - "file": "il6-jak-stat-pathway.bngl", "tags": [ "il6", "jak", @@ -5811,17 +7809,29 @@ "socs" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/il6jakstatpathway/il6-jak-stat-pathway.bngl", + "file": "il6-jak-stat-pathway.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "immune-synapse-formation", "name": "immune synapse formation", "description": "Kinetic Parameters", - "path": "Contributed/BNGPlayground_Examples/biology/immunesynapseformation/immune-synapse-formation.bngl", - "file": "immune-synapse-formation.bngl", "tags": [ "immune", "synapse", @@ -5832,35 +7842,30 @@ "zap70" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Indianapolis-Carmel-Anderson_IN_Indianapolis-Carmel-Anderson_IN", - "name": "Mallela 2022 - COVID-19 MSA Models - Indianapolis-Carmel-Anderson_IN_Indianapolis-Carmel-Anderson_IN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Indianapolis-Carmel-Anderson_IN_Indianapolis-Carmel-Anderson_IN.bngl", - "file": "Indianapolis-Carmel-Anderson_IN_Indianapolis-Carmel-Anderson_IN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/biology/immunesynapseformation/immune-synapse-formation.bngl", + "file": "immune-synapse-formation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "inflammasome-activation", "name": "inflammasome activation", "description": "Rate Constants", - "path": "Contributed/BNGPlayground_Examples/biology/inflammasomeactivation/inflammasome-activation.bngl", - "file": "inflammasome-activation.bngl", "tags": [ "inflammasome", "activation", @@ -5870,35 +7875,30 @@ "il1b" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "InlandEmpire_m13", - "name": "Mallela 2021 - COVID-19 City Models - InlandEmpire_m13", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/InlandEmpire_m13.bngl", - "file": "InlandEmpire_m13.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_Cities" + "path": "Examples/biology/inflammasomeactivation/inflammasome-activation.bngl", + "file": "inflammasome-activation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "innate_immunity", "name": "Korwek 2023", "description": "Immune response", - "path": "Published/innateimmunity/innate_immunity.bngl", - "file": "innate_immunity.bngl", "tags": [ "published", "immunology", @@ -5914,17 +7914,29 @@ "rigi_mrna" ], "category": "immunology", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/innateimmunity/innate_immunity.bngl", + "file": "innate_immunity.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "inositol-phosphate-metabolism", "name": "inositol phosphate metabolism", "description": "Inositol Phosphate (IP) Metabolism: PLC signaling and branch points.", - "path": "Contributed/BNGPlayground_Examples/biology/inositolphosphatemetabolism/inositol-phosphate-metabolism.bngl", - "file": "inositol-phosphate-metabolism.bngl", "tags": [ "inositol", "phosphate", @@ -5936,17 +7948,30 @@ "agonist" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/inositolphosphatemetabolism/inositol-phosphate-metabolism.bngl", + "file": "inositol-phosphate-metabolism.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "insulin-glucose-homeostasis", "name": "insulin glucose homeostasis", "description": "Insulin-Glucose: Compartmentalized transport.", - "path": "Contributed/BNGPlayground_Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis.bngl", - "file": "insulin-glucose-homeostasis.bngl", "tags": [ "insulin", "glucose", @@ -5956,17 +7981,30 @@ "pancreas" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" + ], + "path": "Examples/biology/insulinglucosehomeostasis/insulin-glucose-homeostasis.bngl", + "file": "insulin-glucose-homeostasis.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "interferon-signaling", "name": "interferon signaling", "description": "Rate Constants", - "path": "Contributed/BNGPlayground_Examples/biology/interferonsignaling/interferon-signaling.bngl", - "file": "interferon-signaling.bngl", "tags": [ "interferon", "signaling", @@ -5976,35 +8014,30 @@ "stat1" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Iowa_City_IA_Iowa_City_IA", - "name": "Mallela 2022 - COVID-19 MSA Models - Iowa_City_IA_Iowa_City_IA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Iowa_City_IA_Iowa_City_IA.bngl", - "file": "Iowa_City_IA_Iowa_City_IA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/biology/interferonsignaling/interferon-signaling.bngl", + "file": "interferon-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ire1a-xbp1-er-stress", "name": "ire1a xbp1 er stress", "description": "IRE1a/XBP1 ER Stress: Chaperone buffering and mRNA decay (RIDD).", - "path": "Contributed/BNGPlayground_Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl", - "file": "ire1a-xbp1-er-stress.bngl", "tags": [ "ire1a", "xbp1", @@ -6016,17 +8049,29 @@ "ridd_target" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/ire1axbp1erstress/ire1a-xbp1-er-stress.bngl", + "file": "ire1a-xbp1-er-stress.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "issue_198_short", "name": "issue_198_short", "description": "No description available", - "path": "Contributed/BNGPlayground_Validation/issue198short/issue_198_short.bngl", - "file": "issue_198_short.bngl", "tags": [ "validation", "issue", @@ -6039,71 +8084,29 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null - }, - { - "id": "Jackson_MI_Jackson_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Jackson_MI_Jackson_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Jackson_MI_Jackson_MI.bngl", - "file": "Jackson_MI_Jackson_MI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Jackson_MS_Jackson_MS", - "name": "Mallela 2022 - COVID-19 MSA Models - Jackson_MS_Jackson_MS", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Jackson_MS_Jackson_MS.bngl", - "file": "Jackson_MS_Jackson_MS.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Jacksonville_FL_Jacksonville_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Jacksonville_FL_Jacksonville_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Jacksonville_FL_Jacksonville_FL.bngl", - "file": "Jacksonville_FL_Jacksonville_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/issue198short/issue_198_short.bngl", + "file": "issue_198_short.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "jak-stat-cytokine-signaling", "name": "jak stat cytokine signaling", "description": "Rate Constants", - "path": "Contributed/BNGPlayground_Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling.bngl", - "file": "jak-stat-cytokine-signaling.bngl", "tags": [ "jak", "stat", @@ -6112,35 +8115,30 @@ "receptor" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Janesville-Beloit_WI_Janesville-Beloit_WI", - "name": "Mallela 2022 - COVID-19 MSA Models - Janesville-Beloit_WI_Janesville-Beloit_WI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Janesville-Beloit_WI_Janesville-Beloit_WI.bngl", - "file": "Janesville-Beloit_WI_Janesville-Beloit_WI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/biology/jakstatcytokinesignaling/jak-stat-cytokine-signaling.bngl", + "file": "jak-stat-cytokine-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Jaruszewicz-Blonska_2023", "name": "Jaruszewicz 2023", "description": "T-cell discrimination", - "path": "Published/JaruszewiczBlonska2023/Jaruszewicz-Blonska_2023.bngl", - "file": "Jaruszewicz-Blonska_2023.bngl", "tags": [ "published", "immunology", @@ -6154,17 +8152,29 @@ "nfkb" ], "category": "immunology", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" + ], + "path": "Published/JaruszewiczBlonska2023/Jaruszewicz-Blonska_2023.bngl", + "file": "Jaruszewicz-Blonska_2023.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "jnk-mapk-signaling", "name": "jnk mapk signaling", "description": "JNK MAPK Signaling: Scaffold-mediated activation and feedback.", - "path": "Contributed/BNGPlayground_Examples/biology/jnkmapksignaling/jnk-mapk-signaling.bngl", - "file": "jnk-mapk-signaling.bngl", "tags": [ "jnk", "mapk", @@ -6174,17 +8184,79 @@ "v_dephos" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/jnkmapksignaling/jnk-mapk-signaling.bngl", + "file": "jnk-mapk-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "jobs_ground", + "name": "30-jobs", + "description": "NFsim simulation of the job market", + "tags": [ + "other" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/30-jobs/jobs_ground.bngl", + "file": "jobs_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "jobs_tofit", + "name": "30-jobs", + "description": "NFsim simulation of the job market", + "tags": [ + "other" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/30-jobs/jobs_tofit.bngl", + "file": "jobs_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Jung_2017", "name": "Jung 2017", "description": "M1 receptor signaling", - "path": "Published/Jung2017/Jung_2017.bngl", - "file": "Jung_2017.bngl", "tags": [ "published", "jung", @@ -6199,114 +8271,66 @@ "pp2a" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null - }, - { - "id": "Kalamazoo-Portage_MI_Kalamazoo-Portage_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Kalamazoo-Portage_MI_Kalamazoo-Portage_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Kalamazoo-Portage_MI_Kalamazoo-Portage_MI.bngl", - "file": "Kalamazoo-Portage_MI_Kalamazoo-Portage_MI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/Jung2017/Jung_2017.bngl", + "file": "Jung_2017.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Kankakee_IL_Kankakee_IL", - "name": "Mallela 2022 - COVID-19 MSA Models - Kankakee_IL_Kankakee_IL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Kankakee_IL_Kankakee_IL.bngl", - "file": "Kankakee_IL_Kankakee_IL.bngl", + "id": "Kesseler_2013", + "name": "Kesseler 2013", + "description": "G2/Mitosis transition", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "published", + "kesseler", + "2013", + "mpf", + "cdc25", + "wee1", + "myt1", + "pin1", + "pp2a", + "prox", + "e33" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "signaling", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "path": "Published/Kesseler2013/Kesseler_2013.bngl", + "file": "Kesseler_2013.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Kansas_City_MO-KS_Kansas_City_MO-KS", - "name": "Mallela 2022 - COVID-19 MSA Models - Kansas_City_MO-KS_Kansas_City_MO-KS", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Kansas_City_MO-KS_Kansas_City_MO-KS.bngl", - "file": "Kansas_City_MO-KS_Kansas_City_MO-KS.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Kennewick-Richland_WA_Kennewick-Richland_WA", - "name": "Mallela 2022 - COVID-19 MSA Models - Kennewick-Richland_WA_Kennewick-Richland_WA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Kennewick-Richland_WA_Kennewick-Richland_WA.bngl", - "file": "Kennewick-Richland_WA_Kennewick-Richland_WA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Kesseler_2013", - "name": "Kesseler 2013", - "description": "G2/Mitosis transition", - "path": "Published/Kesseler2013/Kesseler_2013.bngl", - "file": "Kesseler_2013.bngl", - "tags": [ - "published", - "kesseler", - "2013", - "mpf", - "cdc25", - "wee1", - "myt1", - "pin1", - "pp2a", - "prox", - "e33" - ], - "category": "signaling", - "bng2_compatible": false, - "origin": "published", - "visible": false, - "collectionId": null - }, - { - "id": "Kiefhaber_emodel", - "name": "Kiefhaber_emodel", - "description": "Allow molar units to be used for bimolecular rate constants", - "path": "Contributed/BNGPlayground_Validation/Kiefhaberemodel/Kiefhaber_emodel.bngl", - "file": "Kiefhaber_emodel.bngl", + "id": "Kiefhaber_emodel", + "name": "Kiefhaber_emodel", + "description": "Allow molar units to be used for bimolecular rate constants", "tags": [ "validation", "kiefhaber", @@ -6318,53 +8342,29 @@ "a" ], "category": "validation", - "bng2_compatible": false, "origin": "test-case", "visible": false, - "collectionId": null - }, - { - "id": "Killeen-Temple_TX_Killeen-Temple_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - Killeen-Temple_TX_Killeen-Temple_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Killeen-Temple_TX_Killeen-Temple_TX.bngl", - "file": "Killeen-Temple_TX_Killeen-Temple_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Kingston_NY_Kingston_NY", - "name": "Mallela 2022 - COVID-19 MSA Models - Kingston_NY_Kingston_NY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Kingston_NY_Kingston_NY.bngl", - "file": "Kingston_NY_Kingston_NY.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/Kiefhaberemodel/Kiefhaber_emodel.bngl", + "file": "Kiefhaber_emodel.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "kir-channel-regulation", "name": "kir channel regulation", "description": "Kir Channel Regulation: PIP2 modulation and G-protein potentiation.", - "path": "Contributed/BNGPlayground_Examples/biology/kirchannelregulation/kir-channel-regulation.bngl", - "file": "kir-channel-regulation.bngl", "tags": [ "kir", "channel", @@ -6375,35 +8375,29 @@ "v_gbg_factor" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Knoxville_TN_Knoxville_TN", - "name": "Mallela 2022 - COVID-19 MSA Models - Knoxville_TN_Knoxville_TN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Knoxville_TN_Knoxville_TN.bngl", - "file": "Knoxville_TN_Knoxville_TN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/kirchannelregulation/kir-channel-regulation.bngl", + "file": "kir-channel-regulation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Kocieniewski_2012", "name": "Kocieniewski 2012", "description": "Actin dynamics", - "path": "Published/Kocieniewski2012/Kocieniewski_2012.bngl", - "file": "Kocieniewski_2012.bngl", "tags": [ "published", "kocieniewski", @@ -6414,35 +8408,29 @@ "scaff" ], "category": "regulation", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null - }, - { - "id": "Kokomo_IN_Kokomo_IN", - "name": "Mallela 2022 - COVID-19 MSA Models - Kokomo_IN_Kokomo_IN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Kokomo_IN_Kokomo_IN.bngl", - "file": "Kokomo_IN_Kokomo_IN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/Kocieniewski2012/Kocieniewski_2012.bngl", + "file": "Kocieniewski_2012.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Korwek_2023", "name": "Korwek_2023", "description": "This BioNetGen file features the article:", - "path": "Contributed/BNGPlayground_Validation/Korwek2023/Korwek_2023.bngl", - "file": "Korwek_2023.bngl", "tags": [ "validation", "korwek", @@ -6457,17 +8445,29 @@ "rigi_mrna" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/Korwek2023/Korwek_2023.bngl", + "file": "Korwek_2023.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Kozer_2013", "name": "Kozer 2013", "description": "EGFR oligomerization", - "path": "Published/Kozer2013/Kozer_2013.bngl", - "file": "Kozer_2013.bngl", "tags": [ "published", "kozer", @@ -6476,17 +8476,29 @@ "egfr" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Kozer2013/Kozer_2013.bngl", + "file": "Kozer_2013.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Kozer_2014", "name": "Kozer 2014", "description": "Grb2-EGFR recruitment", - "path": "Published/Kozer2014/Kozer_2014.bngl", - "file": "Kozer_2014.bngl", "tags": [ "published", "kozer", @@ -6496,17 +8508,29 @@ "grb2" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Kozer2014/Kozer_2014.bngl", + "file": "Kozer_2014.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "l-type-calcium-channel-dynamics", "name": "l type calcium channel dynamics", "description": "L-type Calcium Channel: Voltage gating and CDI (Calcium-dependent inactivation).", - "path": "Contributed/BNGPlayground_Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics.bngl", - "file": "l-type-calcium-channel-dynamics.bngl", "tags": [ "l", "type", @@ -6519,17 +8543,30 @@ "v_inact" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/ltypecalciumchanneldynamics/l-type-calcium-channel-dynamics.bngl", + "file": "l-type-calcium-channel-dynamics.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "lac-operon-regulation", "name": "lac operon regulation", "description": "Kinetic Parameters", - "path": "Contributed/BNGPlayground_Examples/biology/lacoperonregulation/lac-operon-regulation.bngl", - "file": "lac-operon-regulation.bngl", "tags": [ "lac", "operon", @@ -6542,143 +8579,30 @@ "allolactose" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Lafayette_LA_Lafayette_LA", - "name": "Mallela 2022 - COVID-19 MSA Models - Lafayette_LA_Lafayette_LA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Lafayette_LA_Lafayette_LA.bngl", - "file": "Lafayette_LA_Lafayette_LA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lafayette-West_Lafayette_IN_Lafayette-West_Lafayette_IN", - "name": "Mallela 2022 - COVID-19 MSA Models - Lafayette-West_Lafayette_IN_Lafayette-West_Lafayette_IN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Lafayette-West_Lafayette_IN_Lafayette-West_Lafayette_IN.bngl", - "file": "Lafayette-West_Lafayette_IN_Lafayette-West_Lafayette_IN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lake_Charles_LA_Lake_Charles_LA", - "name": "Mallela 2022 - COVID-19 MSA Models - Lake_Charles_LA_Lake_Charles_LA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Lake_Charles_LA_Lake_Charles_LA.bngl", - "file": "Lake_Charles_LA_Lake_Charles_LA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lake_Havasu_City-Kingman_AZ_Lake_Havasu_City-Kingman_AZ", - "name": "Mallela 2022 - COVID-19 MSA Models - Lake_Havasu_City-Kingman_AZ_Lake_Havasu_City-Kingman_AZ", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Lake_Havasu_City-Kingman_AZ_Lake_Havasu_City-Kingman_AZ.bngl", - "file": "Lake_Havasu_City-Kingman_AZ_Lake_Havasu_City-Kingman_AZ.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lakeland-Winter_Haven_FL_Lakeland-Winter_Haven_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Lakeland-Winter_Haven_FL_Lakeland-Winter_Haven_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Lakeland-Winter_Haven_FL_Lakeland-Winter_Haven_FL.bngl", - "file": "Lakeland-Winter_Haven_FL_Lakeland-Winter_Haven_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "LaLaLand_m2", - "name": "Mallela 2021 - COVID-19 City Models - LaLaLand_m2", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/LaLaLand_m2.bngl", - "file": "LaLaLand_m2.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "Lancaster_PA_Lancaster_PA", - "name": "Mallela 2022 - COVID-19 MSA Models - Lancaster_PA_Lancaster_PA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Lancaster_PA_Lancaster_PA.bngl", - "file": "Lancaster_PA_Lancaster_PA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/biology/lacoperonregulation/lac-operon-regulation.bngl", + "file": "lac-operon-regulation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Lang_2024", "name": "Lang 2024", "description": "Cell cycle regulation", - "path": "Published/Lang2024/Lang_2024.bngl", - "file": "Lang_2024.bngl", "tags": [ "published", "lang", @@ -6693,186 +8617,96 @@ "ensa_arpp19" ], "category": "signaling", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "path": "Published/Lang2024/Lang_2024.bngl", + "file": "Lang_2024.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "Lansing-East_Lansing_MI_Lansing-East_Lansing_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Lansing-East_Lansing_MI_Lansing-East_Lansing_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Lansing-East_Lansing_MI_Lansing-East_Lansing_MI.bngl", - "file": "Lansing-East_Lansing_MI_Lansing-East_Lansing_MI.bngl", + "id": "Ligon_2014", + "name": "Ligon 2014", + "description": "Lipoplex delivery", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "published", + "nfsim", + "ligon", + "2014", + "lext", + "pit", + "lint" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "signaling", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Ligon2014/Ligon_2014.bngl", + "file": "Ligon_2014.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Laredo_TX_Laredo_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - Laredo_TX_Laredo_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Laredo_TX_Laredo_TX.bngl", - "file": "Laredo_TX_Laredo_TX.bngl", + "id": "LilyIgE", + "name": "LilyIgE", + "description": "An example from a real application", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "lilyige", + "ag", + "r", + "syk", + "ship1", + "x", + "pip3", + "h" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", + "category": "validation", + "origin": "test-case", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/LilyIgE/LilyIgE.bngl", + "file": "LilyIgE.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Las_Cruces_NM_Las_Cruces_NM", - "name": "Mallela 2022 - COVID-19 MSA Models - Las_Cruces_NM_Las_Cruces_NM", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Las_Cruces_NM_Las_Cruces_NM.bngl", - "file": "Las_Cruces_NM_Las_Cruces_NM.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Las_Vegas-Henderson-Paradise_NV_Las_Vegas-Henderson-Paradise_NV", - "name": "Mallela 2022 - COVID-19 MSA Models - Las_Vegas-Henderson-Paradise_NV_Las_Vegas-Henderson-Paradise_NV", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Las_Vegas-Henderson-Paradise_NV_Las_Vegas-Henderson-Paradise_NV.bngl", - "file": "Las_Vegas-Henderson-Paradise_NV_Las_Vegas-Henderson-Paradise_NV.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lawton_OK_Lawton_OK", - "name": "Mallela 2022 - COVID-19 MSA Models - Lawton_OK_Lawton_OK", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Lawton_OK_Lawton_OK.bngl", - "file": "Lawton_OK_Lawton_OK.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lebanon_PA_Lebanon_PA", - "name": "Mallela 2022 - COVID-19 MSA Models - Lebanon_PA_Lebanon_PA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Lebanon_PA_Lebanon_PA.bngl", - "file": "Lebanon_PA_Lebanon_PA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lexington-Fayette_KY_Lexington-Fayette_KY", - "name": "Mallela 2022 - COVID-19 MSA Models - Lexington-Fayette_KY_Lexington-Fayette_KY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Lexington-Fayette_KY_Lexington-Fayette_KY.bngl", - "file": "Lexington-Fayette_KY_Lexington-Fayette_KY.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Ligon_2014", - "name": "Ligon 2014", - "description": "Lipoplex delivery", - "path": "Published/Ligon2014/Ligon_2014.bngl", - "file": "Ligon_2014.bngl", - "tags": [ - "published", - "nfsim", - "ligon", - "2014", - "lext", - "pit", - "lint" - ], - "category": "signaling", - "bng2_compatible": false, - "origin": "published", - "visible": false, - "collectionId": null - }, - { - "id": "LilyIgE", - "name": "LilyIgE", - "description": "An example from a real application", - "path": "PyBioNetGen/tests/LilyIgE/LilyIgE.bngl", - "file": "LilyIgE.bngl", - "tags": [ - "lilyige", - "ag", - "r", - "syk", - "ship1", - "x", - "pip3", - "h" - ], - "category": "validation", - "bng2_compatible": true, - "origin": "test-case", - "visible": false, - "collectionId": null - }, - { - "id": "Lin_ERK_2019", - "name": "Lin 2019", - "description": "ERK signaling", - "path": "Published/LinERK2019/Lin_ERK_2019.bngl", - "file": "Lin_ERK_2019.bngl", + "id": "Lin_ERK_2019", + "name": "Lin 2019", + "description": "ERK signaling", "tags": [ "published", "literature", @@ -6889,17 +8723,30 @@ "ekar3" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "developmental" + ], + "path": "Published/LinERK2019/Lin_ERK_2019.bngl", + "file": "Lin_ERK_2019.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Lin_Prion_2019", "name": "Lin 2019", "description": "Prion replication", - "path": "Published/LinPrion2019/Lin_Prion_2019.bngl", - "file": "Lin_Prion_2019.bngl", "tags": [ "published", "literature", @@ -6913,17 +8760,30 @@ "scaledupspecies30" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "neuroscience" + ], + "path": "Published/LinPrion2019/Lin_Prion_2019.bngl", + "file": "Lin_Prion_2019.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Lin_TCR_2019", "name": "Lin 2019", "description": "TCR signaling", - "path": "Published/LinTCR2019/Lin_TCR_2019.bngl", - "file": "Lin_TCR_2019.bngl", "tags": [ "published", "literature", @@ -6939,35 +8799,30 @@ "erk" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null - }, - { - "id": "Lincoln_NE_Lincoln_NE", - "name": "Mallela 2022 - COVID-19 MSA Models - Lincoln_NE_Lincoln_NE", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Lincoln_NE_Lincoln_NE.bngl", - "file": "Lincoln_NE_Lincoln_NE.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "immunology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/LinTCR2019/Lin_TCR_2019.bngl", + "file": "Lin_TCR_2019.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "lipid-mediated-pip3-signaling", "name": "lipid mediated pip3 signaling", "description": "Kinetic Parameters", - "path": "Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl", - "file": "lipid-mediated-pip3-signaling.bngl", "tags": [ "lipid", "mediated", @@ -6979,17 +8834,29 @@ "pdk1" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/lipidmediatedpip3signaling/lipid-mediated-pip3-signaling.bngl", + "file": "lipid-mediated-pip3-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Lisman", "name": "Lisman", "description": "title: auto.bngl", - "path": "Tutorials/NativeTutorials/Lisman/Lisman.bngl", - "file": "Lisman.bngl", "tags": [ "lisman", "k1", @@ -7000,17 +8867,30 @@ "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/Lisman/Lisman.bngl", + "file": "Lisman.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Lisman_bifurcate", "name": "Lisman bifurcate", "description": "title: Lisman_bifurcate.bngl", - "path": "Tutorials/NativeTutorials/Lismanbifurcate/Lisman_bifurcate.bngl", - "file": "Lisman_bifurcate.bngl", "tags": [ "lisman", "bifurcate", @@ -7018,35 +8898,30 @@ "p" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null - }, - { - "id": "Little_Rock-North_Little_Rock-Conway_AR_Little_Rock-North_Little_Rock-Conway_AR", - "name": "Mallela 2022 - COVID-19 MSA Models - Little_Rock-North_Little_Rock-Conway_AR_Little_Rock-North_Little_Rock-Conway_AR", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Little_Rock-North_Little_Rock-Conway_AR_Little_Rock-North_Little_Rock-Conway_AR.bngl", - "file": "Little_Rock-North_Little_Rock-Conway_AR_Little_Rock-North_Little_Rock-Conway_AR.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "native-tutorials" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Tutorials/NativeTutorials/Lismanbifurcate/Lisman_bifurcate.bngl", + "file": "Lisman_bifurcate.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "localfunc", "name": "localfunc", "description": "Test local function expansion", - "path": "Contributed/BNGPlayground_Validation/localfunc/localfunc.bngl", - "file": "localfunc.bngl", "tags": [ "validation", "localfunc", @@ -7057,71 +8932,29 @@ "f_synth" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null - }, - { - "id": "Longview_TX_Longview_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - Longview_TX_Longview_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Longview_TX_Longview_TX.bngl", - "file": "Longview_TX_Longview_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Los_Angeles-Long_Beach-Anaheim_CA_Los_Angeles-Long_Beach-Anaheim_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Los_Angeles-Long_Beach-Anaheim_CA_Los_Angeles-Long_Beach-Anaheim_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Los_Angeles-Long_Beach-Anaheim_CA_Los_Angeles-Long_Beach-Anaheim_CA.bngl", - "file": "Los_Angeles-Long_Beach-Anaheim_CA_Los_Angeles-Long_Beach-Anaheim_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Louisville_Jefferson_County_KY-IN_Louisville_Jefferson_County_KY-IN", - "name": "Mallela 2022 - COVID-19 MSA Models - Louisville_Jefferson_County_KY-IN_Louisville_Jefferson_County_KY-IN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Louisville_Jefferson_County_KY-IN_Louisville_Jefferson_County_KY-IN.bngl", - "file": "Louisville_Jefferson_County_KY-IN_Louisville_Jefferson_County_KY-IN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/localfunc/localfunc.bngl", + "file": "localfunc.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "LR", "name": "LR", "description": "title: LR.bngl", - "path": "Tutorials/NativeTutorials/LR/LR.bngl", - "file": "LR.bngl", "tags": [ "lr", "l", @@ -7129,17 +8962,29 @@ "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/LR/LR.bngl", + "file": "LR.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "LR_comp", "name": "LR comp", "description": "title: LR_comp.bngl", - "path": "Tutorials/NativeTutorials/LRcomp/LR_comp.bngl", - "file": "LR_comp.bngl", "tags": [ "lr", "comp", @@ -7148,34 +8993,58 @@ "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/LRcomp/LR_comp.bngl", + "file": "LR_comp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "LRR", "name": "LRR", "description": "title: LRR.bngl", - "path": "Tutorials/NativeTutorials/LRR/LRR.bngl", - "file": "LRR.bngl", "tags": [ "lrr", "l", "r" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/LRR/LRR.bngl", + "file": "LRR.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "LRR_comp", "name": "LRR comp", "description": "title: LRR_comp.bngl", - "path": "Tutorials/NativeTutorials/LRRcomp/LRR_comp.bngl", - "file": "LRR_comp.bngl", "tags": [ "lrr", "comp", @@ -7184,35 +9053,29 @@ "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null - }, - { - "id": "Lubbock_TX_Lubbock_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - Lubbock_TX_Lubbock_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Lubbock_TX_Lubbock_TX.bngl", - "file": "Lubbock_TX_Lubbock_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Tutorials/NativeTutorials/LRRcomp/LRR_comp.bngl", + "file": "LRR_comp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "LV", "name": "LV", "description": "title: LV.bgl", - "path": "Tutorials/NativeTutorials/LV/LV.bngl", - "file": "LV.bngl", "tags": [ "lv", "s", @@ -7222,17 +9085,30 @@ "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/LV/LV.bngl", + "file": "LV.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "LV_comp", "name": "LV comp", "description": "title: LV_comp.bgl", - "path": "Tutorials/NativeTutorials/LVcomp/LV_comp.bngl", - "file": "LV_comp.bngl", "tags": [ "lv", "comp", @@ -7241,17 +9117,113 @@ "w" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/LVcomp/LV_comp.bngl", + "file": "LV_comp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "m1", + "name": "of a 3-step signaling cascade", + "description": "Toy model of a 3-step signaling cascade", + "tags": [ + "k1", + "k2", + "k3", + "ainit", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/05-threestep/m1.bngl", + "file": "m1.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "m1_ground", + "name": "of a 3-step signaling cascade", + "description": "Toy model of a 3-step signaling cascade", + "tags": [ + "k1", + "k2", + "k3", + "ainit", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/05-threestep/m1_ground.bngl", + "file": "m1_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "machine_tofit", + "name": "translated into BNGL", + "description": "Ensemble model translated into BNGL", + "tags": [ + "signaling" + ], + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/28-mapk/machine_tofit.bngl", + "file": "machine_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Macken_1982", "name": "Macken 1982", "description": "TLBR solution macken 1982", - "path": "Published/Macken1982/tlbr_solution_macken1982.bngl", - "file": "tlbr_solution_macken1982.bngl", "tags": [ "published", "physics", @@ -7259,17 +9231,29 @@ "1982" ], "category": "physics", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "path": "Published/Macken1982/tlbr_solution_macken1982.bngl", + "file": "tlbr_solution_macken1982.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "Macon-Bibb_County_GA_Macon-Bibb_County_GA", - "name": "Mallela 2022 - COVID-19 MSA Models - Macon-Bibb_County_GA_Macon-Bibb_County_GA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Macon-Bibb_County_GA_Macon-Bibb_County_GA.bngl", - "file": "Macon-Bibb_County_GA_Macon-Bibb_County_GA.bngl", + "id": "Mallela2021_Cities", + "name": "Mallela 2021 - COVID-19 City Models", + "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", "tags": [ "covid-19", "epidemiology", @@ -7277,35 +9261,96 @@ "pybionetgen" ], "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Madison_WI_Madison_WI", - "name": "Mallela 2022 - COVID-19 MSA Models - Madison_WI_Madison_WI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Madison_WI_Madison_WI.bngl", - "file": "Madison_WI_Madison_WI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "MagicCity_m7", - "name": "Mallela 2021 - COVID-19 City Models - MagicCity_m7", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/MagicCity_m7.bngl", - "file": "MagicCity_m7.bngl", + "path": "Published/Mallela2021_Cities/Beantown_m11.bngl", + "file": "Beantown_m11.bngl", + "collectionId": "Mallela2021_Cities", + "collection": { + "type": "geographic-variants", + "count": 15, + "variant_key": "city", + "variants": [ + { + "id": "Beantown_m11", + "file": "Beantown_m11.bngl" + }, + { + "id": "BigApple_m1", + "file": "BigApple_m1.bngl" + }, + { + "id": "BigD_m4", + "file": "BigD_m4.bngl" + }, + { + "id": "BrotherlyLove_m8", + "file": "BrotherlyLove_m8.bngl" + }, + { + "id": "DC_m6", + "file": "DC_m6.bngl" + }, + { + "id": "EmeraldCity_m15", + "file": "EmeraldCity_m15.bngl" + }, + { + "id": "Frisco_m12", + "file": "Frisco_m12.bngl" + }, + { + "id": "HTown_m5", + "file": "HTown_m5.bngl" + }, + { + "id": "Hotlanta_m9", + "file": "Hotlanta_m9.bngl" + }, + { + "id": "InlandEmpire_m13", + "file": "InlandEmpire_m13.bngl" + }, + { + "id": "LaLaLand_m2", + "file": "LaLaLand_m2.bngl" + }, + { + "id": "MagicCity_m7", + "file": "MagicCity_m7.bngl" + }, + { + "id": "MotorCity_m14", + "file": "MotorCity_m14.bngl" + }, + { + "id": "Valley_of_the_Sun_m10", + "file": "Valley_of_the_Sun_m10.bngl" + }, + { + "id": "WindyCity_m3", + "file": "WindyCity_m3.bngl" + } + ] + }, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Mallela2021_States", + "name": "Mallela 2021 - COVID-19 State-Level Models", + "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", "tags": [ "covid-19", "epidemiology", @@ -7313,35 +9358,1397 @@ "pybionetgen" ], "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "Manchester-Nashua_NH_Manchester-Nashua_NH", - "name": "Mallela 2022 - COVID-19 MSA Models - Manchester-Nashua_NH_Manchester-Nashua_NH", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Manchester-Nashua_NH_Manchester-Nashua_NH.bngl", - "file": "Manchester-Nashua_NH_Manchester-Nashua_NH.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/Mallela2021/SI_files_Alabama_Alabama.bngl", + "file": "SI_files_Alabama_Alabama.bngl", + "collectionId": "Mallela2021_States", + "collection": { + "type": "geographic-variants", + "count": 50, + "variant_key": "us_state", + "variants": [ + { + "id": "SI_files_Alabama_Alabama", + "file": "SI_files_Alabama_Alabama.bngl" + }, + { + "id": "SI_files_Alaska_Alaska", + "file": "SI_files_Alaska_Alaska.bngl" + }, + { + "id": "SI_files_Arizona_Arizona", + "file": "SI_files_Arizona_Arizona.bngl" + }, + { + "id": "SI_files_Arkansas_Arkansas", + "file": "SI_files_Arkansas_Arkansas.bngl" + }, + { + "id": "SI_files_California_California", + "file": "SI_files_California_California.bngl" + }, + { + "id": "SI_files_Colorado_Colorado", + "file": "SI_files_Colorado_Colorado.bngl" + }, + { + "id": "SI_files_Connecticut_Connecticut", + "file": "SI_files_Connecticut_Connecticut.bngl" + }, + { + "id": "SI_files_Delaware_Delaware", + "file": "SI_files_Delaware_Delaware.bngl" + }, + { + "id": "SI_files_Florida_Florida", + "file": "SI_files_Florida_Florida.bngl" + }, + { + "id": "SI_files_Georgia_Georgia", + "file": "SI_files_Georgia_Georgia.bngl" + }, + { + "id": "SI_files_Hawaii_Hawaii", + "file": "SI_files_Hawaii_Hawaii.bngl" + }, + { + "id": "SI_files_Idaho_Idaho", + "file": "SI_files_Idaho_Idaho.bngl" + }, + { + "id": "SI_files_Illinois_Illinois", + "file": "SI_files_Illinois_Illinois.bngl" + }, + { + "id": "SI_files_Indiana_Indiana", + "file": "SI_files_Indiana_Indiana.bngl" + }, + { + "id": "SI_files_Iowa_Iowa", + "file": "SI_files_Iowa_Iowa.bngl" + }, + { + "id": "SI_files_Kansas_Kansas", + "file": "SI_files_Kansas_Kansas.bngl" + }, + { + "id": "SI_files_Kentucky_Kentucky", + "file": "SI_files_Kentucky_Kentucky.bngl" + }, + { + "id": "SI_files_Louisiana_Louisiana", + "file": "SI_files_Louisiana_Louisiana.bngl" + }, + { + "id": "SI_files_Maine_Maine", + "file": "SI_files_Maine_Maine.bngl" + }, + { + "id": "SI_files_Maryland_Maryland", + "file": "SI_files_Maryland_Maryland.bngl" + }, + { + "id": "SI_files_Massachusetts_Massachusetts", + "file": "SI_files_Massachusetts_Massachusetts.bngl" + }, + { + "id": "SI_files_Michigan_Michigan", + "file": "SI_files_Michigan_Michigan.bngl" + }, + { + "id": "SI_files_Minnesota_Minnesota", + "file": "SI_files_Minnesota_Minnesota.bngl" + }, + { + "id": "SI_files_Mississippi_Mississippi", + "file": "SI_files_Mississippi_Mississippi.bngl" + }, + { + "id": "SI_files_Missouri_Missouri", + "file": "SI_files_Missouri_Missouri.bngl" + }, + { + "id": "SI_files_Montana_Montana", + "file": "SI_files_Montana_Montana.bngl" + }, + { + "id": "SI_files_Nebraska_Nebraska", + "file": "SI_files_Nebraska_Nebraska.bngl" + }, + { + "id": "SI_files_Nevada_Nevada", + "file": "SI_files_Nevada_Nevada.bngl" + }, + { + "id": "SI_files_NewHampshire_NewHampshire", + "file": "SI_files_NewHampshire_NewHampshire.bngl" + }, + { + "id": "SI_files_NewJersey_NewJersey", + "file": "SI_files_NewJersey_NewJersey.bngl" + }, + { + "id": "SI_files_NewMexico_NewMexico", + "file": "SI_files_NewMexico_NewMexico.bngl" + }, + { + "id": "SI_files_NewYork_NewYork", + "file": "SI_files_NewYork_NewYork.bngl" + }, + { + "id": "SI_files_NorthCarolina_NorthCarolina", + "file": "SI_files_NorthCarolina_NorthCarolina.bngl" + }, + { + "id": "SI_files_NorthDakota_NorthDakota", + "file": "SI_files_NorthDakota_NorthDakota.bngl" + }, + { + "id": "SI_files_Ohio_Ohio", + "file": "SI_files_Ohio_Ohio.bngl" + }, + { + "id": "SI_files_Oklahoma_Oklahoma", + "file": "SI_files_Oklahoma_Oklahoma.bngl" + }, + { + "id": "SI_files_Oregon_Oregon", + "file": "SI_files_Oregon_Oregon.bngl" + }, + { + "id": "SI_files_Pennsylvania_Pennsylvania", + "file": "SI_files_Pennsylvania_Pennsylvania.bngl" + }, + { + "id": "SI_files_RhodeIsland_RhodeIsland", + "file": "SI_files_RhodeIsland_RhodeIsland.bngl" + }, + { + "id": "SI_files_SouthCarolina_SouthCarolina", + "file": "SI_files_SouthCarolina_SouthCarolina.bngl" + }, + { + "id": "SI_files_SouthDakota_SouthDakota", + "file": "SI_files_SouthDakota_SouthDakota.bngl" + }, + { + "id": "SI_files_Tennessee_Tennessee", + "file": "SI_files_Tennessee_Tennessee.bngl" + }, + { + "id": "SI_files_Texas_Texas", + "file": "SI_files_Texas_Texas.bngl" + }, + { + "id": "SI_files_Utah_Utah", + "file": "SI_files_Utah_Utah.bngl" + }, + { + "id": "SI_files_Vermont_Vermont", + "file": "SI_files_Vermont_Vermont.bngl" + }, + { + "id": "SI_files_Virginia_Virginia", + "file": "SI_files_Virginia_Virginia.bngl" + }, + { + "id": "SI_files_Washington_Washington", + "file": "SI_files_Washington_Washington.bngl" + }, + { + "id": "SI_files_WestVirginia_WestVirginia", + "file": "SI_files_WestVirginia_WestVirginia.bngl" + }, + { + "id": "SI_files_Wisconsin_Wisconsin", + "file": "SI_files_Wisconsin_Wisconsin.bngl" + }, + { + "id": "SI_files_Wyoming_Wyoming", + "file": "SI_files_Wyoming_Wyoming.bngl" + } + ] + }, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Mallela2022_MSAs", + "name": "Mallela 2022 - COVID-19 MSA Models", + "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", + "tags": [ + "covid-19", + "epidemiology", + "parameter-estimation", + "pybionetgen" + ], + "category": "epidemiology", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/Mallela2022_MSAs/Abilene_TX_Abilene_TX.bngl", + "file": "Abilene_TX_Abilene_TX.bngl", + "collectionId": "Mallela2022_MSAs", + "collection": { + "type": "geographic-variants", + "count": 281, + "variant_key": "metropolitan_area", + "variants": [ + { + "id": "Abilene_TX_Abilene_TX", + "file": "Abilene_TX_Abilene_TX.bngl" + }, + { + "id": "Akron_OH_Akron_OH", + "file": "Akron_OH_Akron_OH.bngl" + }, + { + "id": "Albany-Schenectady-Troy_NY_Albany-Schenectady-Troy_NY", + "file": "Albany-Schenectady-Troy_NY_Albany-Schenectady-Troy_NY.bngl" + }, + { + "id": "Albany_GA_Albany_GA", + "file": "Albany_GA_Albany_GA.bngl" + }, + { + "id": "Albuquerque_NM_Albuquerque_NM", + "file": "Albuquerque_NM_Albuquerque_NM.bngl" + }, + { + "id": "Alexandria_LA_Alexandria_LA", + "file": "Alexandria_LA_Alexandria_LA.bngl" + }, + { + "id": "Allentown-Bethlehem-Easton_PA-NJ_Allentown-Bethlehem-Easton_PA-NJ", + "file": "Allentown-Bethlehem-Easton_PA-NJ_Allentown-Bethlehem-Easton_PA-NJ.bngl" + }, + { + "id": "Amarillo_TX_Amarillo_TX", + "file": "Amarillo_TX_Amarillo_TX.bngl" + }, + { + "id": "Anchorage_AK_Anchorage_AK", + "file": "Anchorage_AK_Anchorage_AK.bngl" + }, + { + "id": "Ann_Arbor_MI_Ann_Arbor_MI", + "file": "Ann_Arbor_MI_Ann_Arbor_MI.bngl" + }, + { + "id": "Appleton_WI_Appleton_WI", + "file": "Appleton_WI_Appleton_WI.bngl" + }, + { + "id": "Asheville_NC_Asheville_NC", + "file": "Asheville_NC_Asheville_NC.bngl" + }, + { + "id": "Athens-Clarke_County_GA_Athens-Clarke_County_GA", + "file": "Athens-Clarke_County_GA_Athens-Clarke_County_GA.bngl" + }, + { + "id": "Atlanta-Sandy_Springs-Alpharetta_GA_Atlanta-Sandy_Springs-Alpharetta_GA", + "file": "Atlanta-Sandy_Springs-Alpharetta_GA_Atlanta-Sandy_Springs-Alpharetta_GA.bngl" + }, + { + "id": "Atlantic_City-Hammonton_NJ_Atlantic_City-Hammonton_NJ", + "file": "Atlantic_City-Hammonton_NJ_Atlantic_City-Hammonton_NJ.bngl" + }, + { + "id": "Auburn-Opelika_AL_Auburn-Opelika_AL", + "file": "Auburn-Opelika_AL_Auburn-Opelika_AL.bngl" + }, + { + "id": "Augusta-Richmond_County_GA-SC_Augusta-Richmond_County_GA-SC", + "file": "Augusta-Richmond_County_GA-SC_Augusta-Richmond_County_GA-SC.bngl" + }, + { + "id": "Austin-Round_Rock_TX_Austin-Round_Rock_TX", + "file": "Austin-Round_Rock_TX_Austin-Round_Rock_TX.bngl" + }, + { + "id": "Bakersfield_CA_Bakersfield_CA", + "file": "Bakersfield_CA_Bakersfield_CA.bngl" + }, + { + "id": "Baltimore-Columbia-Towson_MD_Baltimore-Columbia-Towson_MD", + "file": "Baltimore-Columbia-Towson_MD_Baltimore-Columbia-Towson_MD.bngl" + }, + { + "id": "Barnstable_Town_MA_Barnstable_Town_MA", + "file": "Barnstable_Town_MA_Barnstable_Town_MA.bngl" + }, + { + "id": "Baton_Rouge_LA_Baton_Rouge_LA", + "file": "Baton_Rouge_LA_Baton_Rouge_LA.bngl" + }, + { + "id": "Battle_Creek_MI_Battle_Creek_MI", + "file": "Battle_Creek_MI_Battle_Creek_MI.bngl" + }, + { + "id": "Bay_City_MI_Bay_City_MI", + "file": "Bay_City_MI_Bay_City_MI.bngl" + }, + { + "id": "Beaumont-Port_Arthur_TX_Beaumont-Port_Arthur_TX", + "file": "Beaumont-Port_Arthur_TX_Beaumont-Port_Arthur_TX.bngl" + }, + { + "id": "Bellingham_WA_Bellingham_WA", + "file": "Bellingham_WA_Bellingham_WA.bngl" + }, + { + "id": "Binghamton_NY_Binghamton_NY", + "file": "Binghamton_NY_Binghamton_NY.bngl" + }, + { + "id": "Birmingham-Hoover_AL_Birmingham-Hoover_AL", + "file": "Birmingham-Hoover_AL_Birmingham-Hoover_AL.bngl" + }, + { + "id": "Bloomington_IN_Bloomington_IN", + "file": "Bloomington_IN_Bloomington_IN.bngl" + }, + { + "id": "Bloomsburg-Berwick_PA_Bloomsburg-Berwick_PA", + "file": "Bloomsburg-Berwick_PA_Bloomsburg-Berwick_PA.bngl" + }, + { + "id": "Boise_City_ID_Boise_City_ID", + "file": "Boise_City_ID_Boise_City_ID.bngl" + }, + { + "id": "Boston-Cambridge-Newton_MA-NH_Boston-Cambridge-Newton_MA-NH", + "file": "Boston-Cambridge-Newton_MA-NH_Boston-Cambridge-Newton_MA-NH.bngl" + }, + { + "id": "Boulder_CO_Boulder_CO", + "file": "Boulder_CO_Boulder_CO.bngl" + }, + { + "id": "Bowling_Green_KY_Bowling_Green_KY", + "file": "Bowling_Green_KY_Bowling_Green_KY.bngl" + }, + { + "id": "Bridgeport-Stamford-Norwalk_CT_Bridgeport-Stamford-Norwalk_CT", + "file": "Bridgeport-Stamford-Norwalk_CT_Bridgeport-Stamford-Norwalk_CT.bngl" + }, + { + "id": "Brownsville-Harlingen_TX_Brownsville-Harlingen_TX", + "file": "Brownsville-Harlingen_TX_Brownsville-Harlingen_TX.bngl" + }, + { + "id": "Buffalo-Niagara_Falls_NY_Buffalo-Niagara_Falls_NY", + "file": "Buffalo-Niagara_Falls_NY_Buffalo-Niagara_Falls_NY.bngl" + }, + { + "id": "Burlington-South_Burlington_VT_Burlington-South_Burlington_VT", + "file": "Burlington-South_Burlington_VT_Burlington-South_Burlington_VT.bngl" + }, + { + "id": "Burlington_NC_Burlington_NC", + "file": "Burlington_NC_Burlington_NC.bngl" + }, + { + "id": "California-Lexington_Park_MD_California-Lexington_Park_MD", + "file": "California-Lexington_Park_MD_California-Lexington_Park_MD.bngl" + }, + { + "id": "Canton-Massillon_OH_Canton-Massillon_OH", + "file": "Canton-Massillon_OH_Canton-Massillon_OH.bngl" + }, + { + "id": "Cape_Coral-Fort_Myers_FL_Cape_Coral-Fort_Myers_FL", + "file": "Cape_Coral-Fort_Myers_FL_Cape_Coral-Fort_Myers_FL.bngl" + }, + { + "id": "Carbondale-Marion_IL_Carbondale-Marion_IL", + "file": "Carbondale-Marion_IL_Carbondale-Marion_IL.bngl" + }, + { + "id": "Cedar_Rapids_IA_Cedar_Rapids_IA", + "file": "Cedar_Rapids_IA_Cedar_Rapids_IA.bngl" + }, + { + "id": "Chambersburg-Waynesboro_PA_Chambersburg-Waynesboro_PA", + "file": "Chambersburg-Waynesboro_PA_Chambersburg-Waynesboro_PA.bngl" + }, + { + "id": "Champaign-Urbana_IL_Champaign-Urbana_IL", + "file": "Champaign-Urbana_IL_Champaign-Urbana_IL.bngl" + }, + { + "id": "Charleston-North_Charleston_SC_Charleston-North_Charleston_SC", + "file": "Charleston-North_Charleston_SC_Charleston-North_Charleston_SC.bngl" + }, + { + "id": "Charleston_WV_Charleston_WV", + "file": "Charleston_WV_Charleston_WV.bngl" + }, + { + "id": "Charlotte-Concord-Gastonia_NC-SC_Charlotte-Concord-Gastonia_NC-SC", + "file": "Charlotte-Concord-Gastonia_NC-SC_Charlotte-Concord-Gastonia_NC-SC.bngl" + }, + { + "id": "Charlottesville_VA_Charlottesville_VA", + "file": "Charlottesville_VA_Charlottesville_VA.bngl" + }, + { + "id": "Chattanooga_TN-GA_Chattanooga_TN-GA", + "file": "Chattanooga_TN-GA_Chattanooga_TN-GA.bngl" + }, + { + "id": "Chicago-Naperville-Elgin_IL-IN-WI_Chicago-Naperville-Elgin_IL-IN-WI", + "file": "Chicago-Naperville-Elgin_IL-IN-WI_Chicago-Naperville-Elgin_IL-IN-WI.bngl" + }, + { + "id": "Cincinnati_OH-KY-IN_Cincinnati_OH-KY-IN", + "file": "Cincinnati_OH-KY-IN_Cincinnati_OH-KY-IN.bngl" + }, + { + "id": "Clarksville_TN-KY_Clarksville_TN-KY", + "file": "Clarksville_TN-KY_Clarksville_TN-KY.bngl" + }, + { + "id": "Cleveland-Elyria_OH_Cleveland-Elyria_OH", + "file": "Cleveland-Elyria_OH_Cleveland-Elyria_OH.bngl" + }, + { + "id": "College_Station-Bryan_TX_College_Station-Bryan_TX", + "file": "College_Station-Bryan_TX_College_Station-Bryan_TX.bngl" + }, + { + "id": "Colorado_Springs_CO_Colorado_Springs_CO", + "file": "Colorado_Springs_CO_Colorado_Springs_CO.bngl" + }, + { + "id": "Columbia_SC_Columbia_SC", + "file": "Columbia_SC_Columbia_SC.bngl" + }, + { + "id": "Columbus_GA-AL_Columbus_GA-AL", + "file": "Columbus_GA-AL_Columbus_GA-AL.bngl" + }, + { + "id": "Columbus_IN_Columbus_IN", + "file": "Columbus_IN_Columbus_IN.bngl" + }, + { + "id": "Columbus_OH_Columbus_OH", + "file": "Columbus_OH_Columbus_OH.bngl" + }, + { + "id": "Corpus_Christi_TX_Corpus_Christi_TX", + "file": "Corpus_Christi_TX_Corpus_Christi_TX.bngl" + }, + { + "id": "Crestview-Fort_Walton_Beach-Destin_FL_Crestview-Fort_Walton_Beach-Destin_FL", + "file": "Crestview-Fort_Walton_Beach-Destin_FL_Crestview-Fort_Walton_Beach-Destin_FL.bngl" + }, + { + "id": "Cumberland_MD-WV_Cumberland_MD-WV", + "file": "Cumberland_MD-WV_Cumberland_MD-WV.bngl" + }, + { + "id": "Dallas-Fort_Worth-Arlington_TX_Dallas-Fort_Worth-Arlington_TX", + "file": "Dallas-Fort_Worth-Arlington_TX_Dallas-Fort_Worth-Arlington_TX.bngl" + }, + { + "id": "Dalton_GA_Dalton_GA", + "file": "Dalton_GA_Dalton_GA.bngl" + }, + { + "id": "Daphne-Fairhope-Foley_AL_Daphne-Fairhope-Foley_AL", + "file": "Daphne-Fairhope-Foley_AL_Daphne-Fairhope-Foley_AL.bngl" + }, + { + "id": "Davenport-Moline-Rock_Island_IA-IL_Davenport-Moline-Rock_Island_IA-IL", + "file": "Davenport-Moline-Rock_Island_IA-IL_Davenport-Moline-Rock_Island_IA-IL.bngl" + }, + { + "id": "Dayton_OH_Dayton_OH", + "file": "Dayton_OH_Dayton_OH.bngl" + }, + { + "id": "Deltona-Daytona_Beach-Ormond_Beach_FL_Deltona-Daytona_Beach-Ormond_Beach_FL", + "file": "Deltona-Daytona_Beach-Ormond_Beach_FL_Deltona-Daytona_Beach-Ormond_Beach_FL.bngl" + }, + { + "id": "Denver-Aurora-Lakewood_CO_Denver-Aurora-Lakewood_CO", + "file": "Denver-Aurora-Lakewood_CO_Denver-Aurora-Lakewood_CO.bngl" + }, + { + "id": "Des_Moines-West_Des_Moines_IA_Des_Moines-West_Des_Moines_IA", + "file": "Des_Moines-West_Des_Moines_IA_Des_Moines-West_Des_Moines_IA.bngl" + }, + { + "id": "Detroit-Warren-Dearborn_MI_Detroit-Warren-Dearborn_MI", + "file": "Detroit-Warren-Dearborn_MI_Detroit-Warren-Dearborn_MI.bngl" + }, + { + "id": "Detroit_Warren_Dearborn_MI_Detroit_Warren_Dearborn_MI", + "file": "Detroit_Warren_Dearborn_MI_Detroit_Warren_Dearborn_MI.bngl" + }, + { + "id": "Dothan_AL_Dothan_AL", + "file": "Dothan_AL_Dothan_AL.bngl" + }, + { + "id": "Dover_DE_Dover_DE", + "file": "Dover_DE_Dover_DE.bngl" + }, + { + "id": "Dubuque_IA_Dubuque_IA", + "file": "Dubuque_IA_Dubuque_IA.bngl" + }, + { + "id": "Durham-Chapel_Hill_NC_Durham-Chapel_Hill_NC", + "file": "Durham-Chapel_Hill_NC_Durham-Chapel_Hill_NC.bngl" + }, + { + "id": "East_Stroudsburg_PA_East_Stroudsburg_PA", + "file": "East_Stroudsburg_PA_East_Stroudsburg_PA.bngl" + }, + { + "id": "El_Centro_CA_El_Centro_CA", + "file": "El_Centro_CA_El_Centro_CA.bngl" + }, + { + "id": "El_Paso_TX_El_Paso_TX", + "file": "El_Paso_TX_El_Paso_TX.bngl" + }, + { + "id": "Elkhart-Goshen_IN_Elkhart-Goshen_IN", + "file": "Elkhart-Goshen_IN_Elkhart-Goshen_IN.bngl" + }, + { + "id": "Evansville_IN-KY_Evansville_IN-KY", + "file": "Evansville_IN-KY_Evansville_IN-KY.bngl" + }, + { + "id": "Fargo_ND-MN_Fargo_ND-MN", + "file": "Fargo_ND-MN_Fargo_ND-MN.bngl" + }, + { + "id": "Farmington_NM_Farmington_NM", + "file": "Farmington_NM_Farmington_NM.bngl" + }, + { + "id": "Fayetteville-Springdale-Rogers_AR_Fayetteville-Springdale-Rogers_AR", + "file": "Fayetteville-Springdale-Rogers_AR_Fayetteville-Springdale-Rogers_AR.bngl" + }, + { + "id": "Fayetteville_NC_Fayetteville_NC", + "file": "Fayetteville_NC_Fayetteville_NC.bngl" + }, + { + "id": "Flagstaff_AZ_Flagstaff_AZ", + "file": "Flagstaff_AZ_Flagstaff_AZ.bngl" + }, + { + "id": "Flint_MI_Flint_MI", + "file": "Flint_MI_Flint_MI.bngl" + }, + { + "id": "Florence-Muscle_Shoals_AL_Florence-Muscle_Shoals_AL", + "file": "Florence-Muscle_Shoals_AL_Florence-Muscle_Shoals_AL.bngl" + }, + { + "id": "Florence_SC_Florence_SC", + "file": "Florence_SC_Florence_SC.bngl" + }, + { + "id": "Fort_Collins_CO_Fort_Collins_CO", + "file": "Fort_Collins_CO_Fort_Collins_CO.bngl" + }, + { + "id": "Fort_Wayne_IN_Fort_Wayne_IN", + "file": "Fort_Wayne_IN_Fort_Wayne_IN.bngl" + }, + { + "id": "Fresno_CA_Fresno_CA", + "file": "Fresno_CA_Fresno_CA.bngl" + }, + { + "id": "Gadsden_AL_Gadsden_AL", + "file": "Gadsden_AL_Gadsden_AL.bngl" + }, + { + "id": "Gainesville_FL_Gainesville_FL", + "file": "Gainesville_FL_Gainesville_FL.bngl" + }, + { + "id": "Gainesville_GA_Gainesville_GA", + "file": "Gainesville_GA_Gainesville_GA.bngl" + }, + { + "id": "Glens_Falls_NY_Glens_Falls_NY", + "file": "Glens_Falls_NY_Glens_Falls_NY.bngl" + }, + { + "id": "Goldsboro_NC_Goldsboro_NC", + "file": "Goldsboro_NC_Goldsboro_NC.bngl" + }, + { + "id": "Grand_Forks_ND-MN_Grand_Forks_ND-MN", + "file": "Grand_Forks_ND-MN_Grand_Forks_ND-MN.bngl" + }, + { + "id": "Grand_Island_NE_Grand_Island_NE", + "file": "Grand_Island_NE_Grand_Island_NE.bngl" + }, + { + "id": "Grand_Rapids-Kentwood_MI_Grand_Rapids-Kentwood_MI", + "file": "Grand_Rapids-Kentwood_MI_Grand_Rapids-Kentwood_MI.bngl" + }, + { + "id": "Greeley_CO_Greeley_CO", + "file": "Greeley_CO_Greeley_CO.bngl" + }, + { + "id": "Green_Bay_WI_Green_Bay_WI", + "file": "Green_Bay_WI_Green_Bay_WI.bngl" + }, + { + "id": "Greensboro-High_Point_NC_Greensboro-High_Point_NC", + "file": "Greensboro-High_Point_NC_Greensboro-High_Point_NC.bngl" + }, + { + "id": "Greenville-Anderson_SC_Greenville-Anderson_SC", + "file": "Greenville-Anderson_SC_Greenville-Anderson_SC.bngl" + }, + { + "id": "Greenville_NC_Greenville_NC", + "file": "Greenville_NC_Greenville_NC.bngl" + }, + { + "id": "Gulfport-Biloxi_MS_Gulfport-Biloxi_MS", + "file": "Gulfport-Biloxi_MS_Gulfport-Biloxi_MS.bngl" + }, + { + "id": "Hagerstown-Martinsburg_MD-WV_Hagerstown-Martinsburg_MD-WV", + "file": "Hagerstown-Martinsburg_MD-WV_Hagerstown-Martinsburg_MD-WV.bngl" + }, + { + "id": "Hammond_LA_Hammond_LA", + "file": "Hammond_LA_Hammond_LA.bngl" + }, + { + "id": "Hanford-Corcoran_CA_Hanford-Corcoran_CA", + "file": "Hanford-Corcoran_CA_Hanford-Corcoran_CA.bngl" + }, + { + "id": "Harrisburg-Carlisle_PA_Harrisburg-Carlisle_PA", + "file": "Harrisburg-Carlisle_PA_Harrisburg-Carlisle_PA.bngl" + }, + { + "id": "Harrisonburg_VA_Harrisonburg_VA", + "file": "Harrisonburg_VA_Harrisonburg_VA.bngl" + }, + { + "id": "Hartford-East_Hartford-Middletown_CT_Hartford-East_Hartford-Middletown_CT", + "file": "Hartford-East_Hartford-Middletown_CT_Hartford-East_Hartford-Middletown_CT.bngl" + }, + { + "id": "Hattiesburg_MS_Hattiesburg_MS", + "file": "Hattiesburg_MS_Hattiesburg_MS.bngl" + }, + { + "id": "Hickory-Lenoir-Morganton_NC_Hickory-Lenoir-Morganton_NC", + "file": "Hickory-Lenoir-Morganton_NC_Hickory-Lenoir-Morganton_NC.bngl" + }, + { + "id": "Hilton_Head_Island-Bluffton-Beaufort_SC_Hilton_Head_Island-Bluffton-Beaufort_SC", + "file": "Hilton_Head_Island-Bluffton-Beaufort_SC_Hilton_Head_Island-Bluffton-Beaufort_SC.bngl" + }, + { + "id": "Houma-Thibodaux_LA_Houma-Thibodaux_LA", + "file": "Houma-Thibodaux_LA_Houma-Thibodaux_LA.bngl" + }, + { + "id": "Houston-The_Woodlands-Sugar_Land_TX_Houston-The_Woodlands-Sugar_Land_TX", + "file": "Houston-The_Woodlands-Sugar_Land_TX_Houston-The_Woodlands-Sugar_Land_TX.bngl" + }, + { + "id": "Huntington-Ashland_WV-KY-OH_Huntington-Ashland_WV-KY-OH", + "file": "Huntington-Ashland_WV-KY-OH_Huntington-Ashland_WV-KY-OH.bngl" + }, + { + "id": "Huntsville_AL_Huntsville_AL", + "file": "Huntsville_AL_Huntsville_AL.bngl" + }, + { + "id": "Indianapolis-Carmel-Anderson_IN_Indianapolis-Carmel-Anderson_IN", + "file": "Indianapolis-Carmel-Anderson_IN_Indianapolis-Carmel-Anderson_IN.bngl" + }, + { + "id": "Iowa_City_IA_Iowa_City_IA", + "file": "Iowa_City_IA_Iowa_City_IA.bngl" + }, + { + "id": "Jackson_MI_Jackson_MI", + "file": "Jackson_MI_Jackson_MI.bngl" + }, + { + "id": "Jackson_MS_Jackson_MS", + "file": "Jackson_MS_Jackson_MS.bngl" + }, + { + "id": "Jacksonville_FL_Jacksonville_FL", + "file": "Jacksonville_FL_Jacksonville_FL.bngl" + }, + { + "id": "Janesville-Beloit_WI_Janesville-Beloit_WI", + "file": "Janesville-Beloit_WI_Janesville-Beloit_WI.bngl" + }, + { + "id": "Kalamazoo-Portage_MI_Kalamazoo-Portage_MI", + "file": "Kalamazoo-Portage_MI_Kalamazoo-Portage_MI.bngl" + }, + { + "id": "Kankakee_IL_Kankakee_IL", + "file": "Kankakee_IL_Kankakee_IL.bngl" + }, + { + "id": "Kansas_City_MO-KS_Kansas_City_MO-KS", + "file": "Kansas_City_MO-KS_Kansas_City_MO-KS.bngl" + }, + { + "id": "Kennewick-Richland_WA_Kennewick-Richland_WA", + "file": "Kennewick-Richland_WA_Kennewick-Richland_WA.bngl" + }, + { + "id": "Killeen-Temple_TX_Killeen-Temple_TX", + "file": "Killeen-Temple_TX_Killeen-Temple_TX.bngl" + }, + { + "id": "Kingston_NY_Kingston_NY", + "file": "Kingston_NY_Kingston_NY.bngl" + }, + { + "id": "Knoxville_TN_Knoxville_TN", + "file": "Knoxville_TN_Knoxville_TN.bngl" + }, + { + "id": "Kokomo_IN_Kokomo_IN", + "file": "Kokomo_IN_Kokomo_IN.bngl" + }, + { + "id": "Lafayette-West_Lafayette_IN_Lafayette-West_Lafayette_IN", + "file": "Lafayette-West_Lafayette_IN_Lafayette-West_Lafayette_IN.bngl" + }, + { + "id": "Lafayette_LA_Lafayette_LA", + "file": "Lafayette_LA_Lafayette_LA.bngl" + }, + { + "id": "Lake_Charles_LA_Lake_Charles_LA", + "file": "Lake_Charles_LA_Lake_Charles_LA.bngl" + }, + { + "id": "Lake_Havasu_City-Kingman_AZ_Lake_Havasu_City-Kingman_AZ", + "file": "Lake_Havasu_City-Kingman_AZ_Lake_Havasu_City-Kingman_AZ.bngl" + }, + { + "id": "Lakeland-Winter_Haven_FL_Lakeland-Winter_Haven_FL", + "file": "Lakeland-Winter_Haven_FL_Lakeland-Winter_Haven_FL.bngl" + }, + { + "id": "Lancaster_PA_Lancaster_PA", + "file": "Lancaster_PA_Lancaster_PA.bngl" + }, + { + "id": "Lansing-East_Lansing_MI_Lansing-East_Lansing_MI", + "file": "Lansing-East_Lansing_MI_Lansing-East_Lansing_MI.bngl" + }, + { + "id": "Laredo_TX_Laredo_TX", + "file": "Laredo_TX_Laredo_TX.bngl" + }, + { + "id": "Las_Cruces_NM_Las_Cruces_NM", + "file": "Las_Cruces_NM_Las_Cruces_NM.bngl" + }, + { + "id": "Las_Vegas-Henderson-Paradise_NV_Las_Vegas-Henderson-Paradise_NV", + "file": "Las_Vegas-Henderson-Paradise_NV_Las_Vegas-Henderson-Paradise_NV.bngl" + }, + { + "id": "Lawton_OK_Lawton_OK", + "file": "Lawton_OK_Lawton_OK.bngl" + }, + { + "id": "Lebanon_PA_Lebanon_PA", + "file": "Lebanon_PA_Lebanon_PA.bngl" + }, + { + "id": "Lexington-Fayette_KY_Lexington-Fayette_KY", + "file": "Lexington-Fayette_KY_Lexington-Fayette_KY.bngl" + }, + { + "id": "Lincoln_NE_Lincoln_NE", + "file": "Lincoln_NE_Lincoln_NE.bngl" + }, + { + "id": "Little_Rock-North_Little_Rock-Conway_AR_Little_Rock-North_Little_Rock-Conway_AR", + "file": "Little_Rock-North_Little_Rock-Conway_AR_Little_Rock-North_Little_Rock-Conway_AR.bngl" + }, + { + "id": "Longview_TX_Longview_TX", + "file": "Longview_TX_Longview_TX.bngl" + }, + { + "id": "Los_Angeles-Long_Beach-Anaheim_CA_Los_Angeles-Long_Beach-Anaheim_CA", + "file": "Los_Angeles-Long_Beach-Anaheim_CA_Los_Angeles-Long_Beach-Anaheim_CA.bngl" + }, + { + "id": "Louisville_Jefferson_County_KY-IN_Louisville_Jefferson_County_KY-IN", + "file": "Louisville_Jefferson_County_KY-IN_Louisville_Jefferson_County_KY-IN.bngl" + }, + { + "id": "Lubbock_TX_Lubbock_TX", + "file": "Lubbock_TX_Lubbock_TX.bngl" + }, + { + "id": "Macon-Bibb_County_GA_Macon-Bibb_County_GA", + "file": "Macon-Bibb_County_GA_Macon-Bibb_County_GA.bngl" + }, + { + "id": "Madison_WI_Madison_WI", + "file": "Madison_WI_Madison_WI.bngl" + }, + { + "id": "Manchester-Nashua_NH_Manchester-Nashua_NH", + "file": "Manchester-Nashua_NH_Manchester-Nashua_NH.bngl" + }, + { + "id": "McAllen-Edinburg-Mission_TX_McAllen-Edinburg-Mission_TX", + "file": "McAllen-Edinburg-Mission_TX_McAllen-Edinburg-Mission_TX.bngl" + }, + { + "id": "Memphis_TN-MS-AR_Memphis_TN-MS-AR", + "file": "Memphis_TN-MS-AR_Memphis_TN-MS-AR.bngl" + }, + { + "id": "Merced_CA_Merced_CA", + "file": "Merced_CA_Merced_CA.bngl" + }, + { + "id": "Miami-Fort_Lauderdale-West_Palm_Beach_FL_Miami-Fort_Lauderdale-West_Palm_Beach_FL", + "file": "Miami-Fort_Lauderdale-West_Palm_Beach_FL_Miami-Fort_Lauderdale-West_Palm_Beach_FL.bngl" + }, + { + "id": "Michigan_City-La_Porte_IN_Michigan_City-La_Porte_IN", + "file": "Michigan_City-La_Porte_IN_Michigan_City-La_Porte_IN.bngl" + }, + { + "id": "Milwaukee-Waukesha_WI_Milwaukee-Waukesha_WI", + "file": "Milwaukee-Waukesha_WI_Milwaukee-Waukesha_WI.bngl" + }, + { + "id": "Minneapolis-St._Paul-Bloomington_MN-WI_Minneapolis-St._Paul-Bloomington_MN-WI", + "file": "Minneapolis-St._Paul-Bloomington_MN-WI_Minneapolis-St._Paul-Bloomington_MN-WI.bngl" + }, + { + "id": "Mobile_AL_Mobile_AL", + "file": "Mobile_AL_Mobile_AL.bngl" + }, + { + "id": "Modesto_CA_Modesto_CA", + "file": "Modesto_CA_Modesto_CA.bngl" + }, + { + "id": "Monroe_LA_Monroe_LA", + "file": "Monroe_LA_Monroe_LA.bngl" + }, + { + "id": "Monroe_MI_Monroe_MI", + "file": "Monroe_MI_Monroe_MI.bngl" + }, + { + "id": "Montgomery_AL_Montgomery_AL", + "file": "Montgomery_AL_Montgomery_AL.bngl" + }, + { + "id": "Mount_Vernon-Anacortes_WA_Mount_Vernon-Anacortes_WA", + "file": "Mount_Vernon-Anacortes_WA_Mount_Vernon-Anacortes_WA.bngl" + }, + { + "id": "Muncie_IN_Muncie_IN", + "file": "Muncie_IN_Muncie_IN.bngl" + }, + { + "id": "Muskegon_MI_Muskegon_MI", + "file": "Muskegon_MI_Muskegon_MI.bngl" + }, + { + "id": "Naples-Marco_Island_FL_Naples-Marco_Island_FL", + "file": "Naples-Marco_Island_FL_Naples-Marco_Island_FL.bngl" + }, + { + "id": "Nashville-Davidson-Murfreesboro-Franklin_TN_Nashville-Davidson-Murfreesboro-Franklin_TN", + "file": "Nashville-Davidson-Murfreesboro-Franklin_TN_Nashville-Davidson-Murfreesboro-Franklin_TN.bngl" + }, + { + "id": "New_Haven-Milford_CT_New_Haven-Milford_CT", + "file": "New_Haven-Milford_CT_New_Haven-Milford_CT.bngl" + }, + { + "id": "New_Orleans-Metairie_LA_New_Orleans-Metairie_LA", + "file": "New_Orleans-Metairie_LA_New_Orleans-Metairie_LA.bngl" + }, + { + "id": "New_York-Newark-Jersey_City_NY-NJ-PA_New_York-Newark-Jersey_City_NY-NJ-PA", + "file": "New_York-Newark-Jersey_City_NY-NJ-PA_New_York-Newark-Jersey_City_NY-NJ-PA.bngl" + }, + { + "id": "Niles_MI_Niles_MI", + "file": "Niles_MI_Niles_MI.bngl" + }, + { + "id": "North_Port-Sarasota-Bradenton_FL_North_Port-Sarasota-Bradenton_FL", + "file": "North_Port-Sarasota-Bradenton_FL_North_Port-Sarasota-Bradenton_FL.bngl" + }, + { + "id": "Norwich-New_London_CT_Norwich-New_London_CT", + "file": "Norwich-New_London_CT_Norwich-New_London_CT.bngl" + }, + { + "id": "Ocala_FL_Ocala_FL", + "file": "Ocala_FL_Ocala_FL.bngl" + }, + { + "id": "Ocean_City_NJ_Ocean_City_NJ", + "file": "Ocean_City_NJ_Ocean_City_NJ.bngl" + }, + { + "id": "Ogden-Clearfield_UT_Ogden-Clearfield_UT", + "file": "Ogden-Clearfield_UT_Ogden-Clearfield_UT.bngl" + }, + { + "id": "Oklahoma_City_OK_Oklahoma_City_OK", + "file": "Oklahoma_City_OK_Oklahoma_City_OK.bngl" + }, + { + "id": "Omaha-Council_Bluffs_NE-IA_Omaha-Council_Bluffs_NE-IA", + "file": "Omaha-Council_Bluffs_NE-IA_Omaha-Council_Bluffs_NE-IA.bngl" + }, + { + "id": "Orlando-Kissimmee-Sanford_FL_Orlando-Kissimmee-Sanford_FL", + "file": "Orlando-Kissimmee-Sanford_FL_Orlando-Kissimmee-Sanford_FL.bngl" + }, + { + "id": "Owensboro_KY_Owensboro_KY", + "file": "Owensboro_KY_Owensboro_KY.bngl" + }, + { + "id": "Oxnard-Thousand_Oaks-Ventura_CA_Oxnard-Thousand_Oaks-Ventura_CA", + "file": "Oxnard-Thousand_Oaks-Ventura_CA_Oxnard-Thousand_Oaks-Ventura_CA.bngl" + }, + { + "id": "Palm_Bay-Melbourne-Titusville_FL_Palm_Bay-Melbourne-Titusville_FL", + "file": "Palm_Bay-Melbourne-Titusville_FL_Palm_Bay-Melbourne-Titusville_FL.bngl" + }, + { + "id": "Pensacola-Ferry_Pass-Brent_FL_Pensacola-Ferry_Pass-Brent_FL", + "file": "Pensacola-Ferry_Pass-Brent_FL_Pensacola-Ferry_Pass-Brent_FL.bngl" + }, + { + "id": "Peoria_IL_Peoria_IL", + "file": "Peoria_IL_Peoria_IL.bngl" + }, + { + "id": "Philadelphia-Camden-Wilmington_PA-NJ-DE-MD_Philadelphia-Camden-Wilmington_PA-NJ-DE-MD", + "file": "Philadelphia-Camden-Wilmington_PA-NJ-DE-MD_Philadelphia-Camden-Wilmington_PA-NJ-DE-MD.bngl" + }, + { + "id": "Phoenix-Mesa-Chandler_AZ_Phoenix-Mesa-Chandler_AZ", + "file": "Phoenix-Mesa-Chandler_AZ_Phoenix-Mesa-Chandler_AZ.bngl" + }, + { + "id": "Pine_Bluff_AR_Pine_Bluff_AR", + "file": "Pine_Bluff_AR_Pine_Bluff_AR.bngl" + }, + { + "id": "Pittsburgh_PA_Pittsburgh_PA", + "file": "Pittsburgh_PA_Pittsburgh_PA.bngl" + }, + { + "id": "Pittsfield_MA_Pittsfield_MA", + "file": "Pittsfield_MA_Pittsfield_MA.bngl" + }, + { + "id": "Port_St._Lucie_FL_Port_St._Lucie_FL", + "file": "Port_St._Lucie_FL_Port_St._Lucie_FL.bngl" + }, + { + "id": "Portland-South_Portland_ME_Portland-South_Portland_ME", + "file": "Portland-South_Portland_ME_Portland-South_Portland_ME.bngl" + }, + { + "id": "Portland-Vancouver-Hillsboro_OR-WA_Portland-Vancouver-Hillsboro_OR-WA", + "file": "Portland-Vancouver-Hillsboro_OR-WA_Portland-Vancouver-Hillsboro_OR-WA.bngl" + }, + { + "id": "Poughkeepsie-Newburgh-Middletown_NY_Poughkeepsie-Newburgh-Middletown_NY", + "file": "Poughkeepsie-Newburgh-Middletown_NY_Poughkeepsie-Newburgh-Middletown_NY.bngl" + }, + { + "id": "Prescott_Valley-Prescott_AZ_Prescott_Valley-Prescott_AZ", + "file": "Prescott_Valley-Prescott_AZ_Prescott_Valley-Prescott_AZ.bngl" + }, + { + "id": "Providence-Warwick_RI-MA_Providence-Warwick_RI-MA", + "file": "Providence-Warwick_RI-MA_Providence-Warwick_RI-MA.bngl" + }, + { + "id": "Provo-Orem_UT_Provo-Orem_UT", + "file": "Provo-Orem_UT_Provo-Orem_UT.bngl" + }, + { + "id": "Pueblo_CO_Pueblo_CO", + "file": "Pueblo_CO_Pueblo_CO.bngl" + }, + { + "id": "Punta_Gorda_FL_Punta_Gorda_FL", + "file": "Punta_Gorda_FL_Punta_Gorda_FL.bngl" + }, + { + "id": "Racine_WI_Racine_WI", + "file": "Racine_WI_Racine_WI.bngl" + }, + { + "id": "Raleigh-Cary_NC_Raleigh-Cary_NC", + "file": "Raleigh-Cary_NC_Raleigh-Cary_NC.bngl" + }, + { + "id": "Reading_PA_Reading_PA", + "file": "Reading_PA_Reading_PA.bngl" + }, + { + "id": "Reno_NV_Reno_NV", + "file": "Reno_NV_Reno_NV.bngl" + }, + { + "id": "Richmond_VA_Richmond_VA", + "file": "Richmond_VA_Richmond_VA.bngl" + }, + { + "id": "Riverside-San_Bernardino-Ontario_CA_Riverside-San_Bernardino-Ontario_CA", + "file": "Riverside-San_Bernardino-Ontario_CA_Riverside-San_Bernardino-Ontario_CA.bngl" + }, + { + "id": "Roanoke_VA_Roanoke_VA", + "file": "Roanoke_VA_Roanoke_VA.bngl" + }, + { + "id": "Rochester_MN_Rochester_MN", + "file": "Rochester_MN_Rochester_MN.bngl" + }, + { + "id": "Rochester_NY_Rochester_NY", + "file": "Rochester_NY_Rochester_NY.bngl" + }, + { + "id": "Rockford_IL_Rockford_IL", + "file": "Rockford_IL_Rockford_IL.bngl" + }, + { + "id": "Rocky_Mount_NC_Rocky_Mount_NC", + "file": "Rocky_Mount_NC_Rocky_Mount_NC.bngl" + }, + { + "id": "Rome_GA_Rome_GA", + "file": "Rome_GA_Rome_GA.bngl" + }, + { + "id": "Sacramento-Roseville-Folsom_CA_Sacramento-Roseville-Folsom_CA", + "file": "Sacramento-Roseville-Folsom_CA_Sacramento-Roseville-Folsom_CA.bngl" + }, + { + "id": "Saginaw_MI_Saginaw_MI", + "file": "Saginaw_MI_Saginaw_MI.bngl" + }, + { + "id": "Salem_OR_Salem_OR", + "file": "Salem_OR_Salem_OR.bngl" + }, + { + "id": "Salinas_CA_Salinas_CA", + "file": "Salinas_CA_Salinas_CA.bngl" + }, + { + "id": "Salisbury_MD-DE_Salisbury_MD-DE", + "file": "Salisbury_MD-DE_Salisbury_MD-DE.bngl" + }, + { + "id": "Salt_Lake_City_UT_Salt_Lake_City_UT", + "file": "Salt_Lake_City_UT_Salt_Lake_City_UT.bngl" + }, + { + "id": "San_Antonio-New_Braunfels_TX_San_Antonio-New_Braunfels_TX", + "file": "San_Antonio-New_Braunfels_TX_San_Antonio-New_Braunfels_TX.bngl" + }, + { + "id": "San_Diego-Chula_Vista-Carlsbad_CA_San_Diego-Chula_Vista-Carlsbad_CA", + "file": "San_Diego-Chula_Vista-Carlsbad_CA_San_Diego-Chula_Vista-Carlsbad_CA.bngl" + }, + { + "id": "San_Francisco-Oakland-Berkeley_CA_San_Francisco-Oakland-Berkeley_CA", + "file": "San_Francisco-Oakland-Berkeley_CA_San_Francisco-Oakland-Berkeley_CA.bngl" + }, + { + "id": "San_Jose-Sunnyvale-Santa_Clara_CA_San_Jose-Sunnyvale-Santa_Clara_CA", + "file": "San_Jose-Sunnyvale-Santa_Clara_CA_San_Jose-Sunnyvale-Santa_Clara_CA.bngl" + }, + { + "id": "San_Luis_Obispo-Paso_Robles_CA_San_Luis_Obispo-Paso_Robles_CA", + "file": "San_Luis_Obispo-Paso_Robles_CA_San_Luis_Obispo-Paso_Robles_CA.bngl" + }, + { + "id": "Santa_Maria-Santa_Barbara_CA_Santa_Maria-Santa_Barbara_CA", + "file": "Santa_Maria-Santa_Barbara_CA_Santa_Maria-Santa_Barbara_CA.bngl" + }, + { + "id": "Santa_Rosa-Petaluma_CA_Santa_Rosa-Petaluma_CA", + "file": "Santa_Rosa-Petaluma_CA_Santa_Rosa-Petaluma_CA.bngl" + }, + { + "id": "Savannah_GA_Savannah_GA", + "file": "Savannah_GA_Savannah_GA.bngl" + }, + { + "id": "Scranton-Wilkes-Barre_PA_Scranton-Wilkes-Barre_PA", + "file": "Scranton-Wilkes-Barre_PA_Scranton-Wilkes-Barre_PA.bngl" + }, + { + "id": "Scranton_Wilkes-Barre_PA_Scranton_Wilkes-Barre_PA", + "file": "Scranton_Wilkes-Barre_PA_Scranton_Wilkes-Barre_PA.bngl" + }, + { + "id": "Seattle-Tacoma-Bellevue_WA_Seattle-Tacoma-Bellevue_WA", + "file": "Seattle-Tacoma-Bellevue_WA_Seattle-Tacoma-Bellevue_WA.bngl" + }, + { + "id": "Shreveport-Bossier_City_LA_Shreveport-Bossier_City_LA", + "file": "Shreveport-Bossier_City_LA_Shreveport-Bossier_City_LA.bngl" + }, + { + "id": "Sioux_City_IA-NE-SD_Sioux_City_IA-NE-SD", + "file": "Sioux_City_IA-NE-SD_Sioux_City_IA-NE-SD.bngl" + }, + { + "id": "Sioux_Falls_SD_Sioux_Falls_SD", + "file": "Sioux_Falls_SD_Sioux_Falls_SD.bngl" + }, + { + "id": "South_Bend-Mishawaka_IN-MI_South_Bend-Mishawaka_IN-MI", + "file": "South_Bend-Mishawaka_IN-MI_South_Bend-Mishawaka_IN-MI.bngl" + }, + { + "id": "Spartanburg_SC_Spartanburg_SC", + "file": "Spartanburg_SC_Spartanburg_SC.bngl" + }, + { + "id": "Spokane-Spokane_Valley_WA_Spokane-Spokane_Valley_WA", + "file": "Spokane-Spokane_Valley_WA_Spokane-Spokane_Valley_WA.bngl" + }, + { + "id": "Springfield_IL_Springfield_IL", + "file": "Springfield_IL_Springfield_IL.bngl" + }, + { + "id": "Springfield_MA_Springfield_MA", + "file": "Springfield_MA_Springfield_MA.bngl" + }, + { + "id": "St._Cloud_MN_St._Cloud_MN", + "file": "St._Cloud_MN_St._Cloud_MN.bngl" + }, + { + "id": "St._George_UT_St._George_UT", + "file": "St._George_UT_St._George_UT.bngl" + }, + { + "id": "St._Joseph_MO-KS_St._Joseph_MO-KS", + "file": "St._Joseph_MO-KS_St._Joseph_MO-KS.bngl" + }, + { + "id": "St._Louis_MO-IL_St._Louis_MO-IL", + "file": "St._Louis_MO-IL_St._Louis_MO-IL.bngl" + }, + { + "id": "Stockton_CA_Stockton_CA", + "file": "Stockton_CA_Stockton_CA.bngl" + }, + { + "id": "Sumter_SC_Sumter_SC", + "file": "Sumter_SC_Sumter_SC.bngl" + }, + { + "id": "Syracuse_NY_Syracuse_NY", + "file": "Syracuse_NY_Syracuse_NY.bngl" + }, + { + "id": "Tallahassee_FL_Tallahassee_FL", + "file": "Tallahassee_FL_Tallahassee_FL.bngl" + }, + { + "id": "Tampa-St._Petersburg-Clearwater_FL_Tampa-St._Petersburg-Clearwater_FL", + "file": "Tampa-St._Petersburg-Clearwater_FL_Tampa-St._Petersburg-Clearwater_FL.bngl" + }, + { + "id": "Texarkana_TX-AR_Texarkana_TX-AR", + "file": "Texarkana_TX-AR_Texarkana_TX-AR.bngl" + }, + { + "id": "The_Villages_FL_The_Villages_FL", + "file": "The_Villages_FL_The_Villages_FL.bngl" + }, + { + "id": "Toledo_OH_Toledo_OH", + "file": "Toledo_OH_Toledo_OH.bngl" + }, + { + "id": "Topeka_KS_Topeka_KS", + "file": "Topeka_KS_Topeka_KS.bngl" + }, + { + "id": "Trenton-Princeton_NJ_Trenton-Princeton_NJ", + "file": "Trenton-Princeton_NJ_Trenton-Princeton_NJ.bngl" + }, + { + "id": "Tucson_AZ_Tucson_AZ", + "file": "Tucson_AZ_Tucson_AZ.bngl" + }, + { + "id": "Tulsa_OK_Tulsa_OK", + "file": "Tulsa_OK_Tulsa_OK.bngl" + }, + { + "id": "Tuscaloosa_AL_Tuscaloosa_AL", + "file": "Tuscaloosa_AL_Tuscaloosa_AL.bngl" + }, + { + "id": "Twin_Falls_ID_Twin_Falls_ID", + "file": "Twin_Falls_ID_Twin_Falls_ID.bngl" + }, + { + "id": "Urban_Honolulu_HI_Urban_Honolulu_HI", + "file": "Urban_Honolulu_HI_Urban_Honolulu_HI.bngl" + }, + { + "id": "Utica-Rome_NY_Utica-Rome_NY", + "file": "Utica-Rome_NY_Utica-Rome_NY.bngl" + }, + { + "id": "Valdosta_GA_Valdosta_GA", + "file": "Valdosta_GA_Valdosta_GA.bngl" + }, + { + "id": "Vallejo_CA_Vallejo_CA", + "file": "Vallejo_CA_Vallejo_CA.bngl" + }, + { + "id": "Victoria_TX_Victoria_TX", + "file": "Victoria_TX_Victoria_TX.bngl" + }, + { + "id": "Vineland-Bridgeton_NJ_Vineland-Bridgeton_NJ", + "file": "Vineland-Bridgeton_NJ_Vineland-Bridgeton_NJ.bngl" + }, + { + "id": "Virginia_Beach-Norfolk-Newport_News_VA-NC_Virginia_Beach-Norfolk-Newport_News_VA-NC", + "file": "Virginia_Beach-Norfolk-Newport_News_VA-NC_Virginia_Beach-Norfolk-Newport_News_VA-NC.bngl" + }, + { + "id": "Visalia_CA_Visalia_CA", + "file": "Visalia_CA_Visalia_CA.bngl" + }, + { + "id": "Warner_Robins_GA_Warner_Robins_GA", + "file": "Warner_Robins_GA_Warner_Robins_GA.bngl" + }, + { + "id": "Washington-Arlington-Alexandria_DC-VA-MD-WV_Washington-Arlington-Alexandria_DC-VA-MD-WV", + "file": "Washington-Arlington-Alexandria_DC-VA-MD-WV_Washington-Arlington-Alexandria_DC-VA-MD-WV.bngl" + }, + { + "id": "Waterloo-Cedar_Falls_IA_Waterloo-Cedar_Falls_IA", + "file": "Waterloo-Cedar_Falls_IA_Waterloo-Cedar_Falls_IA.bngl" + }, + { + "id": "Wenatchee_WA_Wenatchee_WA", + "file": "Wenatchee_WA_Wenatchee_WA.bngl" + }, + { + "id": "Wheeling_WV-OH_Wheeling_WV-OH", + "file": "Wheeling_WV-OH_Wheeling_WV-OH.bngl" + }, + { + "id": "Wichita_KS_Wichita_KS", + "file": "Wichita_KS_Wichita_KS.bngl" + }, + { + "id": "Winchester_VA-WV_Winchester_VA-WV", + "file": "Winchester_VA-WV_Winchester_VA-WV.bngl" + }, + { + "id": "Winston-Salem_NC_Winston-Salem_NC", + "file": "Winston-Salem_NC_Winston-Salem_NC.bngl" + }, + { + "id": "Worcester_MA-CT_Worcester_MA-CT", + "file": "Worcester_MA-CT_Worcester_MA-CT.bngl" + }, + { + "id": "Yakima_WA_Yakima_WA", + "file": "Yakima_WA_Yakima_WA.bngl" + }, + { + "id": "York-Hanover_PA_York-Hanover_PA", + "file": "York-Hanover_PA_York-Hanover_PA.bngl" + }, + { + "id": "Youngstown-Warren-Boardman_OH-PA_Youngstown-Warren-Boardman_OH-PA", + "file": "Youngstown-Warren-Boardman_OH-PA_Youngstown-Warren-Boardman_OH-PA.bngl" + }, + { + "id": "Yuma_AZ_Yuma_AZ", + "file": "Yuma_AZ_Yuma_AZ.bngl" + } + ] + }, + "featured": false, + "difficulty": "advanced" }, { "id": "mapk-dimers", "name": "MAPK Dimers", "description": "MAPK dimerization", - "path": "Published/mapkdimers/mapk-dimers.bngl", - "file": "mapk-dimers.bngl", "tags": [ "published", "mapk", @@ -7352,17 +10759,29 @@ "fus3" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/mapkdimers/mapk-dimers.bngl", + "file": "mapk-dimers.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "mapk-monomers", "name": "MAPK Monomers", "description": "MAPK cascade", - "path": "Published/mapkmonomers/mapk-monomers.bngl", - "file": "mapk-monomers.bngl", "tags": [ "published", "mapk", @@ -7373,17 +10792,29 @@ "fus3" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/mapkmonomers/mapk-monomers.bngl", + "file": "mapk-monomers.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "mapk-signaling-cascade", "name": "mapk signaling cascade", "description": "Rate Constants", - "path": "Contributed/BNGPlayground_Examples/biology/mapksignalingcascade/mapk-signaling-cascade.bngl", - "file": "mapk-signaling-cascade.bngl", "tags": [ "mapk", "signaling", @@ -7394,52 +10825,59 @@ "mapkk" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/mapksignalingcascade/mapk-signaling-cascade.bngl", + "file": "mapk-signaling-cascade.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Massole_2023", "name": "Massole 2023", "description": "Epo receptor signaling", - "path": "Published/Massole2023/Massole_2023.bngl", - "file": "Massole_2023.bngl", "tags": [ "published", "massole", "2023" ], "category": "signaling", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null - }, - { - "id": "McAllen-Edinburg-Mission_TX_McAllen-Edinburg-Mission_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - McAllen-Edinburg-Mission_TX_McAllen-Edinburg-Mission_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/McAllen-Edinburg-Mission_TX_McAllen-Edinburg-Mission_TX.bngl", - "file": "McAllen-Edinburg-Mission_TX_McAllen-Edinburg-Mission_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/Massole2023/Massole_2023.bngl", + "file": "Massole_2023.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "mCaMKII_Ca_Spike", "name": "Ordyan 2020: mCaMKII Ca Spike", "description": "mCaMKII Ca Spike model", - "path": "Published/Ordyan2020/mCaMKIICaSpike/mCaMKII_Ca_Spike.bngl", - "file": "mCaMKII_Ca_Spike.bngl", "tags": [ "published", "neuroscience", @@ -7453,17 +10891,29 @@ "time_counter" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "path": "Published/Ordyan2020/mCaMKIICaSpike/mCaMKII_Ca_Spike.bngl", + "file": "mCaMKII_Ca_Spike.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "McMillan_2021", "name": "McMillan 2021", "description": "TNF signaling", - "path": "Published/McMillan2021/McMillan_2021.bngl", - "file": "McMillan_2021.bngl", "tags": [ "published", "nfsim", @@ -7477,233 +10927,29 @@ "simulate_ode" ], "category": "signaling", - "bng2_compatible": false, - "origin": "published", - "visible": false, - "collectionId": null - }, - { - "id": "MEK_isoform_aMCMC_MEK1_KO", - "name": "Miller 2025 - MEK Isoform Models - MEK_isoform_aMCMC_MEK1_KO", - "description": "MEK isoform variant models curated for PyBioNetGen.", - "path": "Published/Miller2025_MEK/MEK_isoform_aMCMC_MEK1_KO.bngl", - "file": "MEK_isoform_aMCMC_MEK1_KO.bngl", - "tags": [ - "mek", - "isoforms", - "signaling", - "pybionetgen" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK_isoform_aMCMC_MEK1_N78G", - "name": "Miller 2025 - MEK Isoform Models - MEK_isoform_aMCMC_MEK1_N78G", - "description": "MEK isoform variant models curated for PyBioNetGen.", - "path": "Published/Miller2025_MEK/MEK_isoform_aMCMC_MEK1_N78G.bngl", - "file": "MEK_isoform_aMCMC_MEK1_N78G.bngl", - "tags": [ - "mek", - "isoforms", - "signaling", - "pybionetgen" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK_isoform_aMCMC_MEK1_T292A", - "name": "Miller 2025 - MEK Isoform Models - MEK_isoform_aMCMC_MEK1_T292A", - "description": "MEK isoform variant models curated for PyBioNetGen.", - "path": "Published/Miller2025_MEK/MEK_isoform_aMCMC_MEK1_T292A.bngl", - "file": "MEK_isoform_aMCMC_MEK1_T292A.bngl", - "tags": [ - "mek", - "isoforms", - "signaling", - "pybionetgen" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK_isoform_aMCMC_MEK1_T292D", - "name": "Miller 2025 - MEK Isoform Models - MEK_isoform_aMCMC_MEK1_T292D", - "description": "MEK isoform variant models curated for PyBioNetGen.", - "path": "Published/Miller2025_MEK/MEK_isoform_aMCMC_MEK1_T292D.bngl", - "file": "MEK_isoform_aMCMC_MEK1_T292D.bngl", - "tags": [ - "mek", - "isoforms", - "signaling", - "pybionetgen" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK_isoform_aMCMC_MEK1_WT", - "name": "Miller 2025 - MEK Isoform Models - MEK_isoform_aMCMC_MEK1_WT", - "description": "MEK isoform variant models curated for PyBioNetGen.", - "path": "Published/Miller2025_MEK/MEK_isoform_aMCMC_MEK1_WT.bngl", - "file": "MEK_isoform_aMCMC_MEK1_WT.bngl", - "tags": [ - "mek", - "isoforms", - "signaling", - "pybionetgen" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK_isoform_optimization_DE_MEK1_KO", - "name": "Miller 2025 - MEK Isoform Models - MEK_isoform_optimization_DE_MEK1_KO", - "description": "MEK isoform variant models curated for PyBioNetGen.", - "path": "Published/Miller2025_MEK/MEK_isoform_optimization_DE_MEK1_KO.bngl", - "file": "MEK_isoform_optimization_DE_MEK1_KO.bngl", - "tags": [ - "mek", - "isoforms", - "signaling", - "pybionetgen" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK_isoform_optimization_DE_MEK1_N78G", - "name": "Miller 2025 - MEK Isoform Models - MEK_isoform_optimization_DE_MEK1_N78G", - "description": "MEK isoform variant models curated for PyBioNetGen.", - "path": "Published/Miller2025_MEK/MEK_isoform_optimization_DE_MEK1_N78G.bngl", - "file": "MEK_isoform_optimization_DE_MEK1_N78G.bngl", - "tags": [ - "mek", - "isoforms", - "signaling", - "pybionetgen" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK_isoform_optimization_DE_MEK1_T292A", - "name": "Miller 2025 - MEK Isoform Models - MEK_isoform_optimization_DE_MEK1_T292A", - "description": "MEK isoform variant models curated for PyBioNetGen.", - "path": "Published/Miller2025_MEK/MEK_isoform_optimization_DE_MEK1_T292A.bngl", - "file": "MEK_isoform_optimization_DE_MEK1_T292A.bngl", - "tags": [ - "mek", - "isoforms", - "signaling", - "pybionetgen" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK_isoform_optimization_DE_MEK1_T292D", - "name": "Miller 2025 - MEK Isoform Models - MEK_isoform_optimization_DE_MEK1_T292D", - "description": "MEK isoform variant models curated for PyBioNetGen.", - "path": "Published/Miller2025_MEK/MEK_isoform_optimization_DE_MEK1_T292D.bngl", - "file": "MEK_isoform_optimization_DE_MEK1_T292D.bngl", - "tags": [ - "mek", - "isoforms", - "signaling", - "pybionetgen" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK_isoform_optimization_DE_MEK1_WT", - "name": "Miller 2025 - MEK Isoform Models - MEK_isoform_optimization_DE_MEK1_WT", - "description": "MEK isoform variant models curated for PyBioNetGen.", - "path": "Published/Miller2025_MEK/MEK_isoform_optimization_DE_MEK1_WT.bngl", - "file": "MEK_isoform_optimization_DE_MEK1_WT.bngl", - "tags": [ - "mek", - "isoforms", - "signaling", - "pybionetgen" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "Memphis_TN-MS-AR_Memphis_TN-MS-AR", - "name": "Mallela 2022 - COVID-19 MSA Models - Memphis_TN-MS-AR_Memphis_TN-MS-AR", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Memphis_TN-MS-AR_Memphis_TN-MS-AR.bngl", - "file": "Memphis_TN-MS-AR_Memphis_TN-MS-AR.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Merced_CA_Merced_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Merced_CA_Merced_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Merced_CA_Merced_CA.bngl", - "file": "Merced_CA_Merced_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "immunology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/McMillan2021/McMillan_2021.bngl", + "file": "McMillan_2021.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Mertins_2023", "name": "Mertins 2023", "description": "DNA damage response", - "path": "Published/Mertins2023/Mertins_2023.bngl", - "file": "Mertins_2023.bngl", "tags": [ "published", "mertins", @@ -7718,17 +10964,29 @@ "caspase" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Mertins2023/Mertins_2023.bngl", + "file": "Mertins_2023.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "meta_formal_game_theory", "name": "meta formal game theory", "description": "Model: meta_formal_game_theory.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/metaformalgametheory/meta_formal_game_theory.bngl", - "file": "meta_formal_game_theory.bngl", "tags": [ "meta", "formal", @@ -7741,17 +10999,29 @@ "payoffd" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/meta/metaformalgametheory/meta_formal_game_theory.bngl", + "file": "meta_formal_game_theory.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "meta_formal_molecular_clock", "name": "meta formal molecular clock", "description": "Model: meta_formal_molecular_clock.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/metaformalmolecularclock/meta_formal_molecular_clock.bngl", - "file": "meta_formal_molecular_clock.bngl", "tags": [ "meta", "formal", @@ -7763,17 +11033,29 @@ "slowd" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/meta/metaformalmolecularclock/meta_formal_molecular_clock.bngl", + "file": "meta_formal_molecular_clock.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "meta_formal_petri_net", "name": "meta formal petri net", "description": "Model: meta_formal_petri_net.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/metaformalpetrinet/meta_formal_petri_net.bngl", - "file": "meta_formal_petri_net.bngl", "tags": [ "meta", "formal", @@ -7785,35 +11067,29 @@ "p4" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Miami-Fort_Lauderdale-West_Palm_Beach_FL_Miami-Fort_Lauderdale-West_Palm_Beach_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Miami-Fort_Lauderdale-West_Palm_Beach_FL_Miami-Fort_Lauderdale-West_Palm_Beach_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Miami-Fort_Lauderdale-West_Palm_Beach_FL_Miami-Fort_Lauderdale-West_Palm_Beach_FL.bngl", - "file": "Miami-Fort_Lauderdale-West_Palm_Beach_FL_Miami-Fort_Lauderdale-West_Palm_Beach_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/meta/metaformalpetrinet/meta_formal_petri_net.bngl", + "file": "meta_formal_petri_net.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "michaelis-menten-kinetics", "name": "michaelis menten kinetics", "description": "Kinetic Constants", - "path": "Contributed/BNGPlayground_Examples/biology/michaelismentenkinetics/michaelis-menten-kinetics.bngl", - "file": "michaelis-menten-kinetics.bngl", "tags": [ "michaelis", "menten", @@ -7826,35 +11102,30 @@ "writesbml" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Michigan_City-La_Porte_IN_Michigan_City-La_Porte_IN", - "name": "Mallela 2022 - COVID-19 MSA Models - Michigan_City-La_Porte_IN_Michigan_City-La_Porte_IN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Michigan_City-La_Porte_IN_Michigan_City-La_Porte_IN.bngl", - "file": "Michigan_City-La_Porte_IN_Michigan_City-La_Porte_IN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/biology/michaelismentenkinetics/michaelis-menten-kinetics.bngl", + "file": "michaelis-menten-kinetics.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "michment", "name": "michment", "description": "Michaelis Menten", - "path": "Contributed/BNGPlayground_Validation/michment/michment.bngl", - "file": "michment.bngl", "tags": [ "validation", "michment", @@ -7863,17 +11134,29 @@ "generate_network" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/michment/michment.bngl", + "file": "michment.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "michment_cont", "name": "michment_cont", "description": "Michaelis Menten Continue", - "path": "Contributed/BNGPlayground_Validation/michmentcont/michment_cont.bngl", - "file": "michment_cont.bngl", "tags": [ "validation", "michment", @@ -7884,53 +11167,187 @@ "addconcentration" ], "category": "validation", - "bng2_compatible": false, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/michmentcont/michment_cont.bngl", + "file": "michment_cont.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Milwaukee-Waukesha_WI_Milwaukee-Waukesha_WI", - "name": "Mallela 2022 - COVID-19 MSA Models - Milwaukee-Waukesha_WI_Milwaukee-Waukesha_WI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Milwaukee-Waukesha_WI_Milwaukee-Waukesha_WI.bngl", - "file": "Milwaukee-Waukesha_WI_Milwaukee-Waukesha_WI.bngl", + "id": "Miller2022_NavajoNation", + "name": "Miller 2022 - Navajo Nation Models", + "description": "COVID-19 epidemiological models fit to Navajo Nation regional data.", "tags": [ "covid-19", "epidemiology", - "parameter-estimation", "pybionetgen" ], "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Minneapolis-St._Paul-Bloomington_MN-WI_Minneapolis-St._Paul-Bloomington_MN-WI", - "name": "Mallela 2022 - COVID-19 MSA Models - Minneapolis-St._Paul-Bloomington_MN-WI_Minneapolis-St._Paul-Bloomington_MN-WI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Minneapolis-St._Paul-Bloomington_MN-WI_Minneapolis-St._Paul-Bloomington_MN-WI.bngl", - "file": "Minneapolis-St._Paul-Bloomington_MN-WI_Minneapolis-St._Paul-Bloomington_MN-WI.bngl", + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" + ], + "path": "Published/Miller2022_NavajoNation/supplementary_material_Arizona_Arizona.bngl", + "file": "supplementary_material_Arizona_Arizona.bngl", + "collectionId": "Miller2022_NavajoNation", + "collection": { + "type": "geographic-variants", + "count": 5, + "variant_key": "region", + "variants": [ + { + "id": "supplementary_material_Arizona_Arizona", + "file": "supplementary_material_Arizona_Arizona.bngl" + }, + { + "id": "supplementary_material_Colorado_Colorado", + "file": "supplementary_material_Colorado_Colorado.bngl" + }, + { + "id": "supplementary_material_NavajoNation_NavajoNation", + "file": "supplementary_material_NavajoNation_NavajoNation.bngl" + }, + { + "id": "supplementary_material_NewMexico_NewMexico", + "file": "supplementary_material_NewMexico_NewMexico.bngl" + }, + { + "id": "supplementary_material_Utah_Utah", + "file": "supplementary_material_Utah_Utah.bngl" + } + ] + }, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Miller2025_MEK", + "name": "Miller 2025 - MEK Isoform Models", + "description": "MEK isoform variant models curated for PyBioNetGen.", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", + "mek", + "isoforms", + "signaling", "pybionetgen" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "signaling", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "path": "Published/Miller2025_MEK/MEK_isoform_aMCMC_MEK1_KO.bngl", + "file": "MEK_isoform_aMCMC_MEK1_KO.bngl", + "collectionId": "Miller2025_MEK", + "collection": { + "type": "parameter-fit-variants", + "count": 10, + "variant_key": "isoform", + "variants": [ + { + "id": "MEK_isoform_aMCMC_MEK1_KO", + "file": "MEK_isoform_aMCMC_MEK1_KO.bngl" + }, + { + "id": "MEK_isoform_aMCMC_MEK1_N78G", + "file": "MEK_isoform_aMCMC_MEK1_N78G.bngl" + }, + { + "id": "MEK_isoform_aMCMC_MEK1_T292A", + "file": "MEK_isoform_aMCMC_MEK1_T292A.bngl" + }, + { + "id": "MEK_isoform_aMCMC_MEK1_T292D", + "file": "MEK_isoform_aMCMC_MEK1_T292D.bngl" + }, + { + "id": "MEK_isoform_aMCMC_MEK1_WT", + "file": "MEK_isoform_aMCMC_MEK1_WT.bngl" + }, + { + "id": "MEK_isoform_optimization_DE_MEK1_KO", + "file": "MEK_isoform_optimization_DE_MEK1_KO.bngl" + }, + { + "id": "MEK_isoform_optimization_DE_MEK1_N78G", + "file": "MEK_isoform_optimization_DE_MEK1_N78G.bngl" + }, + { + "id": "MEK_isoform_optimization_DE_MEK1_T292A", + "file": "MEK_isoform_optimization_DE_MEK1_T292A.bngl" + }, + { + "id": "MEK_isoform_optimization_DE_MEK1_T292D", + "file": "MEK_isoform_optimization_DE_MEK1_T292D.bngl" + }, + { + "id": "MEK_isoform_optimization_DE_MEK1_WT", + "file": "MEK_isoform_optimization_DE_MEK1_WT.bngl" + } + ] + }, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "Mitra2019_02_egfr_bnf1_InputFiles_egfr", + "name": "InputFiles", + "description": "EGFR model", + "tags": [ + "signaling" + ], + "category": "signaling", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/02-egfr/bnf1/InputFiles/egfr.bngl", + "file": "egfr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "ml_gradient_descent", "name": "ml gradient descent", "description": "Gradient Descent Optimizer in BNGL", - "path": "Contributed/BNGPlayground_Examples/ml/mlgradientdescent/ml_gradient_descent.bngl", - "file": "ml_gradient_descent.bngl", "tags": [ "ml", "gradient", @@ -7942,17 +11359,30 @@ "loss" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/ml/mlgradientdescent/ml_gradient_descent.bngl", + "file": "ml_gradient_descent.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ml_hopfield", "name": "ml hopfield", "description": "Model: ml_hopfield.bngl", - "path": "Contributed/BNGPlayground_Examples/ml/mlhopfield/ml_hopfield.bngl", - "file": "ml_hopfield.bngl", "tags": [ "ml", "hopfield", @@ -7963,17 +11393,30 @@ "target1" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/ml/mlhopfield/ml_hopfield.bngl", + "file": "ml_hopfield.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ml_kmeans", "name": "ml kmeans", "description": "Model: ml_kmeans.bngl", - "path": "Contributed/BNGPlayground_Examples/ml/mlkmeans/ml_kmeans.bngl", - "file": "ml_kmeans.bngl", "tags": [ "ml", "kmeans", @@ -7983,17 +11426,30 @@ "by" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/ml/mlkmeans/ml_kmeans.bngl", + "file": "ml_kmeans.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ml_q_learning", "name": "ml q learning", "description": "Q-Learning Agent in BNGL", - "path": "Contributed/BNGPlayground_Examples/ml/mlqlearning/ml_q_learning.bngl", - "file": "ml_q_learning.bngl", "tags": [ "ml", "q", @@ -8005,17 +11461,30 @@ "action" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/ml/mlqlearning/ml_q_learning.bngl", + "file": "ml_q_learning.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ml_svm", "name": "ml svm", "description": "Model: ml_svm.bngl", - "path": "Contributed/BNGPlayground_Examples/ml/mlsvm/ml_svm.bngl", - "file": "ml_svm.bngl", "tags": [ "ml", "svm", @@ -8026,35 +11495,30 @@ "dw1_dt" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Mobile_AL_Mobile_AL", - "name": "Mallela 2022 - COVID-19 MSA Models - Mobile_AL_Mobile_AL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Mobile_AL_Mobile_AL.bngl", - "file": "Mobile_AL_Mobile_AL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/ml/mlsvm/ml_svm.bngl", + "file": "ml_svm.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "model", "name": "model", "description": "filename: model.bngl", - "path": "PyBioNetGen/core/model/model.bngl", - "file": "model.bngl", "tags": [ "model", "ag", @@ -8066,17 +11530,29 @@ "h" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/model/model.bngl", + "file": "model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "model", "name": "model", "description": "A model of IgE receptor signaling", - "path": "PyBioNetGen/core/model_Degranulation_aMCMC/model.bngl", - "file": "model.bngl", "tags": [ "model", "ag", @@ -8088,17 +11564,97 @@ "h" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/model_Degranulation_aMCMC/model.bngl", + "file": "model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "model_ground", + "name": "model_ground.bngl", + "description": "filename: model_ground.bngl", + "tags": [ + "x_tot__free", + "k_xoff__free", + "k_xon__free", + "kase__free", + "kdegx__free", + "kdegran__free", + "km_ship1__free", + "km_syk__free", + "km_x__free", + "koff__free", + "kp_ship1__free", + "kp_syk__free", + "kp_x__free", + "kpten__free", + "ksynth1__free", + "pase__free", + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/model_ground.bngl", + "file": "model_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "model_tofit", "name": "model tofit", "description": "A model of IgE receptor signaling", - "path": "PyBioNetGen/core/modeltofit/model_tofit.bngl", - "file": "model_tofit.bngl", "tags": [ "model", "tofit", @@ -8111,17 +11667,29 @@ "h" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/modeltofit/model_tofit.bngl", + "file": "model_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Model_ZAP", "name": "Model ZAP", "description": "ZAP-70 recruitment", - "path": "Published/ModelZAP/Model_ZAP.bngl", - "file": "Model_ZAP.bngl", "tags": [ "published", "immunology", @@ -8138,89 +11706,29 @@ "dead" ], "category": "immunology", - "bng2_compatible": false, - "origin": "published", - "visible": false, - "collectionId": null - }, - { - "id": "Modesto_CA_Modesto_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Modesto_CA_Modesto_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Modesto_CA_Modesto_CA.bngl", - "file": "Modesto_CA_Modesto_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Monroe_LA_Monroe_LA", - "name": "Mallela 2022 - COVID-19 MSA Models - Monroe_LA_Monroe_LA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Monroe_LA_Monroe_LA.bngl", - "file": "Monroe_LA_Monroe_LA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Monroe_MI_Monroe_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Monroe_MI_Monroe_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Monroe_MI_Monroe_MI.bngl", - "file": "Monroe_MI_Monroe_MI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Montgomery_AL_Montgomery_AL", - "name": "Mallela 2022 - COVID-19 MSA Models - Montgomery_AL_Montgomery_AL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Montgomery_AL_Montgomery_AL.bngl", - "file": "Montgomery_AL_Montgomery_AL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "immunology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/ModelZAP/Model_ZAP.bngl", + "file": "Model_ZAP.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Motivating_example", "name": "Motivating_example", "description": "Signal Transduction with receptor internalization", - "path": "Contributed/BNGPlayground_Validation/Motivatingexample/Motivating_example.bngl", - "file": "Motivating_example.bngl", "tags": [ "validation", "motivating", @@ -8235,17 +11743,29 @@ "p2" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/Motivatingexample/Motivating_example.bngl", + "file": "Motivating_example.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Motivating_example_cBNGL", "name": "Motivating_example_cBNGL", "description": "Signal transduction with receptor internalization", - "path": "Contributed/BNGPlayground_Validation/MotivatingexamplecBNGL/Motivating_example_cBNGL.bngl", - "file": "Motivating_example_cBNGL.bngl", "tags": [ "validation", "motivating", @@ -8261,17 +11781,29 @@ "p2" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/MotivatingexamplecBNGL/Motivating_example_cBNGL.bngl", + "file": "Motivating_example_cBNGL.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "motor", "name": "motor", "description": "Motor protein", - "path": "Contributed/BNGPlayground_Validation/motor/motor.bngl", - "file": "motor.bngl", "tags": [ "validation", "motor", @@ -8280,53 +11812,29 @@ "kminus" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null - }, - { - "id": "MotorCity_m14", - "name": "Mallela 2021 - COVID-19 City Models - MotorCity_m14", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/MotorCity_m14.bngl", - "file": "MotorCity_m14.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "Mount_Vernon-Anacortes_WA_Mount_Vernon-Anacortes_WA", - "name": "Mallela 2022 - COVID-19 MSA Models - Mount_Vernon-Anacortes_WA_Mount_Vernon-Anacortes_WA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Mount_Vernon-Anacortes_WA_Mount_Vernon-Anacortes_WA.bngl", - "file": "Mount_Vernon-Anacortes_WA_Mount_Vernon-Anacortes_WA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/motor/motor.bngl", + "file": "motor.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "mt_arithmetic_compiler", "name": "mt arithmetic compiler", "description": "Model: mt_arithmetic_compiler.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/mtarithmeticcompiler/mt_arithmetic_compiler.bngl", - "file": "mt_arithmetic_compiler.bngl", "tags": [ "mt", "arithmetic", @@ -8336,17 +11844,30 @@ "target_mult" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/meta/mtarithmeticcompiler/mt_arithmetic_compiler.bngl", + "file": "mt_arithmetic_compiler.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "mt_bngl_interpreter", "name": "mt bngl interpreter", "description": "Model: mt_bngl_interpreter.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/mtbnglinterpreter/mt_bngl_interpreter.bngl", - "file": "mt_bngl_interpreter.bngl", "tags": [ "mt", "bngl", @@ -8358,17 +11879,30 @@ "simulate" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/meta/mtbnglinterpreter/mt_bngl_interpreter.bngl", + "file": "mt_bngl_interpreter.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "mt_music_sequencer", "name": "mt music sequencer", "description": "Music Sequencer / Chord Synthesizer in BNGL", - "path": "Contributed/BNGPlayground_Examples/meta/mtmusicsequencer/mt_music_sequencer.bngl", - "file": "mt_music_sequencer.bngl", "tags": [ "mt", "music", @@ -8383,17 +11917,30 @@ "chordphase" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/meta/mtmusicsequencer/mt_music_sequencer.bngl", + "file": "mt_music_sequencer.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "mt_pascal_triangle", "name": "mt pascal triangle", "description": "Model: mt_pascal_triangle.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/mtpascaltriangle/mt_pascal_triangle.bngl", - "file": "mt_pascal_triangle.bngl", "tags": [ "mt", "pascal", @@ -8401,17 +11948,30 @@ "node" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/meta/mtpascaltriangle/mt_pascal_triangle.bngl", + "file": "mt_pascal_triangle.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "mt_quine", "name": "mt quine", "description": "Model: mt_quine.bngl", - "path": "Contributed/BNGPlayground_Examples/meta/mtquine/mt_quine.bngl", - "file": "mt_quine.bngl", "tags": [ "mt", "quine", @@ -8419,17 +11979,30 @@ "protein" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cs", + "test-models" + ], + "path": "Examples/meta/mtquine/mt_quine.bngl", + "file": "mt_quine.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "mtor-signaling", "name": "mtor signaling", "description": "mTOR Signaling Pathway", - "path": "Contributed/BNGPlayground_Examples/biology/mtorsignaling/mtor-signaling.bngl", - "file": "mtor-signaling.bngl", "tags": [ "mtor", "signaling", @@ -8439,17 +12012,30 @@ "ampk" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/mtorsignaling/mtor-signaling.bngl", + "file": "mtor-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "mtorc2-signaling", "name": "mtorc2 signaling", "description": "mTORC2 signaling regulates cell survival and growth via AKT and SGK1.", - "path": "Contributed/BNGPlayground_Examples/biology/mtorc2signaling/mtorc2-signaling.bngl", - "file": "mtorc2-signaling.bngl", "tags": [ "mtorc2", "signaling", @@ -8461,17 +12047,29 @@ "pip3" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/mtorc2signaling/mtorc2-signaling.bngl", + "file": "mtorc2-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Mukhopadhyay_2013", "name": "Mukhopadhyay 2013", "description": "FceRI signaling", - "path": "Published/Mukhopadhyay2013/Mukhopadhyay_2013.bngl", - "file": "Mukhopadhyay_2013.bngl", "tags": [ "published", "immunology", @@ -8483,53 +12081,29 @@ "z" ], "category": "immunology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": null - }, - { - "id": "Muncie_IN_Muncie_IN", - "name": "Mallela 2022 - COVID-19 MSA Models - Muncie_IN_Muncie_IN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Muncie_IN_Muncie_IN.bngl", - "file": "Muncie_IN_Muncie_IN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Muskegon_MI_Muskegon_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Muskegon_MI_Muskegon_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Muskegon_MI_Muskegon_MI.bngl", - "file": "Muskegon_MI_Muskegon_MI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/Mukhopadhyay2013/Mukhopadhyay_2013.bngl", + "file": "Mukhopadhyay_2013.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "mwc", "name": "mwc", "description": "Monod-Wyman-Changeux model", - "path": "Contributed/BNGPlayground_Validation/mwc/mwc.bngl", - "file": "mwc.bngl", "tags": [ "validation", "mwc", @@ -8539,17 +12113,29 @@ "b" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/mwc/mwc.bngl", + "file": "mwc.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "myogenic-differentiation", "name": "myogenic differentiation", "description": "Myogenic Differentiation", - "path": "Contributed/BNGPlayground_Examples/biology/myogenicdifferentiation/myogenic-differentiation.bngl", - "file": "myogenic-differentiation.bngl", "tags": [ "myogenic", "differentiation", @@ -8558,17 +12144,30 @@ "mef2" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/myogenicdifferentiation/myogenic-differentiation.bngl", + "file": "myogenic-differentiation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", "name": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", "description": "Runtime-only BNGL model migrated from public/models: Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", - "path": "Contributed/BNGPlayground_PublicRuntime/MyrtleBeachConwayNorthMyrtleBeachSCNC/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl", - "file": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl", "tags": [ "myrtle", "beach", @@ -8578,17 +12177,29 @@ "nc" ], "category": "other", - "bng2_compatible": true, "origin": "contributed", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/MyrtleBeachConwayNorthMyrtleBeachSCNC/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl", + "file": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Nag_2009", "name": "Nag 2009", "description": "LAT-Grb2-SOS1 signaling", - "path": "Published/Nag2009/Nag_2009.bngl", - "file": "Nag_2009.bngl", "tags": [ "published", "nag", @@ -8602,53 +12213,29 @@ "sos" ], "category": "signaling", - "bng2_compatible": false, - "origin": "published", - "visible": false, - "collectionId": null - }, - { - "id": "Naples-Marco_Island_FL_Naples-Marco_Island_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Naples-Marco_Island_FL_Naples-Marco_Island_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Naples-Marco_Island_FL_Naples-Marco_Island_FL.bngl", - "file": "Naples-Marco_Island_FL_Naples-Marco_Island_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Nashville-Davidson-Murfreesboro-Franklin_TN_Nashville-Davidson-Murfreesboro-Franklin_TN", - "name": "Mallela 2022 - COVID-19 MSA Models - Nashville-Davidson-Murfreesboro-Franklin_TN_Nashville-Davidson-Murfreesboro-Franklin_TN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Nashville-Davidson-Murfreesboro-Franklin_TN_Nashville-Davidson-Murfreesboro-Franklin_TN.bngl", - "file": "Nashville-Davidson-Murfreesboro-Franklin_TN_Nashville-Davidson-Murfreesboro-Franklin_TN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/Nag2009/Nag_2009.bngl", + "file": "Nag_2009.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "negative-feedback-loop", "name": "negative feedback loop", "description": "Negative Feedback Loop", - "path": "Contributed/BNGPlayground_Examples/biology/negativefeedbackloop/negative-feedback-loop.bngl", - "file": "negative-feedback-loop.bngl", "tags": [ "negative", "feedback", @@ -8658,17 +12245,29 @@ "protein" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/negativefeedbackloop/negative-feedback-loop.bngl", + "file": "negative-feedback-loop.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "neurotransmitter-release", "name": "neurotransmitter release", "description": "Neurotransmitter Release", - "path": "Contributed/BNGPlayground_Examples/biology/neurotransmitterrelease/neurotransmitter-release.bngl", - "file": "neurotransmitter-release.bngl", "tags": [ "neurotransmitter", "release", @@ -8678,71 +12277,30 @@ "postsynaptic" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "New_Haven-Milford_CT_New_Haven-Milford_CT", - "name": "Mallela 2022 - COVID-19 MSA Models - New_Haven-Milford_CT_New_Haven-Milford_CT", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/New_Haven-Milford_CT_New_Haven-Milford_CT.bngl", - "file": "New_Haven-Milford_CT_New_Haven-Milford_CT.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/biology/neurotransmitterrelease/neurotransmitter-release.bngl", + "file": "neurotransmitter-release.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "New_Orleans-Metairie_LA_New_Orleans-Metairie_LA", - "name": "Mallela 2022 - COVID-19 MSA Models - New_Orleans-Metairie_LA_New_Orleans-Metairie_LA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/New_Orleans-Metairie_LA_New_Orleans-Metairie_LA.bngl", - "file": "New_Orleans-Metairie_LA_New_Orleans-Metairie_LA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "New_York-Newark-Jersey_City_NY-NJ-PA_New_York-Newark-Jersey_City_NY-NJ-PA", - "name": "Mallela 2022 - COVID-19 MSA Models - New_York-Newark-Jersey_City_NY-NJ-PA_New_York-Newark-Jersey_City_NY-NJ-PA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/New_York-Newark-Jersey_City_NY-NJ-PA_New_York-Newark-Jersey_City_NY-NJ-PA.bngl", - "file": "New_York-Newark-Jersey_City_NY-NJ-PA_New_York-Newark-Jersey_City_NY-NJ-PA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "nfkb", - "name": "nfkb", - "description": "NF-kB signaling pathway", - "path": "Contributed/BNGPlayground_Validation/nfkb/nfkb.bngl", - "file": "nfkb.bngl", + "id": "nfkb", + "name": "nfkb", + "description": "NF-kB signaling pathway", "tags": [ "validation", "nfkb", @@ -8755,17 +12313,29 @@ "competitor" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/nfkb/nfkb.bngl", + "file": "nfkb.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "nfkb_illustrating_protocols", "name": "nfkb_illustrating_protocols", "description": "NF-kB signaling pathway", - "path": "Contributed/BNGPlayground_Validation/nfkbillustratingprotocols/nfkb_illustrating_protocols.bngl", - "file": "nfkb_illustrating_protocols.bngl", "tags": [ "validation", "nfkb", @@ -8780,17 +12350,29 @@ "competitor" ], "category": "validation", - "bng2_compatible": false, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/nfkbillustratingprotocols/nfkb_illustrating_protocols.bngl", + "file": "nfkb_illustrating_protocols.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "nfkb-feedback", "name": "nfkb feedback", "description": "TNFalpha-induced NF-kB signaling with IkappaB-alpha feedback.", - "path": "Contributed/BNGPlayground_Examples/biology/nfkbfeedback/nfkb-feedback.bngl", - "file": "nfkb-feedback.bngl", "tags": [ "nfkb", "feedback", @@ -8799,17 +12381,29 @@ "a20" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/nfkbfeedback/nfkb-feedback.bngl", + "file": "nfkb-feedback.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "NFmodel", "name": "NFmodel", "description": "BioNetGen model: NFmodel", - "path": "PyBioNetGen/tests/NFmodel/NFmodel.bngl", - "file": "NFmodel.bngl", "tags": [ "nfmodel", "ag", @@ -8817,17 +12411,29 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/NFmodel/NFmodel.bngl", + "file": "NFmodel.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "nfsim_aggregation_gelation", "name": "nfsim aggregation gelation", "description": "Model: nfsim_aggregation_gelation.bngl", - "path": "Contributed/BNGPlayground_Examples/nfsim/nfsimaggregationgelation/nfsim_aggregation_gelation.bngl", - "file": "nfsim_aggregation_gelation.bngl", "tags": [ "nfsim", "aggregation", @@ -8835,17 +12441,29 @@ "m" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/nfsim/nfsimaggregationgelation/nfsim_aggregation_gelation.bngl", + "file": "nfsim_aggregation_gelation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "nfsim_coarse_graining", "name": "nfsim coarse graining", "description": "Model: nfsim_coarse_graining.bngl", - "path": "Contributed/BNGPlayground_Examples/nfsim/nfsimcoarsegraining/nfsim_coarse_graining.bngl", - "file": "nfsim_coarse_graining.bngl", "tags": [ "nfsim", "coarse", @@ -8853,17 +12471,29 @@ "droplet" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/nfsim/nfsimcoarsegraining/nfsim_coarse_graining.bngl", + "file": "nfsim_coarse_graining.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "nfsim_dynamic_compartments", "name": "nfsim dynamic compartments", "description": "Model: nfsim_dynamic_compartments.bngl", - "path": "Contributed/BNGPlayground_Examples/nfsim/nfsimdynamiccompartments/nfsim_dynamic_compartments.bngl", - "file": "nfsim_dynamic_compartments.bngl", "tags": [ "nfsim", "dynamic", @@ -8873,17 +12503,29 @@ "simulate" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/nfsim/nfsimdynamiccompartments/nfsim_dynamic_compartments.bngl", + "file": "nfsim_dynamic_compartments.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "nfsim_hybrid_particle_field", "name": "nfsim hybrid particle field", "description": "Model: nfsim_hybrid_particle_field.bngl", - "path": "Contributed/BNGPlayground_Examples/nfsim/nfsimhybridparticlefield/nfsim_hybrid_particle_field.bngl", - "file": "nfsim_hybrid_particle_field.bngl", "tags": [ "nfsim", "hybrid", @@ -8891,17 +12533,29 @@ "field" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/nfsim/nfsimhybridparticlefield/nfsim_hybrid_particle_field.bngl", + "file": "nfsim_hybrid_particle_field.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "nfsim_ring_closure_polymer", "name": "nfsim ring closure polymer", "description": "Model: nfsim_ring_closure_polymer.bngl", - "path": "Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer.bngl", - "file": "nfsim_ring_closure_polymer.bngl", "tags": [ "nfsim", "ring", @@ -8912,35 +12566,29 @@ "simulate" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Niles_MI_Niles_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Niles_MI_Niles_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Niles_MI_Niles_MI.bngl", - "file": "Niles_MI_Niles_MI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/nfsim/nfsimringclosurepolymer/nfsim_ring_closure_polymer.bngl", + "file": "nfsim_ring_closure_polymer.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "nn_xor", "name": "nn xor", "description": "Model: nn_xor.bngl", - "path": "Contributed/BNGPlayground_Examples/ml/nnxor/nn_xor.bngl", - "file": "nn_xor.bngl", "tags": [ "nn", "xor", @@ -8953,17 +12601,30 @@ "dopamine" ], "category": "computer-science", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/ml/nnxor/nn_xor.bngl", + "file": "nn_xor.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "no_frees", "name": "no frees", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/nofrees/no_frees.bngl", - "file": "no_frees.bngl", "tags": [ "no", "frees", @@ -8973,17 +12634,29 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/nofrees/no_frees.bngl", + "file": "no_frees.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "no_generate_network", "name": "no generate network", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/nogeneratenetwork/no_generate_network.bngl", - "file": "no_generate_network.bngl", "tags": [ "no", "generate", @@ -8993,17 +12666,29 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/nogeneratenetwork/no_generate_network.bngl", + "file": "no_generate_network.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "no_suffix", "name": "no suffix", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/nosuffix/no_suffix.bngl", - "file": "no_suffix.bngl", "tags": [ "no", "suffix", @@ -9013,17 +12698,29 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/nosuffix/no_suffix.bngl", + "file": "no_suffix.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "no-cgmp-signaling", "name": "no cgmp signaling", "description": "Nitric Oxide (NO) / cGMP signaling pathway.", - "path": "Contributed/BNGPlayground_Examples/biology/nocgmpsignaling/no-cgmp-signaling.bngl", - "file": "no-cgmp-signaling.bngl", "tags": [ "no", "cgmp", @@ -9032,53 +12729,30 @@ "pkg" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "North_Port-Sarasota-Bradenton_FL_North_Port-Sarasota-Bradenton_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - North_Port-Sarasota-Bradenton_FL_North_Port-Sarasota-Bradenton_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/North_Port-Sarasota-Bradenton_FL_North_Port-Sarasota-Bradenton_FL.bngl", - "file": "North_Port-Sarasota-Bradenton_FL_North_Port-Sarasota-Bradenton_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Norwich-New_London_CT_Norwich-New_London_CT", - "name": "Mallela 2022 - COVID-19 MSA Models - Norwich-New_London_CT_Norwich-New_London_CT", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Norwich-New_London_CT_Norwich-New_London_CT.bngl", - "file": "Norwich-New_London_CT_Norwich-New_London_CT.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "metabolism", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/biology/nocgmpsignaling/no-cgmp-signaling.bngl", + "file": "no-cgmp-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Nosbisch_2022", "name": "Nosbisch 2022", "description": "RTK-PLCgamma1 signaling", - "path": "Published/Nosbisch2022/Nosbisch_2022.bngl", - "file": "Nosbisch_2022.bngl", "tags": [ "published", "nosbisch", @@ -9088,17 +12762,29 @@ "generate_network" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Nosbisch2022/Nosbisch_2022.bngl", + "file": "Nosbisch_2022.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "notch", "name": "Notch", "description": "Notch signaling", - "path": "Published/notch/notch.bngl", - "file": "notch.bngl", "tags": [ "published", "notch", @@ -9111,17 +12797,29 @@ "maml" ], "category": "regulation", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "path": "Published/notch/notch.bngl", + "file": "notch.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "notch-delta-lateral-inhibition", "name": "notch delta lateral inhibition", "description": "Notch-Delta Lateral Inhibition", - "path": "Contributed/BNGPlayground_Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition.bngl", - "file": "notch-delta-lateral-inhibition.bngl", "tags": [ "notch", "delta", @@ -9131,17 +12829,30 @@ "celldelta" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/notchdeltalateralinhibition/notch-delta-lateral-inhibition.bngl", + "file": "notch-delta-lateral-inhibition.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "NYC", "name": "NYC", "description": "- This model is intended to be consistent with the compartmental model", - "path": "Published/VaxAndVariants/NYC/NYC.bngl", - "file": "NYC.bngl", "tags": [ "nyc", "counter", @@ -9154,107 +12865,29 @@ "v" ], "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": null - }, - { - "id": "Ocala_FL_Ocala_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Ocala_FL_Ocala_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Ocala_FL_Ocala_FL.bngl", - "file": "Ocala_FL_Ocala_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Ocean_City_NJ_Ocean_City_NJ", - "name": "Mallela 2022 - COVID-19 MSA Models - Ocean_City_NJ_Ocean_City_NJ", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Ocean_City_NJ_Ocean_City_NJ.bngl", - "file": "Ocean_City_NJ_Ocean_City_NJ.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Ogden-Clearfield_UT_Ogden-Clearfield_UT", - "name": "Mallela 2022 - COVID-19 MSA Models - Ogden-Clearfield_UT_Ogden-Clearfield_UT", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Ogden-Clearfield_UT_Ogden-Clearfield_UT.bngl", - "file": "Ogden-Clearfield_UT_Ogden-Clearfield_UT.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Oklahoma_City_OK_Oklahoma_City_OK", - "name": "Mallela 2022 - COVID-19 MSA Models - Oklahoma_City_OK_Oklahoma_City_OK", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Oklahoma_City_OK_Oklahoma_City_OK.bngl", - "file": "Oklahoma_City_OK_Oklahoma_City_OK.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Omaha-Council_Bluffs_NE-IA_Omaha-Council_Bluffs_NE-IA", - "name": "Mallela 2022 - COVID-19 MSA Models - Omaha-Council_Bluffs_NE-IA_Omaha-Council_Bluffs_NE-IA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Omaha-Council_Bluffs_NE-IA_Omaha-Council_Bluffs_NE-IA.bngl", - "file": "Omaha-Council_Bluffs_NE-IA_Omaha-Council_Bluffs_NE-IA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/VaxAndVariants/NYC/NYC.bngl", + "file": "NYC.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "organelle_transport", "name": "organelle transport", "description": "title: organelle_transport.bngl", - "path": "Tutorials/NativeTutorials/organelletransport/organelle_transport.bngl", - "file": "organelle_transport.bngl", "tags": [ "organelle", "transport", @@ -9268,17 +12901,29 @@ "t2" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/organelletransport/organelle_transport.bngl", + "file": "organelle_transport.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "organelle_transport_struct", "name": "organelle transport struct", "description": "title: organelle_transport_abcd.bngl", - "path": "Tutorials/NativeTutorials/organelletransportstruct/organelle_transport_struct.bngl", - "file": "organelle_transport_struct.bngl", "tags": [ "organelle", "transport", @@ -9289,53 +12934,29 @@ "t2" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null - }, - { - "id": "Orlando-Kissimmee-Sanford_FL_Orlando-Kissimmee-Sanford_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Orlando-Kissimmee-Sanford_FL_Orlando-Kissimmee-Sanford_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Orlando-Kissimmee-Sanford_FL_Orlando-Kissimmee-Sanford_FL.bngl", - "file": "Orlando-Kissimmee-Sanford_FL_Orlando-Kissimmee-Sanford_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Owensboro_KY_Owensboro_KY", - "name": "Mallela 2022 - COVID-19 MSA Models - Owensboro_KY_Owensboro_KY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Owensboro_KY_Owensboro_KY.bngl", - "file": "Owensboro_KY_Owensboro_KY.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Tutorials/NativeTutorials/organelletransportstruct/organelle_transport_struct.bngl", + "file": "organelle_transport_struct.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "oxidative-stress-response", "name": "oxidative stress response", "description": "Oxidative Stress Response (Keap1-Nrf2 Pathway)", - "path": "Contributed/BNGPlayground_Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl", - "file": "oxidative-stress-response.bngl", "tags": [ "oxidative", "stress", @@ -9346,35 +12967,29 @@ "antioxidant" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Oxnard-Thousand_Oaks-Ventura_CA_Oxnard-Thousand_Oaks-Ventura_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Oxnard-Thousand_Oaks-Ventura_CA_Oxnard-Thousand_Oaks-Ventura_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Oxnard-Thousand_Oaks-Ventura_CA_Oxnard-Thousand_Oaks-Ventura_CA.bngl", - "file": "Oxnard-Thousand_Oaks-Ventura_CA_Oxnard-Thousand_Oaks-Ventura_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/oxidativestressresponse/oxidative-stress-response.bngl", + "file": "oxidative-stress-response.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "p38-mapk-signaling", "name": "p38 mapk signaling", "description": "p38 MAPK stress signaling cascade.", - "path": "Contributed/BNGPlayground_Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl", - "file": "p38-mapk-signaling.bngl", "tags": [ "p38", "mapk", @@ -9384,17 +12999,30 @@ "v_thermal" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/p38mapksignaling/p38-mapk-signaling.bngl", + "file": "p38-mapk-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "p53-mdm2-oscillator", "name": "p53 mdm2 oscillator", "description": "BioNetGen model: p53 mdm2 oscillator", - "path": "Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl", - "file": "p53-mdm2-oscillator.bngl", "tags": [ "p53", "mdm2", @@ -9402,35 +13030,30 @@ "generate_network" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Palm_Bay-Melbourne-Titusville_FL_Palm_Bay-Melbourne-Titusville_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Palm_Bay-Melbourne-Titusville_FL_Palm_Bay-Melbourne-Titusville_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Palm_Bay-Melbourne-Titusville_FL_Palm_Bay-Melbourne-Titusville_FL.bngl", - "file": "Palm_Bay-Melbourne-Titusville_FL_Palm_Bay-Melbourne-Titusville_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/p53mdm2oscillator/p53-mdm2-oscillator.bngl", + "file": "p53-mdm2-oscillator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "parabola", "name": "parabola", "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", - "path": "PyBioNetGen/core/parabola/parabola.bngl", - "file": "parabola.bngl", "tags": [ "parabola", "counter", @@ -9440,17 +13063,29 @@ "simulate" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/parabola/parabola.bngl", + "file": "parabola.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "parabola", "name": "parabola", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/core/parabola_demo/parabola.bngl", - "file": "parabola.bngl", "tags": [ "parabola", "counter", @@ -9459,17 +13094,29 @@ "simulate" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/parabola_demo/parabola.bngl", + "file": "parabola.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "parabola", "name": "parabola", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/parabola/parabola.bngl", - "file": "parabola.bngl", "tags": [ "parabola", "counter", @@ -9479,17 +13126,29 @@ "resetconcentrations" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/parabola/parabola.bngl", + "file": "parabola.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "parabola", "name": "parabola", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/parabola_bngl_files/parabola.bngl", - "file": "parabola.bngl", "tags": [ "parabola", "counter", @@ -9498,17 +13157,29 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/parabola_bngl_files/parabola.bngl", + "file": "parabola.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "parabola", "name": "parabola", "description": "Original values used to generate parabola.exp", - "path": "PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola.bngl", - "file": "parabola.bngl", "tags": [ "parabola", "counter", @@ -9517,17 +13188,29 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check/parabola.bngl", + "file": "parabola.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "parabola_ground", "name": "parabola ground", "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", - "path": "PyBioNetGen/core/parabolaground/parabola_ground.bngl", - "file": "parabola_ground.bngl", "tags": [ "parabola", "ground", @@ -9538,17 +13221,29 @@ "simulate" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/parabolaground/parabola_ground.bngl", + "file": "parabola_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "parabola2", "name": "parabola2", "description": "A file for testing behavior with duplicate file names", - "path": "PyBioNetGen/tests/parabola2/parabola2.bngl", - "file": "parabola2.bngl", "tags": [ "parabola2", "counter", @@ -9558,17 +13253,29 @@ "resetconcentrations" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/parabola2/parabola2.bngl", + "file": "parabola2.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ParamsEverywhere", "name": "ParamsEverywhere", "description": "An example from a real application", - "path": "PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere.bngl", - "file": "ParamsEverywhere.bngl", "tags": [ "paramseverywhere", "ag", @@ -9576,17 +13283,29 @@ "h" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/ParamsEverywhere/ParamsEverywhere.bngl", + "file": "ParamsEverywhere.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "parp1-mediated-dna-repair", "name": "parp1 mediated dna repair", "description": "PARP1-mediated DNA damage sensing and repair.", - "path": "Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl", - "file": "parp1-mediated-dna-repair.bngl", "tags": [ "parp1", "mediated", @@ -9597,17 +13316,30 @@ "v_parylate" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/parp1mediateddnarepair/parp1-mediated-dna-repair.bngl", + "file": "parp1-mediated-dna-repair.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Pekalski_2013", "name": "Pekalski 2013", "description": "Spontaneous signaling", - "path": "Published/Pekalski2013/Pekalski_2013.bngl", - "file": "Pekalski_2013.bngl", "tags": [ "published", "pekalski", @@ -9622,53 +13354,29 @@ "nfkb" ], "category": "regulation", - "bng2_compatible": false, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "path": "Published/Pekalski2013/Pekalski_2013.bngl", + "file": "Pekalski_2013.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "Pensacola-Ferry_Pass-Brent_FL_Pensacola-Ferry_Pass-Brent_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Pensacola-Ferry_Pass-Brent_FL_Pensacola-Ferry_Pass-Brent_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Pensacola-Ferry_Pass-Brent_FL_Pensacola-Ferry_Pass-Brent_FL.bngl", - "file": "Pensacola-Ferry_Pass-Brent_FL_Pensacola-Ferry_Pass-Brent_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Peoria_IL_Peoria_IL", - "name": "Mallela 2022 - COVID-19 MSA Models - Peoria_IL_Peoria_IL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Peoria_IL_Peoria_IL.bngl", - "file": "Peoria_IL_Peoria_IL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "ph_lorenz_attractor", - "name": "ph lorenz attractor", - "description": "Lorenz Attractor in BNGL", - "path": "Contributed/BNGPlayground_Examples/physics/phlorenzattractor/ph_lorenz_attractor.bngl", - "file": "ph_lorenz_attractor.bngl", + "id": "ph_lorenz_attractor", + "name": "ph lorenz attractor", + "description": "Lorenz Attractor in BNGL", "tags": [ "ph", "lorenz", @@ -9680,17 +13388,30 @@ "y" ], "category": "physics", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "path": "Examples/physics/phlorenzattractor/ph_lorenz_attractor.bngl", + "file": "ph_lorenz_attractor.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ph_nbody_gravity", "name": "ph nbody gravity", "description": "Model: ph_nbody_gravity.bngl", - "path": "Contributed/BNGPlayground_Examples/physics/phnbodygravity/ph_nbody_gravity.bngl", - "file": "ph_nbody_gravity.bngl", "tags": [ "ph", "nbody", @@ -9699,34 +13420,60 @@ "r2" ], "category": "physics", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "path": "Examples/physics/phnbodygravity/ph_nbody_gravity.bngl", + "file": "ph_nbody_gravity.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ph_schrodinger", "name": "ph schrodinger", "description": "Model: ph_schrodinger.bngl", - "path": "Contributed/BNGPlayground_Examples/physics/phschrodinger/ph_schrodinger.bngl", - "file": "ph_schrodinger.bngl", "tags": [ "ph", "schrodinger", "psi" ], "category": "physics", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "path": "Examples/physics/phschrodinger/ph_schrodinger.bngl", + "file": "ph_schrodinger.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ph_wave_equation", "name": "ph wave equation", "description": "Model: ph_wave_equation.bngl", - "path": "Contributed/BNGPlayground_Examples/physics/phwaveequation/ph_wave_equation.bngl", - "file": "ph_wave_equation.bngl", "tags": [ "ph", "wave", @@ -9734,35 +13481,30 @@ "node" ], "category": "physics", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Philadelphia-Camden-Wilmington_PA-NJ-DE-MD_Philadelphia-Camden-Wilmington_PA-NJ-DE-MD", - "name": "Mallela 2022 - COVID-19 MSA Models - Philadelphia-Camden-Wilmington_PA-NJ-DE-MD_Philadelphia-Camden-Wilmington_PA-NJ-DE-MD", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Philadelphia-Camden-Wilmington_PA-NJ-DE-MD_Philadelphia-Camden-Wilmington_PA-NJ-DE-MD.bngl", - "file": "Philadelphia-Camden-Wilmington_PA-NJ-DE-MD_Philadelphia-Camden-Wilmington_PA-NJ-DE-MD.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/physics/phwaveequation/ph_wave_equation.bngl", + "file": "ph_wave_equation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Phoenix", "name": "Phoenix", "description": "- This model is intended to be consistent with the compartmental model", - "path": "Published/VaxAndVariants/Phoenix/Phoenix.bngl", - "file": "Phoenix.bngl", "tags": [ "phoenix", "counter", @@ -9775,35 +13517,29 @@ "v" ], "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null - }, - { - "id": "Phoenix-Mesa-Chandler_AZ_Phoenix-Mesa-Chandler_AZ", - "name": "Mallela 2022 - COVID-19 MSA Models - Phoenix-Mesa-Chandler_AZ_Phoenix-Mesa-Chandler_AZ", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Phoenix-Mesa-Chandler_AZ_Phoenix-Mesa-Chandler_AZ.bngl", - "file": "Phoenix-Mesa-Chandler_AZ_Phoenix-Mesa-Chandler_AZ.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "epidemiology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/VaxAndVariants/Phoenix/Phoenix.bngl", + "file": "Phoenix.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "phosphorelay-chain", "name": "phosphorelay chain", "description": "BioNetGen model: phosphorelay chain", - "path": "Contributed/BNGPlayground_Examples/biology/phosphorelaychain/phosphorelay-chain.bngl", - "file": "phosphorelay-chain.bngl", "tags": [ "phosphorelay", "chain", @@ -9812,71 +13548,29 @@ "output" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Pine_Bluff_AR_Pine_Bluff_AR", - "name": "Mallela 2022 - COVID-19 MSA Models - Pine_Bluff_AR_Pine_Bluff_AR", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Pine_Bluff_AR_Pine_Bluff_AR.bngl", - "file": "Pine_Bluff_AR_Pine_Bluff_AR.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Pittsburgh_PA_Pittsburgh_PA", - "name": "Mallela 2022 - COVID-19 MSA Models - Pittsburgh_PA_Pittsburgh_PA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Pittsburgh_PA_Pittsburgh_PA.bngl", - "file": "Pittsburgh_PA_Pittsburgh_PA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Pittsfield_MA_Pittsfield_MA", - "name": "Mallela 2022 - COVID-19 MSA Models - Pittsfield_MA_Pittsfield_MA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Pittsfield_MA_Pittsfield_MA.bngl", - "file": "Pittsfield_MA_Pittsfield_MA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/phosphorelaychain/phosphorelay-chain.bngl", + "file": "phosphorelay-chain.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "platelet-activation", "name": "platelet activation", "description": "BioNetGen model: platelet activation", - "path": "Contributed/BNGPlayground_Examples/biology/plateletactivation/platelet-activation.bngl", - "file": "platelet-activation.bngl", "tags": [ "platelet", "activation", @@ -9886,17 +13580,30 @@ "thromboxane" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/plateletactivation/platelet-activation.bngl", + "file": "platelet-activation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "polymer", "name": "polymer", "description": "Polymerization model", - "path": "Tutorials/General/polymer/polymer.bngl", - "file": "polymer.bngl", "tags": [ "published", "tutorials", @@ -9908,17 +13615,29 @@ "simulate_nf" ], "category": "tutorial", - "bng2_compatible": false, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "tutorials" + ], + "path": "Tutorials/General/polymer/polymer.bngl", + "file": "polymer.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "polymer_draft", "name": "polymer draft", "description": "Polymerization (draft)", - "path": "Tutorials/General/polymerdraft/polymer_draft.bngl", - "file": "polymer_draft.bngl", "tags": [ "published", "tutorials", @@ -9931,33 +13650,57 @@ "simulate_nf" ], "category": "tutorial", - "bng2_compatible": false, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "tutorials" + ], + "path": "Tutorials/General/polymerdraft/polymer_draft.bngl", + "file": "polymer_draft.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "polymer_fixed", "name": "polymer_fixed", "description": "Runtime-only BNGL model migrated from public/models: polymer_fixed", - "path": "Contributed/BNGPlayground_PublicRuntime/polymerfixed/polymer_fixed.bngl", - "file": "polymer_fixed.bngl", "tags": [ "polymer", "fixed" ], "category": "other", - "bng2_compatible": true, "origin": "contributed", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Tutorials/polymerfixed/polymer_fixed.bngl", + "file": "polymer_fixed.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "polynomial", "name": "polynomial", "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", - "path": "PyBioNetGen/core/polynomial/polynomial.bngl", - "file": "polynomial.bngl", "tags": [ "polynomial", "counter", @@ -9969,17 +13712,29 @@ "resetconcentrations" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/polynomial/polynomial.bngl", + "file": "polynomial.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "polynomial", "name": "polynomial", "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", - "path": "PyBioNetGen/tests/polynomial/polynomial.bngl", - "file": "polynomial.bngl", "tags": [ "polynomial", "counter", @@ -9991,17 +13746,29 @@ "resetconcentrations" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/polynomial/polynomial.bngl", + "file": "polynomial.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "polynomial", "name": "polynomial", "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", - "path": "PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial.bngl", - "file": "polynomial.bngl", "tags": [ "polynomial", "counter", @@ -10013,17 +13780,29 @@ "resetconcentrations" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/polynomial_full_tests_T6-check/polynomial.bngl", + "file": "polynomial.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "polynomial_ground", "name": "polynomial ground", "description": "Implementation of the parabola from the Mitra constrained optimization manuscript Fig. 1", - "path": "PyBioNetGen/core/polynomialground/polynomial_ground.bngl", - "file": "polynomial_ground.bngl", "tags": [ "polynomial", "ground", @@ -10036,71 +13815,29 @@ "resetconcentrations" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null - }, - { - "id": "Port_St._Lucie_FL_Port_St._Lucie_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Port_St._Lucie_FL_Port_St._Lucie_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Port_St._Lucie_FL_Port_St._Lucie_FL.bngl", - "file": "Port_St._Lucie_FL_Port_St._Lucie_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Portland-South_Portland_ME_Portland-South_Portland_ME", - "name": "Mallela 2022 - COVID-19 MSA Models - Portland-South_Portland_ME_Portland-South_Portland_ME", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Portland-South_Portland_ME_Portland-South_Portland_ME.bngl", - "file": "Portland-South_Portland_ME_Portland-South_Portland_ME.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Portland-Vancouver-Hillsboro_OR-WA_Portland-Vancouver-Hillsboro_OR-WA", - "name": "Mallela 2022 - COVID-19 MSA Models - Portland-Vancouver-Hillsboro_OR-WA_Portland-Vancouver-Hillsboro_OR-WA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Portland-Vancouver-Hillsboro_OR-WA_Portland-Vancouver-Hillsboro_OR-WA.bngl", - "file": "Portland-Vancouver-Hillsboro_OR-WA_Portland-Vancouver-Hillsboro_OR-WA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/polynomialground/polynomial_ground.bngl", + "file": "polynomial_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Posner_1995", "name": "Posner 1995", "description": "BLBR rings", - "path": "Published/Posner1995/blbr_rings_posner1995.bngl", - "file": "blbr_rings_posner1995.bngl", "tags": [ "published", "physics", @@ -10108,17 +13845,29 @@ "1995" ], "category": "physics", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" + ], + "path": "Published/Posner1995/blbr_rings_posner1995.bngl", + "file": "blbr_rings_posner1995.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Posner_2004", "name": "Posner 2004", "description": "BLBR cooperativity", - "path": "Published/Posner2004/blbr_cooperativity_posner2004.bngl", - "file": "blbr_cooperativity_posner2004.bngl", "tags": [ "published", "physics", @@ -10126,133 +13875,822 @@ "2004" ], "category": "physics", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null - }, - { - "id": "Poughkeepsie-Newburgh-Middletown_NY_Poughkeepsie-Newburgh-Middletown_NY", - "name": "Mallela 2022 - COVID-19 MSA Models - Poughkeepsie-Newburgh-Middletown_NY_Poughkeepsie-Newburgh-Middletown_NY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Poughkeepsie-Newburgh-Middletown_NY_Poughkeepsie-Newburgh-Middletown_NY.bngl", - "file": "Poughkeepsie-Newburgh-Middletown_NY_Poughkeepsie-Newburgh-Middletown_NY.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/Posner2004/blbr_cooperativity_posner2004.bngl", + "file": "blbr_cooperativity_posner2004.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "predator-prey-dynamics", "name": "predator prey dynamics", "description": "BioNetGen model: predator prey dynamics", - "path": "Contributed/BNGPlayground_Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl", - "file": "predator-prey-dynamics.bngl", "tags": [ "predator", "prey", "dynamics" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/predatorpreydynamics/predator-prey-dynamics.bngl", + "file": "predator-prey-dynamics.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "Prescott_Valley-Prescott_AZ_Prescott_Valley-Prescott_AZ", - "name": "Mallela 2022 - COVID-19 MSA Models - Prescott_Valley-Prescott_AZ_Prescott_Valley-Prescott_AZ", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Prescott_Valley-Prescott_AZ_Prescott_Valley-Prescott_AZ.bngl", - "file": "Prescott_Valley-Prescott_AZ_Prescott_Valley-Prescott_AZ.bngl", + "id": "prion_model", + "name": "ERK_model.bngl", + "description": "filename: ERK_model.bngl", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "egf", + "erkpp_sos1_fb", + "erkpp_mek_fb", + "erkpp_raf1_fb", + "lambda", + "egfr_tot", + "ras_tot", + "sos_tot", + "rasgap_tot", + "raf_tot", + "mek_tot", + "erk_tot", + "ekar3_tot", + "erktr_tot", + "a1", + "d1", + "b1", + "u1a", + "u1b", + "b2a", + "u2a", + "b2b", + "u2b", + "k2a", + "k2b", + "b3", + "u3", + "k3", + "a2", + "d2", + "p1", + "q1", + "p2", + "q2", + "p3", + "q3", + "p4", + "q4", + "q5", + "p6", + "q6", + "a0_ekar3", + "d0_ekar3", + "a0_erktr", + "d0_erktr", + "species" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "other", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "process_actin_treadmilling", - "name": "process actin treadmilling", - "description": "Model: process_actin_treadmilling.bngl", - "path": "Contributed/BNGPlayground_Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl", - "file": "process_actin_treadmilling.bngl", + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "path": "Published/Lin2019/prion_model.bngl", + "file": "prion_model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem_quant_model_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", "tags": [ - "process", - "actin", - "treadmilling", - "generate_network", - "simulate" + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" ], "category": "other", - "bng2_compatible": true, - "origin": "ai-generated", + "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem_quant/model_tofit.bngl", + "file": "model_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "process_autophagy_flux", - "name": "process autophagy flux", - "description": "Model: process_autophagy_flux.bngl", - "path": "Contributed/BNGPlayground_Examples/processes/processautophagyflux/process_autophagy_flux.bngl", - "file": "process_autophagy_flux.bngl", + "id": "problem16_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", "tags": [ - "process", - "autophagy", - "flux", - "phagophore", - "autophagosome", - "lysosome", - "autolysosome", - "cargo" + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" ], "category": "other", - "bng2_compatible": true, - "origin": "ai-generated", + "origin": "published", "visible": false, - "collectionId": null - }, - { - "id": "process_cell_adhesion_strength", - "name": "process cell adhesion strength", - "description": "Model: process_cell_adhesion_strength.bngl", - "path": "Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl", - "file": "process_cell_adhesion_strength.bngl", + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem16_3cat/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem16_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", "tags": [ - "process", - "cell", - "adhesion", - "strength", - "c1", - "c2", - "generate_network", - "simulate" + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" ], "category": "other", - "bng2_compatible": true, - "origin": "ai-generated", + "origin": "published", "visible": false, - "collectionId": null - }, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem16/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem32_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem32_3cat/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem32_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem32/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem4_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem4_3cat/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem4_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem4/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem64_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem64_3cat/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem64_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem64/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem8_3cat_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem8_3cat/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "problem8_model0_tofit", + "name": "model.bngl", + "description": "filename: model.bngl", + "tags": [ + "f", + "na", + "t", + "vchannel", + "nchannel", + "vcyt", + "ag_tot_0", + "ag_conc1", + "r_tot", + "syk_tot", + "ship1_tot", + "kon", + "koff", + "kase", + "pase", + "kp_syk", + "km_syk", + "kp_ship1", + "km_ship1", + "ksynth1", + "kdeg1", + "kpten", + "h_tot", + "kdegran", + "kdegx", + "k_xon", + "k_xoff", + "kp_x", + "km_x", + "molecules" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Likelihood/problem8/model0_tofit.bngl", + "file": "model0_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "process_actin_treadmilling", + "name": "process actin treadmilling", + "description": "Model: process_actin_treadmilling.bngl", + "tags": [ + "process", + "actin", + "treadmilling", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/processes/processactintreadmilling/process_actin_treadmilling.bngl", + "file": "process_actin_treadmilling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "process_autophagy_flux", + "name": "process autophagy flux", + "description": "Model: process_autophagy_flux.bngl", + "tags": [ + "process", + "autophagy", + "flux", + "phagophore", + "autophagosome", + "lysosome", + "autolysosome", + "cargo" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/processes/processautophagyflux/process_autophagy_flux.bngl", + "file": "process_autophagy_flux.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "process_cell_adhesion_strength", + "name": "process cell adhesion strength", + "description": "Model: process_cell_adhesion_strength.bngl", + "tags": [ + "process", + "cell", + "adhesion", + "strength", + "c1", + "c2", + "generate_network", + "simulate" + ], + "category": "other", + "origin": "ai-generated", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/processes/processcelladhesionstrength/process_cell_adhesion_strength.bngl", + "file": "process_cell_adhesion_strength.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, { "id": "process_kinetic_proofreading_tcr", "name": "process kinetic proofreading tcr", "description": "Model: process_kinetic_proofreading_tcr.bngl", - "path": "Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl", - "file": "process_kinetic_proofreading_tcr.bngl", "tags": [ "process", "kinetic", @@ -10261,17 +14699,29 @@ "l" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/processes/processkineticproofreadingtcr/process_kinetic_proofreading_tcr.bngl", + "file": "process_kinetic_proofreading_tcr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "process_quorum_sensing_switch", "name": "process quorum sensing switch", "description": "Model: process_quorum_sensing_switch.bngl", - "path": "Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl", - "file": "process_quorum_sensing_switch.bngl", "tags": [ "process", "quorum", @@ -10283,53 +14733,29 @@ "gene_light" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Providence-Warwick_RI-MA_Providence-Warwick_RI-MA", - "name": "Mallela 2022 - COVID-19 MSA Models - Providence-Warwick_RI-MA_Providence-Warwick_RI-MA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Providence-Warwick_RI-MA_Providence-Warwick_RI-MA.bngl", - "file": "Providence-Warwick_RI-MA_Providence-Warwick_RI-MA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Provo-Orem_UT_Provo-Orem_UT", - "name": "Mallela 2022 - COVID-19 MSA Models - Provo-Orem_UT_Provo-Orem_UT", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Provo-Orem_UT_Provo-Orem_UT.bngl", - "file": "Provo-Orem_UT_Provo-Orem_UT.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/processes/processquorumsensingswitch/process_quorum_sensing_switch.bngl", + "file": "process_quorum_sensing_switch.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "pt303", "name": "pt303", "description": "c = 0.20 /d t_1/2 = 3.5 d (inferred)", - "path": "PyBioNetGen/HIVdynamics/pt303/pt303.bngl", - "file": "pt303.bngl", "tags": [ "pt303", "counter", @@ -10341,17 +14767,29 @@ "lnv_tangent" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/HIVdynamics/pt303/pt303.bngl", + "file": "pt303.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "pt403", "name": "pt403", "description": "c = 0.23 /d t_1/2 = 3.0 d (inferred)", - "path": "PyBioNetGen/HIVdynamics/pt403/pt403.bngl", - "file": "pt403.bngl", "tags": [ "pt403", "counter", @@ -10363,17 +14801,29 @@ "lnv_tangent" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/HIVdynamics/pt403/pt403.bngl", + "file": "pt403.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "pt409", "name": "pt409", "description": "c = 0.39 /d t_1/2 = 1.8 d (inferred)", - "path": "PyBioNetGen/HIVdynamics/pt409/pt409.bngl", - "file": "pt409.bngl", "tags": [ "pt409", "counter", @@ -10385,53 +14835,75 @@ "lnv_tangent" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null - }, - { - "id": "Pueblo_CO_Pueblo_CO", - "name": "Mallela 2022 - COVID-19 MSA Models - Pueblo_CO_Pueblo_CO", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Pueblo_CO_Pueblo_CO.bngl", - "file": "Pueblo_CO_Pueblo_CO.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Punta_Gorda_FL_Punta_Gorda_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Punta_Gorda_FL_Punta_Gorda_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Punta_Gorda_FL_Punta_Gorda_FL.bngl", - "file": "Punta_Gorda_FL_Punta_Gorda_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "path": "Published/PyBioNetGen/HIVdynamics/pt409/pt409.bngl", + "file": "pt409.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "PyBNF_fitting_setup_190127_CHO_EGFR_forBNF", + "name": "PyBNF-fitting-setup", + "description": "BNGL model: 190127_CHO_EGFR_forBNF", + "tags": [ + "kdephosy1068_f", + "kdephosy1173_f", + "kphos_f", + "grb2_f", + "ratio_kdephosy1173", + "ratio_kphosy1173", + "offrate_f", + "onrate_f", + "kdephosy1068_pre", + "kdephosy1173_pre", + "kdephosyn_pre", + "kphosy1068_pre", + "kphosy1173_pre", + "kphosyn_pre", + "kdephosy1068", + "kdephosy1173", + "kdephosyn", + "kphosy1068", + "kphosy1173", + "kphosyn", + "ratio_kphos_receiver", + "molecules" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "other", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Salazar-Cavazos2019/PyBNF-fitting-setup/190127_CHO_EGFR_forBNF.bngl", + "file": "190127_CHO_EGFR_forBNF.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "quasi_equilibrium", "name": "quasi equilibrium", "description": "Quasi-equilibrium approximation", - "path": "Tutorials/General/quasiequilibrium/quasi_equilibrium.bngl", - "file": "quasi_equilibrium.bngl", "tags": [ "published", "toy models", @@ -10442,17 +14914,30 @@ "c" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials", + "native-tutorials" + ], + "path": "Tutorials/General/quasiequilibrium/quasi_equilibrium.bngl", + "file": "quasi_equilibrium.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "quorum-sensing-circuit", "name": "quorum sensing circuit", "description": "BioNetGen model: quorum sensing circuit", - "path": "Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl", - "file": "quorum-sensing-circuit.bngl", "tags": [ "quorum", "sensing", @@ -10463,17 +14948,501 @@ "protein" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/quorumsensingcircuit/quorum-sensing-circuit.bngl", + "file": "quorum-sensing-circuit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "rab_mon1ccz1_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/rab_mon1ccz1_ox.bngl", + "file": "rab_mon1ccz1_ox.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_mon1ccz1_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/pybnf_files/rab_mon1ccz1_ox.bngl", + "file": "rab_mon1ccz1_ox.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_rab5_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/rab_rab5_ox.bngl", + "file": "rab_rab5_ox.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_rab5_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/pybnf_files/rab_rab5_ox.bngl", + "file": "rab_rab5_ox.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_rab7_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/rab_rab7_ox.bngl", + "file": "rab_rab7_ox.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_rab7_ox", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/pybnf_files/rab_rab7_ox.bngl", + "file": "rab_rab7_ox.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_wt", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "kd_rabgef1__free", + "d_hill__free", + "d_threshold__free", + "k_deg__free", + "k_dephos__free", + "k_deub__free", + "k_extract__free", + "k_insert__free", + "k_recyc__free", + "k_synth__free", + "k_to_endo__free", + "kcat_rab5__free", + "kcat_rab7__free", + "kf_rab5_mon1__free", + "kf_rab5_rabep1__free", + "kf_ptyr_sh2__free", + "kr_kub_uim__free", + "kr_rab5_mon1__free", + "kr_rab5_rabep1__free", + "kr_ptyr_sh2__free", + "py_basal_coef__free", + "py_half_coef__free", + "py_hill_coef__free", + "py_scale_coef__free", + "r_hill__free", + "r_threshold__free", + "ub_basal_coef__free", + "ub_half_coef__free", + "ub_hill_coef__free", + "ub_scale_coef__free", + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/rab_wt.bngl", + "file": "rab_wt.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" + }, + { + "id": "rab_wt", + "name": "rab_mon1ccz1_ox.bngl", + "description": "filename:rab_mon1ccz1_ox.bngl", + "tags": [ + "rab5_expr", + "rab7_expr", + "mon1_expr", + "ccz1_expr", + "kf_mon1_ccz1", + "kr_mon1_ccz1", + "egf_conc_ngml", + "ub_hill_coef", + "ub_half_coef", + "ub_basal_coef", + "ub_scale_coef", + "py_hill_coef", + "py_half_coef", + "py_basal_coef", + "py_scale_coef", + "gtp_to_gdp_ratio", + "kcatgtp_rab5", + "k_gdp_gef_eff", + "kcatgtp_rab7", + "molecules", + "0" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019Rab/pybnf_files/rab_wt.bngl", + "file": "rab_wt.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "rab-gtpase-cycle", "name": "rab gtpase cycle", "description": "BioNetGen model: rab gtpase cycle", - "path": "Contributed/BNGPlayground_Examples/biology/rabgtpasecycle/rab-gtpase-cycle.bngl", - "file": "rab-gtpase-cycle.bngl", "tags": [ "rab", "gtpase", @@ -10483,35 +15452,29 @@ "effector" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Racine_WI_Racine_WI", - "name": "Mallela 2022 - COVID-19 MSA Models - Racine_WI_Racine_WI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Racine_WI_Racine_WI.bngl", - "file": "Racine_WI_Racine_WI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/rabgtpasecycle/rab-gtpase-cycle.bngl", + "file": "rab-gtpase-cycle.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "RAFi", "name": "RAFi", "description": "BioNetGen model: RAFi", - "path": "PyBioNetGen/core/RAFi/RAFi.bngl", - "file": "RAFi.bngl", "tags": [ "rafi", "r", @@ -10520,17 +15483,29 @@ "activity" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/RAFi/RAFi.bngl", + "file": "RAFi.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "RAFi_ground", "name": "RAFi ground", "description": "BioNetGen model: RAFi ground", - "path": "PyBioNetGen/core/RAFiground/RAFi_ground.bngl", - "file": "RAFi_ground.bngl", "tags": [ "rafi", "ground", @@ -10540,35 +15515,29 @@ "activity" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null - }, - { - "id": "Raleigh-Cary_NC_Raleigh-Cary_NC", - "name": "Mallela 2022 - COVID-19 MSA Models - Raleigh-Cary_NC_Raleigh-Cary_NC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Raleigh-Cary_NC_Raleigh-Cary_NC.bngl", - "file": "Raleigh-Cary_NC_Raleigh-Cary_NC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/PyBioNetGen/core/RAFiground/RAFi_ground.bngl", + "file": "RAFi_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "rankl-rank-signaling", "name": "rankl rank signaling", "description": "RANKL-RANK-OPG signaling in bone remodeling.", - "path": "Contributed/BNGPlayground_Examples/biology/ranklranksignaling/rankl-rank-signaling.bngl", - "file": "rankl-rank-signaling.bngl", "tags": [ "rankl", "rank", @@ -10578,17 +15547,30 @@ "traf6" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/ranklranksignaling/rankl-rank-signaling.bngl", + "file": "rankl-rank-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "ras-gef-gap-cycle", "name": "ras gef gap cycle", "description": "Ras-GEF-GAP cycle with explicit nucleotide exchange.", - "path": "Contributed/BNGPlayground_Examples/biology/rasgefgapcycle/ras-gef-gap-cycle.bngl", - "file": "ras-gef-gap-cycle.bngl", "tags": [ "ras", "gef", @@ -10600,35 +15582,30 @@ "v_gap" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Reading_PA_Reading_PA", - "name": "Mallela 2022 - COVID-19 MSA Models - Reading_PA_Reading_PA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Reading_PA_Reading_PA.bngl", - "file": "Reading_PA_Reading_PA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/rasgefgapcycle/ras-gef-gap-cycle.bngl", + "file": "ras-gef-gap-cycle.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "rec_dim", "name": "rec_dim", "description": "Ligand-receptor binding", - "path": "Contributed/BNGPlayground_Validation/recdim/rec_dim.bngl", - "file": "rec_dim.bngl", "tags": [ "validation", "rec", @@ -10639,17 +15616,29 @@ "simulate" ], "category": "validation", - "bng2_compatible": false, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/recdim/rec_dim.bngl", + "file": "rec_dim.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "rec_dim_comp", "name": "rec_dim_comp", "description": "name dimension volume contained_by", - "path": "Contributed/BNGPlayground_Validation/recdimcomp/rec_dim_comp.bngl", - "file": "rec_dim_comp.bngl", "tags": [ "validation", "rec", @@ -10663,17 +15652,56 @@ "simulate" ], "category": "validation", - "bng2_compatible": false, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/recdimcomp/rec_dim_comp.bngl", + "file": "rec_dim_comp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "receptor", + "name": "13-receptor", + "description": "A simple model", + "tags": [ + "ligand_ispresent", + "molecules", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/13-receptor/receptor.bngl", + "file": "receptor.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "receptor", "name": "receptor", "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", - "path": "PyBioNetGen/core/receptor/receptor.bngl", - "file": "receptor.bngl", "tags": [ "receptor", "l", @@ -10681,17 +15709,29 @@ "func" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/receptor/receptor.bngl", + "file": "receptor.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "receptor_nf", "name": "receptor nf", "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", - "path": "PyBioNetGen/core/receptornf/receptor_nf.bngl", - "file": "receptor_nf.bngl", "tags": [ "receptor", "nf", @@ -10699,17 +15739,29 @@ "r" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/receptornf/receptor_nf.bngl", + "file": "receptor_nf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "receptor_nf", "name": "receptor nf", "description": "A simple model of ligand/receptor binding and receptor phosphorylation.", - "path": "PyBioNetGen/tests/receptornf/receptor_nf.bngl", - "file": "receptor_nf.bngl", "tags": [ "receptor", "nf", @@ -10717,35 +15769,29 @@ "r" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null - }, - { - "id": "Reno_NV_Reno_NV", - "name": "Mallela 2022 - COVID-19 MSA Models - Reno_NV_Reno_NV", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Reno_NV_Reno_NV.bngl", - "file": "Reno_NV_Reno_NV.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/receptornf/receptor_nf.bngl", + "file": "receptor_nf.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Repressilator", "name": "Repressilator", "description": "Repressilator circuit", - "path": "Tutorials/NativeTutorials/Repressilator/Repressilator.bngl", - "file": "Repressilator.bngl", "tags": [ "published", "tutorial", @@ -10761,17 +15807,31 @@ "pci" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "synbio", + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/Repressilator/Repressilator.bngl", + "file": "Repressilator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "repressilator-oscillator", "name": "repressilator oscillator", "description": "BioNetGen model: repressilator oscillator", - "path": "Contributed/BNGPlayground_Examples/biology/repressilatoroscillator/repressilator-oscillator.bngl", - "file": "repressilator-oscillator.bngl", "tags": [ "repressilator", "oscillator", @@ -10785,17 +15845,29 @@ "proteinb" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/repressilatoroscillator/repressilator-oscillator.bngl", + "file": "repressilator-oscillator.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "retinoic-acid-signaling", "name": "retinoic acid signaling", "description": "BioNetGen model: retinoic acid signaling", - "path": "Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling/retinoic-acid-signaling.bngl", - "file": "retinoic-acid-signaling.bngl", "tags": [ "retinoic", "acid", @@ -10806,17 +15878,30 @@ "targetgene" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/retinoicacidsignaling/retinoic-acid-signaling.bngl", + "file": "retinoic-acid-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "rho-gtpase-actin-cytoskeleton", "name": "rho gtpase actin cytoskeleton", "description": "RhoA-GTPase regulation of the actin cytoskeleton.", - "path": "Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton.bngl", - "file": "rho-gtpase-actin-cytoskeleton.bngl", "tags": [ "rho", "gtpase", @@ -10828,161 +15913,29 @@ "cofilin" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Richmond_VA_Richmond_VA", - "name": "Mallela 2022 - COVID-19 MSA Models - Richmond_VA_Richmond_VA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Richmond_VA_Richmond_VA.bngl", - "file": "Richmond_VA_Richmond_VA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Riverside-San_Bernardino-Ontario_CA_Riverside-San_Bernardino-Ontario_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Riverside-San_Bernardino-Ontario_CA_Riverside-San_Bernardino-Ontario_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Riverside-San_Bernardino-Ontario_CA_Riverside-San_Bernardino-Ontario_CA.bngl", - "file": "Riverside-San_Bernardino-Ontario_CA_Riverside-San_Bernardino-Ontario_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Roanoke_VA_Roanoke_VA", - "name": "Mallela 2022 - COVID-19 MSA Models - Roanoke_VA_Roanoke_VA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Roanoke_VA_Roanoke_VA.bngl", - "file": "Roanoke_VA_Roanoke_VA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Rochester_MN_Rochester_MN", - "name": "Mallela 2022 - COVID-19 MSA Models - Rochester_MN_Rochester_MN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Rochester_MN_Rochester_MN.bngl", - "file": "Rochester_MN_Rochester_MN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Rochester_NY_Rochester_NY", - "name": "Mallela 2022 - COVID-19 MSA Models - Rochester_NY_Rochester_NY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Rochester_NY_Rochester_NY.bngl", - "file": "Rochester_NY_Rochester_NY.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Rockford_IL_Rockford_IL", - "name": "Mallela 2022 - COVID-19 MSA Models - Rockford_IL_Rockford_IL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Rockford_IL_Rockford_IL.bngl", - "file": "Rockford_IL_Rockford_IL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Rocky_Mount_NC_Rocky_Mount_NC", - "name": "Mallela 2022 - COVID-19 MSA Models - Rocky_Mount_NC_Rocky_Mount_NC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Rocky_Mount_NC_Rocky_Mount_NC.bngl", - "file": "Rocky_Mount_NC_Rocky_Mount_NC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Rome_GA_Rome_GA", - "name": "Mallela 2022 - COVID-19 MSA Models - Rome_GA_Rome_GA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Rome_GA_Rome_GA.bngl", - "file": "Rome_GA_Rome_GA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/rhogtpaseactincytoskeleton/rho-gtpase-actin-cytoskeleton.bngl", + "file": "rho-gtpase-actin-cytoskeleton.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Rule_based_egfr_compart", "name": "Rule based egfr compart", "description": "Compartmental EGFR model", - "path": "Published/Rulebasedegfrcompart/Rule_based_egfr_compart.bngl", - "file": "Rule_based_egfr_compart.bngl", "tags": [ "published", "rule", @@ -10995,17 +15948,29 @@ "generate_network" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "signaling" + ], + "path": "Published/Rulebasedegfrcompart/Rule_based_egfr_compart.bngl", + "file": "Rule_based_egfr_compart.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Rule_based_egfr_tutorial", "name": "Faeder 2009", "description": "EGFR signaling", - "path": "Published/Rulebasedegfrtutorial/Rule_based_egfr_tutorial.bngl", - "file": "Rule_based_egfr_tutorial.bngl", "tags": [ "published", "rule", @@ -11018,17 +15983,29 @@ "generate_network" ], "category": "signaling", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer" + ], + "path": "Published/Rulebasedegfrtutorial/Rule_based_egfr_tutorial.bngl", + "file": "Rule_based_egfr_tutorial.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Rule_based_Ran_transport", "name": "Rule based Ran transport", "description": "Nuclear Ran transport", - "path": "Published/RulebasedRantransport/Rule_based_Ran_transport.bngl", - "file": "Rule_based_Ran_transport.bngl", "tags": [ "published", "rule", @@ -11040,17 +16017,29 @@ "generate_network" ], "category": "regulation", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "path": "Published/RulebasedRantransport/Rule_based_Ran_transport.bngl", + "file": "Rule_based_Ran_transport.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Rule_based_Ran_transport_draft", "name": "Rule based Ran transport draft", "description": "Ran transport (draft)", - "path": "Published/RulebasedRantransportdraft/Rule_based_Ran_transport_draft.bngl", - "file": "Rule_based_Ran_transport_draft.bngl", "tags": [ "published", "rule", @@ -11063,1282 +16052,144 @@ "generate_network" ], "category": "regulation", - "bng2_compatible": false, - "origin": "published", - "visible": false, - "collectionId": null - }, - { - "id": "Sacramento-Roseville-Folsom_CA_Sacramento-Roseville-Folsom_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Sacramento-Roseville-Folsom_CA_Sacramento-Roseville-Folsom_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Sacramento-Roseville-Folsom_CA_Sacramento-Roseville-Folsom_CA.bngl", - "file": "Sacramento-Roseville-Folsom_CA_Sacramento-Roseville-Folsom_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Saginaw_MI_Saginaw_MI", - "name": "Mallela 2022 - COVID-19 MSA Models - Saginaw_MI_Saginaw_MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Saginaw_MI_Saginaw_MI.bngl", - "file": "Saginaw_MI_Saginaw_MI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Salem_OR_Salem_OR", - "name": "Mallela 2022 - COVID-19 MSA Models - Salem_OR_Salem_OR", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Salem_OR_Salem_OR.bngl", - "file": "Salem_OR_Salem_OR.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Salinas_CA_Salinas_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Salinas_CA_Salinas_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Salinas_CA_Salinas_CA.bngl", - "file": "Salinas_CA_Salinas_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Salisbury_MD-DE_Salisbury_MD-DE", - "name": "Mallela 2022 - COVID-19 MSA Models - Salisbury_MD-DE_Salisbury_MD-DE", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Salisbury_MD-DE_Salisbury_MD-DE.bngl", - "file": "Salisbury_MD-DE_Salisbury_MD-DE.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Salt_Lake_City_UT_Salt_Lake_City_UT", - "name": "Mallela 2022 - COVID-19 MSA Models - Salt_Lake_City_UT_Salt_Lake_City_UT", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Salt_Lake_City_UT_Salt_Lake_City_UT.bngl", - "file": "Salt_Lake_City_UT_Salt_Lake_City_UT.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "San_Antonio-New_Braunfels_TX_San_Antonio-New_Braunfels_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - San_Antonio-New_Braunfels_TX_San_Antonio-New_Braunfels_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/San_Antonio-New_Braunfels_TX_San_Antonio-New_Braunfels_TX.bngl", - "file": "San_Antonio-New_Braunfels_TX_San_Antonio-New_Braunfels_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "San_Diego-Chula_Vista-Carlsbad_CA_San_Diego-Chula_Vista-Carlsbad_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - San_Diego-Chula_Vista-Carlsbad_CA_San_Diego-Chula_Vista-Carlsbad_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/San_Diego-Chula_Vista-Carlsbad_CA_San_Diego-Chula_Vista-Carlsbad_CA.bngl", - "file": "San_Diego-Chula_Vista-Carlsbad_CA_San_Diego-Chula_Vista-Carlsbad_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "San_Francisco-Oakland-Berkeley_CA_San_Francisco-Oakland-Berkeley_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - San_Francisco-Oakland-Berkeley_CA_San_Francisco-Oakland-Berkeley_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/San_Francisco-Oakland-Berkeley_CA_San_Francisco-Oakland-Berkeley_CA.bngl", - "file": "San_Francisco-Oakland-Berkeley_CA_San_Francisco-Oakland-Berkeley_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "San_Jose-Sunnyvale-Santa_Clara_CA_San_Jose-Sunnyvale-Santa_Clara_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - San_Jose-Sunnyvale-Santa_Clara_CA_San_Jose-Sunnyvale-Santa_Clara_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/San_Jose-Sunnyvale-Santa_Clara_CA_San_Jose-Sunnyvale-Santa_Clara_CA.bngl", - "file": "San_Jose-Sunnyvale-Santa_Clara_CA_San_Jose-Sunnyvale-Santa_Clara_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "San_Luis_Obispo-Paso_Robles_CA_San_Luis_Obispo-Paso_Robles_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - San_Luis_Obispo-Paso_Robles_CA_San_Luis_Obispo-Paso_Robles_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/San_Luis_Obispo-Paso_Robles_CA_San_Luis_Obispo-Paso_Robles_CA.bngl", - "file": "San_Luis_Obispo-Paso_Robles_CA_San_Luis_Obispo-Paso_Robles_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Santa_Maria-Santa_Barbara_CA_Santa_Maria-Santa_Barbara_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Santa_Maria-Santa_Barbara_CA_Santa_Maria-Santa_Barbara_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Santa_Maria-Santa_Barbara_CA_Santa_Maria-Santa_Barbara_CA.bngl", - "file": "Santa_Maria-Santa_Barbara_CA_Santa_Maria-Santa_Barbara_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Santa_Rosa-Petaluma_CA_Santa_Rosa-Petaluma_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Santa_Rosa-Petaluma_CA_Santa_Rosa-Petaluma_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Santa_Rosa-Petaluma_CA_Santa_Rosa-Petaluma_CA.bngl", - "file": "Santa_Rosa-Petaluma_CA_Santa_Rosa-Petaluma_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Savannah_GA_Savannah_GA", - "name": "Mallela 2022 - COVID-19 MSA Models - Savannah_GA_Savannah_GA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Savannah_GA_Savannah_GA.bngl", - "file": "Savannah_GA_Savannah_GA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Scranton_Wilkes-Barre_PA_Scranton_Wilkes-Barre_PA", - "name": "Mallela 2022 - COVID-19 MSA Models - Scranton_Wilkes-Barre_PA_Scranton_Wilkes-Barre_PA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Scranton_Wilkes-Barre_PA_Scranton_Wilkes-Barre_PA.bngl", - "file": "Scranton_Wilkes-Barre_PA_Scranton_Wilkes-Barre_PA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Scranton-Wilkes-Barre_PA_Scranton-Wilkes-Barre_PA", - "name": "Mallela 2022 - COVID-19 MSA Models - Scranton-Wilkes-Barre_PA_Scranton-Wilkes-Barre_PA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Scranton-Wilkes-Barre_PA_Scranton-Wilkes-Barre_PA.bngl", - "file": "Scranton-Wilkes-Barre_PA_Scranton-Wilkes-Barre_PA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Seattle-Tacoma-Bellevue_WA_Seattle-Tacoma-Bellevue_WA", - "name": "Mallela 2022 - COVID-19 MSA Models - Seattle-Tacoma-Bellevue_WA_Seattle-Tacoma-Bellevue_WA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Seattle-Tacoma-Bellevue_WA_Seattle-Tacoma-Bellevue_WA.bngl", - "file": "Seattle-Tacoma-Bellevue_WA_Seattle-Tacoma-Bellevue_WA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "SHP2_base_model", - "name": "SHP2_base_model", - "description": "Base model of Shp2 regulation", - "path": "Contributed/BNGPlayground_Validation/SHP2basemodel/SHP2_base_model.bngl", - "file": "SHP2_base_model.bngl", - "tags": [ - "validation", - "shp2", - "base", - "model", - "r", - "s", - "exclude_reactants" - ], - "category": "validation", - "bng2_compatible": true, - "origin": "test-case", - "visible": true, - "collectionId": null - }, - { - "id": "shp2-phosphatase-regulation", - "name": "shp2 phosphatase regulation", - "description": "SHP2 phosphatase regulation via autoinhibition and SH2 binding.", - "path": "Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation.bngl", - "file": "shp2-phosphatase-regulation.bngl", - "tags": [ - "shp2", - "phosphatase", - "regulation", - "rtk", - "substrate", - "v_dephos" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "ai-generated", - "visible": false, - "collectionId": null - }, - { - "id": "Shreveport-Bossier_City_LA_Shreveport-Bossier_City_LA", - "name": "Mallela 2022 - COVID-19 MSA Models - Shreveport-Bossier_City_LA_Shreveport-Bossier_City_LA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Shreveport-Bossier_City_LA_Shreveport-Bossier_City_LA.bngl", - "file": "Shreveport-Bossier_City_LA_Shreveport-Bossier_City_LA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "SI_files_Alabama_Alabama", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Alabama_Alabama", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Alabama_Alabama.bngl", - "file": "SI_files_Alabama_Alabama.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Alaska_Alaska", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Alaska_Alaska", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Alaska_Alaska.bngl", - "file": "SI_files_Alaska_Alaska.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Arizona_Arizona", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Arizona_Arizona", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Arizona_Arizona.bngl", - "file": "SI_files_Arizona_Arizona.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Arkansas_Arkansas", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Arkansas_Arkansas", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Arkansas_Arkansas.bngl", - "file": "SI_files_Arkansas_Arkansas.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_California_California", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_California_California", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_California_California.bngl", - "file": "SI_files_California_California.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Colorado_Colorado", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Colorado_Colorado", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Colorado_Colorado.bngl", - "file": "SI_files_Colorado_Colorado.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Connecticut_Connecticut", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Connecticut_Connecticut", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Connecticut_Connecticut.bngl", - "file": "SI_files_Connecticut_Connecticut.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Delaware_Delaware", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Delaware_Delaware", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Delaware_Delaware.bngl", - "file": "SI_files_Delaware_Delaware.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Florida_Florida", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Florida_Florida", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Florida_Florida.bngl", - "file": "SI_files_Florida_Florida.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Georgia_Georgia", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Georgia_Georgia", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Georgia_Georgia.bngl", - "file": "SI_files_Georgia_Georgia.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Hawaii_Hawaii", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Hawaii_Hawaii", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Hawaii_Hawaii.bngl", - "file": "SI_files_Hawaii_Hawaii.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Idaho_Idaho", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Idaho_Idaho", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Idaho_Idaho.bngl", - "file": "SI_files_Idaho_Idaho.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Illinois_Illinois", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Illinois_Illinois", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Illinois_Illinois.bngl", - "file": "SI_files_Illinois_Illinois.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Indiana_Indiana", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Indiana_Indiana", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Indiana_Indiana.bngl", - "file": "SI_files_Indiana_Indiana.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Iowa_Iowa", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Iowa_Iowa", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Iowa_Iowa.bngl", - "file": "SI_files_Iowa_Iowa.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Kansas_Kansas", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Kansas_Kansas", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Kansas_Kansas.bngl", - "file": "SI_files_Kansas_Kansas.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Kentucky_Kentucky", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Kentucky_Kentucky", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Kentucky_Kentucky.bngl", - "file": "SI_files_Kentucky_Kentucky.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Louisiana_Louisiana", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Louisiana_Louisiana", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Louisiana_Louisiana.bngl", - "file": "SI_files_Louisiana_Louisiana.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Maine_Maine", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Maine_Maine", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Maine_Maine.bngl", - "file": "SI_files_Maine_Maine.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Maryland_Maryland", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Maryland_Maryland", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Maryland_Maryland.bngl", - "file": "SI_files_Maryland_Maryland.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Massachusetts_Massachusetts", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Massachusetts_Massachusetts", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Massachusetts_Massachusetts.bngl", - "file": "SI_files_Massachusetts_Massachusetts.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Michigan_Michigan", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Michigan_Michigan", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Michigan_Michigan.bngl", - "file": "SI_files_Michigan_Michigan.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Minnesota_Minnesota", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Minnesota_Minnesota", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Minnesota_Minnesota.bngl", - "file": "SI_files_Minnesota_Minnesota.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Mississippi_Mississippi", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Mississippi_Mississippi", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Mississippi_Mississippi.bngl", - "file": "SI_files_Mississippi_Mississippi.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Missouri_Missouri", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Missouri_Missouri", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Missouri_Missouri.bngl", - "file": "SI_files_Missouri_Missouri.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Montana_Montana", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Montana_Montana", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Montana_Montana.bngl", - "file": "SI_files_Montana_Montana.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Nebraska_Nebraska", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Nebraska_Nebraska", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Nebraska_Nebraska.bngl", - "file": "SI_files_Nebraska_Nebraska.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Nevada_Nevada", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Nevada_Nevada", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Nevada_Nevada.bngl", - "file": "SI_files_Nevada_Nevada.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_NewHampshire_NewHampshire", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_NewHampshire_NewHampshire", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_NewHampshire_NewHampshire.bngl", - "file": "SI_files_NewHampshire_NewHampshire.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_NewJersey_NewJersey", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_NewJersey_NewJersey", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_NewJersey_NewJersey.bngl", - "file": "SI_files_NewJersey_NewJersey.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_NewMexico_NewMexico", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_NewMexico_NewMexico", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_NewMexico_NewMexico.bngl", - "file": "SI_files_NewMexico_NewMexico.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_NewYork_NewYork", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_NewYork_NewYork", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_NewYork_NewYork.bngl", - "file": "SI_files_NewYork_NewYork.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_NorthCarolina_NorthCarolina", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_NorthCarolina_NorthCarolina", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_NorthCarolina_NorthCarolina.bngl", - "file": "SI_files_NorthCarolina_NorthCarolina.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_NorthDakota_NorthDakota", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_NorthDakota_NorthDakota", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_NorthDakota_NorthDakota.bngl", - "file": "SI_files_NorthDakota_NorthDakota.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Ohio_Ohio", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Ohio_Ohio", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Ohio_Ohio.bngl", - "file": "SI_files_Ohio_Ohio.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Oklahoma_Oklahoma", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Oklahoma_Oklahoma", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Oklahoma_Oklahoma.bngl", - "file": "SI_files_Oklahoma_Oklahoma.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Oregon_Oregon", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Oregon_Oregon", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Oregon_Oregon.bngl", - "file": "SI_files_Oregon_Oregon.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Pennsylvania_Pennsylvania", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Pennsylvania_Pennsylvania", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Pennsylvania_Pennsylvania.bngl", - "file": "SI_files_Pennsylvania_Pennsylvania.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_RhodeIsland_RhodeIsland", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_RhodeIsland_RhodeIsland", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_RhodeIsland_RhodeIsland.bngl", - "file": "SI_files_RhodeIsland_RhodeIsland.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_SouthCarolina_SouthCarolina", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_SouthCarolina_SouthCarolina", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_SouthCarolina_SouthCarolina.bngl", - "file": "SI_files_SouthCarolina_SouthCarolina.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_SouthDakota_SouthDakota", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_SouthDakota_SouthDakota", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_SouthDakota_SouthDakota.bngl", - "file": "SI_files_SouthDakota_SouthDakota.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Tennessee_Tennessee", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Tennessee_Tennessee", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Tennessee_Tennessee.bngl", - "file": "SI_files_Tennessee_Tennessee.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Texas_Texas", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Texas_Texas", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Texas_Texas.bngl", - "file": "SI_files_Texas_Texas.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Utah_Utah", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Utah_Utah", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Utah_Utah.bngl", - "file": "SI_files_Utah_Utah.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Vermont_Vermont", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Vermont_Vermont", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Vermont_Vermont.bngl", - "file": "SI_files_Vermont_Vermont.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SI_files_Virginia_Virginia", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Virginia_Virginia", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Virginia_Virginia.bngl", - "file": "SI_files_Virginia_Virginia.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": "Mallela2021_States" + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "path": "Published/RulebasedRantransportdraft/Rule_based_Ran_transport_draft.bngl", + "file": "Rule_based_Ran_transport_draft.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "SI_files_Washington_Washington", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Washington_Washington", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Washington_Washington.bngl", - "file": "SI_files_Washington_Washington.bngl", + "id": "Scaff-22_ground", + "name": "18-mapk", + "description": "For \"ground truth\" model, use median values such that hierarchy H1 occurs, as shown in Table 3.", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "signaling" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "signaling", "origin": "published", "visible": false, - "collectionId": "Mallela2021_States" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/18-mapk/Scaff-22_ground.bngl", + "file": "Scaff-22_ground.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "SI_files_WestVirginia_WestVirginia", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_WestVirginia_WestVirginia", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_WestVirginia_WestVirginia.bngl", - "file": "SI_files_WestVirginia_WestVirginia.bngl", + "id": "Scaff-22_tofit", + "name": "18-mapk", + "description": "For \"ground truth\" model, use median values such that hierarchy H1 occurs, as shown in Table 3.", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "signaling" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "signaling", "origin": "published", "visible": false, - "collectionId": "Mallela2021_States" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [], + "path": "Published/Mitra2019/18-mapk/Scaff-22_tofit.bngl", + "file": "Scaff-22_tofit.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "SI_files_Wisconsin_Wisconsin", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Wisconsin_Wisconsin", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Wisconsin_Wisconsin.bngl", - "file": "SI_files_Wisconsin_Wisconsin.bngl", + "id": "SHP2_base_model", + "name": "SHP2_base_model", + "description": "Base model of Shp2 regulation", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "validation", + "shp2", + "base", + "model", + "r", + "s", + "exclude_reactants" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_States" + "category": "validation", + "origin": "test-case", + "visible": true, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/SHP2basemodel/SHP2_base_model.bngl", + "file": "SHP2_base_model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "SI_files_Wyoming_Wyoming", - "name": "Mallela 2021 - COVID-19 State-Level Models - SI_files_Wyoming_Wyoming", - "description": "Parameter-fit COVID-19 epidemiological models for all 50 US states.", - "path": "Published/Mallela2021/SI_files_Wyoming_Wyoming.bngl", - "file": "SI_files_Wyoming_Wyoming.bngl", + "id": "shp2-phosphatase-regulation", + "name": "shp2 phosphatase regulation", + "description": "SHP2 phosphatase regulation via autoinhibition and SH2 binding.", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "shp2", + "phosphatase", + "regulation", + "rtk", + "substrate", + "v_dephos" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, - "collectionId": "Mallela2021_States" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/shp2phosphataseregulation/shp2-phosphatase-regulation.bngl", + "file": "shp2-phosphatase-regulation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "signal-amplification-cascade", "name": "signal amplification cascade", "description": "BioNetGen model: signal amplification cascade", - "path": "Contributed/BNGPlayground_Examples/biology/signalamplificationcascade/signal-amplification-cascade.bngl", - "file": "signal-amplification-cascade.bngl", "tags": [ "signal", "amplification", @@ -12349,17 +16200,29 @@ "messenger" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/signalamplificationcascade/signal-amplification-cascade.bngl", + "file": "signal-amplification-cascade.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "simple", "name": "simple", "description": "Simple binding model", - "path": "Tutorials/General/simple/simple.bngl", - "file": "simple.bngl", "tags": [ "published", "tutorials", @@ -12370,17 +16233,29 @@ "trash" ], "category": "tutorial", - "bng2_compatible": false, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "path": "Tutorials/General/simple/simple.bngl", + "file": "simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Simple", "name": "Simple", "description": "An example from a real application", - "path": "PyBioNetGen/tests/Simple/Simple.bngl", - "file": "Simple.bngl", "tags": [ "simple", "setoption", @@ -12389,17 +16264,29 @@ "h" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/Simple/Simple.bngl", + "file": "Simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Simple_AddActions", "name": "Simple AddActions", "description": "An example from a real application", - "path": "PyBioNetGen/tests/SimpleAddActions/Simple_AddActions.bngl", - "file": "Simple_AddActions.bngl", "tags": [ "simple", "addactions", @@ -12409,17 +16296,29 @@ "h" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/SimpleAddActions/Simple_AddActions.bngl", + "file": "Simple_AddActions.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Simple_Answer", "name": "Simple Answer", "description": "An example from a real application", - "path": "PyBioNetGen/tests/SimpleAnswer/Simple_Answer.bngl", - "file": "Simple_Answer.bngl", "tags": [ "simple", "answer", @@ -12429,17 +16328,29 @@ "h" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/SimpleAnswer/Simple_Answer.bngl", + "file": "Simple_Answer.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Simple_GenOnly", "name": "Simple GenOnly", "description": "An example from a real application", - "path": "PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly.bngl", - "file": "Simple_GenOnly.bngl", "tags": [ "simple", "genonly", @@ -12449,17 +16360,29 @@ "h" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/SimpleGenOnly/Simple_GenOnly.bngl", + "file": "Simple_GenOnly.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "simple_nf_seed", "name": "simple nf seed", "description": "BioNetGen model: simple nf seed", - "path": "PyBioNetGen/tests/simplenfseed/simple_nf_seed.bngl", - "file": "simple_nf_seed.bngl", "tags": [ "simple", "nf", @@ -12470,34 +16393,58 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/simplenfseed/simple_nf_seed.bngl", + "file": "simple_nf_seed.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "simple_nfsim_test", "name": "simple_nfsim_test", "description": "Runtime-only BNGL model migrated from public/models: simple_nfsim_test", - "path": "Contributed/BNGPlayground_PublicRuntime/simplenfsimtest/simple_nfsim_test.bngl", - "file": "simple_nfsim_test.bngl", "tags": [ "simple", "nfsim", "test" ], "category": "other", - "bng2_compatible": true, "origin": "contributed", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "path": "Tutorials/simplenfsimtest/simple_nfsim_test.bngl", + "file": "simple_nfsim_test.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Simple_nogen", "name": "Simple nogen", "description": "An example from a real application", - "path": "PyBioNetGen/tests/Simplenogen/Simple_nogen.bngl", - "file": "Simple_nogen.bngl", "tags": [ "simple", "nogen", @@ -12506,17 +16453,29 @@ "h" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/Simplenogen/Simple_nogen.bngl", + "file": "Simple_nogen.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "simple_sbml_import", "name": "simple_sbml_import", "description": "SBML import test", - "path": "Contributed/BNGPlayground_Validation/simplesbmlimport/simple_sbml_import.bngl", - "file": "simple_sbml_import.bngl", "tags": [ "validation", "simple", @@ -12527,17 +16486,29 @@ "simulate" ], "category": "validation", - "bng2_compatible": false, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/simplesbmlimport/simple_sbml_import.bngl", + "file": "simple_sbml_import.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "simple_system", "name": "simple_system", "description": "Simple binding system", - "path": "Contributed/BNGPlayground_Validation/simplesystem/simple_system.bngl", - "file": "simple_system.bngl", "tags": [ "validation", "simple", @@ -12546,17 +16517,29 @@ "y" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/simplesystem/simple_system.bngl", + "file": "simple_system.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "simple-dimerization", "name": "simple dimerization", "description": "BioNetGen model: simple dimerization", - "path": "Contributed/BNGPlayground_Examples/biology/simpledimerization/simple-dimerization.bngl", - "file": "simple-dimerization.bngl", "tags": [ "simple", "dimerization", @@ -12566,70 +16549,59 @@ "simulate" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Sioux_City_IA-NE-SD_Sioux_City_IA-NE-SD", - "name": "Mallela 2022 - COVID-19 MSA Models - Sioux_City_IA-NE-SD_Sioux_City_IA-NE-SD", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Sioux_City_IA-NE-SD_Sioux_City_IA-NE-SD.bngl", - "file": "Sioux_City_IA-NE-SD_Sioux_City_IA-NE-SD.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Sioux_Falls_SD_Sioux_Falls_SD", - "name": "Mallela 2022 - COVID-19 MSA Models - Sioux_Falls_SD_Sioux_Falls_SD", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Sioux_Falls_SD_Sioux_Falls_SD.bngl", - "file": "Sioux_Falls_SD_Sioux_Falls_SD.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/simpledimerization/simple-dimerization.bngl", + "file": "simple-dimerization.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "SIR", "name": "SIR", "description": "BioNetGen model: SIR", - "path": "Tutorials/NativeTutorials/SIR/SIR.bngl", - "file": "SIR.bngl", "tags": [ "sir", "saveconcentrations", "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/SIR/SIR.bngl", + "file": "SIR.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "sir-epidemic-model", "name": "sir epidemic model", "description": "BioNetGen model: sir epidemic model", - "path": "Contributed/BNGPlayground_Examples/biology/sirepidemicmodel/sir-epidemic-model.bngl", - "file": "sir-epidemic-model.bngl", "tags": [ "sir", "epidemic", @@ -12639,17 +16611,31 @@ "simulate" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "tutorials", + "test-models" + ], + "path": "Examples/biology/sirepidemicmodel/sir-epidemic-model.bngl", + "file": "sir-epidemic-model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "smad-tgf-beta-signaling", "name": "smad tgf beta signaling", "description": "BioNetGen model: smad tgf beta signaling", - "path": "Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling.bngl", - "file": "smad-tgf-beta-signaling.bngl", "tags": [ "smad", "tgf", @@ -12661,266 +16647,169 @@ "smad4" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/smadtgfbetasignaling/smad-tgf-beta-signaling.bngl", + "file": "smad-tgf-beta-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "sonic-hedgehog-gradient", "name": "sonic hedgehog gradient", "description": "Sonic Hedgehog (Shh) morphogen gradient formation.", - "path": "Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient.bngl", - "file": "sonic-hedgehog-gradient.bngl", "tags": [ "sonic", - "hedgehog", - "gradient", - "shh", - "ptc1", - "v_prod" - ], - "category": "signaling", - "bng2_compatible": true, - "origin": "ai-generated", - "visible": false, - "collectionId": null - }, - { - "id": "South_Bend-Mishawaka_IN-MI_South_Bend-Mishawaka_IN-MI", - "name": "Mallela 2022 - COVID-19 MSA Models - South_Bend-Mishawaka_IN-MI_South_Bend-Mishawaka_IN-MI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/South_Bend-Mishawaka_IN-MI_South_Bend-Mishawaka_IN-MI.bngl", - "file": "South_Bend-Mishawaka_IN-MI_South_Bend-Mishawaka_IN-MI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "sp_fourier_synthesizer", - "name": "sp fourier synthesizer", - "description": "Fourier Series Synthesizer in BNGL", - "path": "Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl", - "file": "sp_fourier_synthesizer.bngl", - "tags": [ - "sp", - "fourier", - "synthesizer", - "s1", - "s3", - "s5", - "s7", - "s9", - "wave", - "c1" - ], - "category": "computer-science", - "bng2_compatible": true, - "origin": "ai-generated", - "visible": false, - "collectionId": null - }, - { - "id": "sp_image_convolution", - "name": "sp image convolution", - "description": "Image Convolution Filter in BNGL", - "path": "Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution/sp_image_convolution.bngl", - "file": "sp_image_convolution.bngl", - "tags": [ - "sp", - "image", - "convolution", - "px", - "ex", - "sink" - ], - "category": "computer-science", - "bng2_compatible": true, - "origin": "ai-generated", - "visible": false, - "collectionId": null - }, - { - "id": "sp_kalman_filter", - "name": "sp kalman filter", - "description": "Kalman Filter in BNGL", - "path": "Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter/sp_kalman_filter.bngl", - "file": "sp_kalman_filter.bngl", - "tags": [ - "sp", - "kalman", - "filter", - "truex", - "obs", - "estx", - "estv", - "variance", - "innovation" - ], - "category": "computer-science", - "bng2_compatible": true, - "origin": "ai-generated", - "visible": false, - "collectionId": null - }, - { - "id": "Spartanburg_SC_Spartanburg_SC", - "name": "Mallela 2022 - COVID-19 MSA Models - Spartanburg_SC_Spartanburg_SC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Spartanburg_SC_Spartanburg_SC.bngl", - "file": "Spartanburg_SC_Spartanburg_SC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Spokane-Spokane_Valley_WA_Spokane-Spokane_Valley_WA", - "name": "Mallela 2022 - COVID-19 MSA Models - Spokane-Spokane_Valley_WA_Spokane-Spokane_Valley_WA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Spokane-Spokane_Valley_WA_Spokane-Spokane_Valley_WA.bngl", - "file": "Spokane-Spokane_Valley_WA_Spokane-Spokane_Valley_WA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Springfield_IL_Springfield_IL", - "name": "Mallela 2022 - COVID-19 MSA Models - Springfield_IL_Springfield_IL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Springfield_IL_Springfield_IL.bngl", - "file": "Springfield_IL_Springfield_IL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Springfield_MA_Springfield_MA", - "name": "Mallela 2022 - COVID-19 MSA Models - Springfield_MA_Springfield_MA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Springfield_MA_Springfield_MA.bngl", - "file": "Springfield_MA_Springfield_MA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "St._Cloud_MN_St._Cloud_MN", - "name": "Mallela 2022 - COVID-19 MSA Models - St._Cloud_MN_St._Cloud_MN", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/St._Cloud_MN_St._Cloud_MN.bngl", - "file": "St._Cloud_MN_St._Cloud_MN.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "hedgehog", + "gradient", + "shh", + "ptc1", + "v_prod" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", + "category": "signaling", + "origin": "ai-generated", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/sonichedgehoggradient/sonic-hedgehog-gradient.bngl", + "file": "sonic-hedgehog-gradient.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "St._George_UT_St._George_UT", - "name": "Mallela 2022 - COVID-19 MSA Models - St._George_UT_St._George_UT", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/St._George_UT_St._George_UT.bngl", - "file": "St._George_UT_St._George_UT.bngl", + "id": "sp_fourier_synthesizer", + "name": "sp fourier synthesizer", + "description": "Fourier Series Synthesizer in BNGL", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "sp", + "fourier", + "synthesizer", + "s1", + "s3", + "s5", + "s7", + "s9", + "wave", + "c1" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", + "category": "computer-science", + "origin": "ai-generated", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/signal-processing/spfouriersynthesizer/sp_fourier_synthesizer.bngl", + "file": "sp_fourier_synthesizer.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "St._Joseph_MO-KS_St._Joseph_MO-KS", - "name": "Mallela 2022 - COVID-19 MSA Models - St._Joseph_MO-KS_St._Joseph_MO-KS", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/St._Joseph_MO-KS_St._Joseph_MO-KS.bngl", - "file": "St._Joseph_MO-KS_St._Joseph_MO-KS.bngl", + "id": "sp_image_convolution", + "name": "sp image convolution", + "description": "Image Convolution Filter in BNGL", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "sp", + "image", + "convolution", + "px", + "ex", + "sink" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", + "category": "computer-science", + "origin": "ai-generated", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/signal-processing/spimageconvolution/sp_image_convolution.bngl", + "file": "sp_image_convolution.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { - "id": "St._Louis_MO-IL_St._Louis_MO-IL", - "name": "Mallela 2022 - COVID-19 MSA Models - St._Louis_MO-IL_St._Louis_MO-IL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/St._Louis_MO-IL_St._Louis_MO-IL.bngl", - "file": "St._Louis_MO-IL_St._Louis_MO-IL.bngl", + "id": "sp_kalman_filter", + "name": "sp kalman filter", + "description": "Kalman Filter in BNGL", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "sp", + "kalman", + "filter", + "truex", + "obs", + "estx", + "estv", + "variance", + "innovation" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", + "category": "computer-science", + "origin": "ai-generated", "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ml-signal", + "test-models" + ], + "path": "Examples/signal-processing/spkalmanfilter/sp_kalman_filter.bngl", + "file": "sp_kalman_filter.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "stat3-mediated-transcription", "name": "stat3 mediated transcription", "description": "STAT3-mediated transcription and feedback.", - "path": "Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription.bngl", - "file": "stat3-mediated-transcription.bngl", "tags": [ "stat3", "mediated", @@ -12930,35 +16819,29 @@ "mrna" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Stockton_CA_Stockton_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Stockton_CA_Stockton_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Stockton_CA_Stockton_CA.bngl", - "file": "Stockton_CA_Stockton_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/stat3mediatedtranscription/stat3-mediated-transcription.bngl", + "file": "stat3-mediated-transcription.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "stress-response-adaptation", "name": "stress response adaptation", "description": "BioNetGen model: stress response adaptation", - "path": "Contributed/BNGPlayground_Examples/biology/stressresponseadaptation/stress-response-adaptation.bngl", - "file": "stress-response-adaptation.bngl", "tags": [ "stress", "response", @@ -12968,17 +16851,29 @@ "enzyme" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/stressresponseadaptation/stress-response-adaptation.bngl", + "file": "stress-response-adaptation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Suderman_2013", "name": "Suderman 2013", "description": "Ensemble model translated into BNGL", - "path": "Tutorials/NativeTutorials/Suderman2013/Suderman_2013.bngl", - "file": "Suderman_2013.bngl", "tags": [ "suderman", "2013", @@ -12992,120 +16887,29 @@ "ste20" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null - }, - { - "id": "Sumter_SC_Sumter_SC", - "name": "Mallela 2022 - COVID-19 MSA Models - Sumter_SC_Sumter_SC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Sumter_SC_Sumter_SC.bngl", - "file": "Sumter_SC_Sumter_SC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "supplementary_material_Arizona_Arizona", - "name": "Miller 2022 - Navajo Nation Models - supplementary_material_Arizona_Arizona", - "description": "COVID-19 epidemiological models fit to Navajo Nation regional data.", - "path": "Published/Miller2022_NavajoNation/supplementary_material_Arizona_Arizona.bngl", - "file": "supplementary_material_Arizona_Arizona.bngl", - "tags": [ - "covid-19", - "epidemiology", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2022_NavajoNation" - }, - { - "id": "supplementary_material_Colorado_Colorado", - "name": "Miller 2022 - Navajo Nation Models - supplementary_material_Colorado_Colorado", - "description": "COVID-19 epidemiological models fit to Navajo Nation regional data.", - "path": "Published/Miller2022_NavajoNation/supplementary_material_Colorado_Colorado.bngl", - "file": "supplementary_material_Colorado_Colorado.bngl", - "tags": [ - "covid-19", - "epidemiology", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2022_NavajoNation" - }, - { - "id": "supplementary_material_NavajoNation_NavajoNation", - "name": "Miller 2022 - Navajo Nation Models - supplementary_material_NavajoNation_NavajoNation", - "description": "COVID-19 epidemiological models fit to Navajo Nation regional data.", - "path": "Published/Miller2022_NavajoNation/supplementary_material_NavajoNation_NavajoNation.bngl", - "file": "supplementary_material_NavajoNation_NavajoNation.bngl", - "tags": [ - "covid-19", - "epidemiology", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2022_NavajoNation" - }, - { - "id": "supplementary_material_NewMexico_NewMexico", - "name": "Miller 2022 - Navajo Nation Models - supplementary_material_NewMexico_NewMexico", - "description": "COVID-19 epidemiological models fit to Navajo Nation regional data.", - "path": "Published/Miller2022_NavajoNation/supplementary_material_NewMexico_NewMexico.bngl", - "file": "supplementary_material_NewMexico_NewMexico.bngl", - "tags": [ - "covid-19", - "epidemiology", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2022_NavajoNation" - }, - { - "id": "supplementary_material_Utah_Utah", - "name": "Miller 2022 - Navajo Nation Models - supplementary_material_Utah_Utah", - "description": "COVID-19 epidemiological models fit to Navajo Nation regional data.", - "path": "Published/Miller2022_NavajoNation/supplementary_material_Utah_Utah.bngl", - "file": "supplementary_material_Utah_Utah.bngl", - "tags": [ - "covid-19", - "epidemiology", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Miller2022_NavajoNation" + "path": "Tutorials/NativeTutorials/Suderman2013/Suderman_2013.bngl", + "file": "Suderman_2013.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "synaptic-plasticity-ltp", "name": "synaptic plasticity ltp", "description": "Initial Concentrations", - "path": "Contributed/BNGPlayground_Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp.bngl", - "file": "synaptic-plasticity-ltp.bngl", "tags": [ "synaptic", "plasticity", @@ -13118,17 +16922,30 @@ "glusource" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "neuroscience", + "test-models" + ], + "path": "Examples/biology/synapticplasticityltp/synaptic-plasticity-ltp.bngl", + "file": "synaptic-plasticity-ltp.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "synbio_band_pass_filter", "name": "synbio band pass filter", "description": "Model: synbio_band_pass_filter.bngl", - "path": "Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter.bngl", - "file": "synbio_band_pass_filter.bngl", "tags": [ "synbio", "band", @@ -13140,17 +16957,30 @@ "out" ], "category": "synthetic-biology", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/synbio/synbiobandpassfilter/synbio_band_pass_filter.bngl", + "file": "synbio_band_pass_filter.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "synbio_counter_molecular", "name": "synbio counter molecular", "description": "Model: synbio_counter_molecular.bngl", - "path": "Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl", - "file": "synbio_counter_molecular.bngl", "tags": [ "synbio", "counter", @@ -13159,17 +16989,30 @@ "input" ], "category": "synthetic-biology", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/synbio/synbiocountermolecular/synbio_counter_molecular.bngl", + "file": "synbio_counter_molecular.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "synbio_edge_detector", "name": "synbio edge detector", "description": "Model: synbio_edge_detector.bngl", - "path": "Contributed/BNGPlayground_Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl", - "file": "synbio_edge_detector.bngl", "tags": [ "synbio", "edge", @@ -13179,17 +17022,30 @@ "z" ], "category": "synthetic-biology", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/synbio/synbioedgedetector/synbio_edge_detector.bngl", + "file": "synbio_edge_detector.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "synbio_logic_gates_enzymatic", "name": "synbio logic gates enzymatic", "description": "Model: synbio_logic_gates_enzymatic.bngl", - "path": "Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl", - "file": "synbio_logic_gates_enzymatic.bngl", "tags": [ "synbio", "logic", @@ -13203,17 +17059,30 @@ "outor" ], "category": "synthetic-biology", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/synbio/synbiologicgatesenzymatic/synbio_logic_gates_enzymatic.bngl", + "file": "synbio_logic_gates_enzymatic.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "synbio_oscillator_synchronization", "name": "synbio oscillator synchronization", "description": "Model: synbio_oscillator_synchronization.bngl", - "path": "Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl", - "file": "synbio_oscillator_synchronization.bngl", "tags": [ "synbio", "oscillator", @@ -13223,35 +17092,30 @@ "signal" ], "category": "synthetic-biology", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Syracuse_NY_Syracuse_NY", - "name": "Mallela 2022 - COVID-19 MSA Models - Syracuse_NY_Syracuse_NY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Syracuse_NY_Syracuse_NY.bngl", - "file": "Syracuse_NY_Syracuse_NY.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/synbio/synbiooscillatorsynchronization/synbio_oscillator_synchronization.bngl", + "file": "synbio_oscillator_synchronization.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "t-cell-activation", "name": "t cell activation", "description": "BioNetGen model: t cell activation", - "path": "Contributed/BNGPlayground_Examples/biology/tcellactivation/t-cell-activation.bngl", - "file": "t-cell-activation.bngl", "tags": [ "t", "cell", @@ -13261,53 +17125,30 @@ "cytokine" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Tallahassee_FL_Tallahassee_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Tallahassee_FL_Tallahassee_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Tallahassee_FL_Tallahassee_FL.bngl", - "file": "Tallahassee_FL_Tallahassee_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Tampa-St._Petersburg-Clearwater_FL_Tampa-St._Petersburg-Clearwater_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - Tampa-St._Petersburg-Clearwater_FL_Tampa-St._Petersburg-Clearwater_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Tampa-St._Petersburg-Clearwater_FL_Tampa-St._Petersburg-Clearwater_FL.bngl", - "file": "Tampa-St._Petersburg-Clearwater_FL_Tampa-St._Petersburg-Clearwater_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/biology/tcellactivation/t-cell-activation.bngl", + "file": "t-cell-activation.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "tcr", "name": "tcr", "description": "A model of T cell receptor signaling", - "path": "PyBioNetGen/core/tcr/tcr.bngl", - "file": "tcr.bngl", "tags": [ "tcr", "lig1", @@ -13319,17 +17160,100 @@ "zap70" ], "category": "other", - "bng2_compatible": true, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "nf" + ] + }, + "gallery": [ + "other" + ], + "path": "Published/PyBioNetGen/core/tcr/tcr.bngl", + "file": "tcr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" + }, + { + "id": "TCR_model", + "name": "ERK_model.bngl", + "description": "filename: ERK_model.bngl", + "tags": [ + "egf", + "erkpp_sos1_fb", + "erkpp_mek_fb", + "erkpp_raf1_fb", + "lambda", + "egfr_tot", + "ras_tot", + "sos_tot", + "rasgap_tot", + "raf_tot", + "mek_tot", + "erk_tot", + "ekar3_tot", + "erktr_tot", + "a1", + "d1", + "b1", + "u1a", + "u1b", + "b2a", + "u2a", + "b2b", + "u2b", + "k2a", + "k2b", + "b3", + "u3", + "k3", + "a2", + "d2", + "p1", + "q1", + "p2", + "q2", + "p3", + "q3", + "p4", + "q4", + "q5", + "p6", + "q6", + "a0_ekar3", + "d0_ekar3", + "a0_erktr", + "d0_erktr", + "species" + ], + "category": "other", + "origin": "published", + "visible": false, + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode", + "ssa" + ] + }, + "gallery": [], + "path": "Published/Lin2019/TCR_model.bngl", + "file": "TCR_model.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "test_ANG_synthesis_simple", "name": "test_ANG_synthesis_simple", "description": "Synthesis network test", - "path": "Contributed/BNGPlayground_Validation/testANGsynthesissimple/test_ANG_synthesis_simple.bngl", - "file": "test_ANG_synthesis_simple.bngl", "tags": [ "validation", "test", @@ -13344,17 +17268,29 @@ "generate_network" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testANGsynthesissimple/test_ANG_synthesis_simple.bngl", + "file": "test_ANG_synthesis_simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "test_fixed", "name": "test_fixed", "description": "# actions ##", - "path": "Contributed/BNGPlayground_Validation/testfixed/test_fixed.bngl", - "file": "test_fixed.bngl", "tags": [ "validation", "test", @@ -13365,17 +17301,29 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testfixed/test_fixed.bngl", + "file": "test_fixed.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "test_MM", "name": "test_MM", "description": "Kinetic constants", - "path": "Contributed/BNGPlayground_Validation/testMM/test_MM.bngl", - "file": "test_MM.bngl", "tags": [ "validation", "test", @@ -13386,17 +17334,29 @@ "generate_network" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testMM/test_MM.bngl", + "file": "test_MM.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "test_mratio", "name": "test_mratio", "description": "Reaction ratio test", - "path": "Contributed/BNGPlayground_Validation/testmratio/test_mratio.bngl", - "file": "test_mratio.bngl", "tags": [ "validation", "test", @@ -13408,17 +17368,29 @@ "c_lower" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testmratio/test_mratio.bngl", + "file": "test_mratio.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "test_network_gen", "name": "test_network_gen", "description": "fceri model with network generation", - "path": "Contributed/BNGPlayground_Validation/testnetworkgen/test_network_gen.bngl", - "file": "test_network_gen.bngl", "tags": [ "validation", "test", @@ -13430,17 +17402,29 @@ "rec" ], "category": "validation", - "bng2_compatible": false, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testnetworkgen/test_network_gen.bngl", + "file": "test_network_gen.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "test_sat", "name": "test_sat", "description": "Kinetic constants", - "path": "Contributed/BNGPlayground_Validation/testsat/test_sat.bngl", - "file": "test_sat.bngl", "tags": [ "validation", "test", @@ -13451,17 +17435,29 @@ "generate_network" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testsat/test_sat.bngl", + "file": "test_sat.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "test_synthesis_cBNGL_simple", "name": "test_synthesis_cBNGL_simple", "description": "Compartmental synthesis", - "path": "Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl", - "file": "test_synthesis_cBNGL_simple.bngl", "tags": [ "validation", "test", @@ -13476,17 +17472,29 @@ "source2" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testsynthesiscBNGLsimple/test_synthesis_cBNGL_simple.bngl", + "file": "test_synthesis_cBNGL_simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "test_synthesis_complex", "name": "test_synthesis_complex", "description": "Complex synthesis test", - "path": "Contributed/BNGPlayground_Validation/testsynthesiscomplex/test_synthesis_complex.bngl", - "file": "test_synthesis_complex.bngl", "tags": [ "validation", "test", @@ -13500,17 +17508,29 @@ "source2" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testsynthesiscomplex/test_synthesis_complex.bngl", + "file": "test_synthesis_complex.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "test_synthesis_complex_0_cBNGL", "name": "test_synthesis_complex_0_cBNGL", "description": "volume-surface", - "path": "Contributed/BNGPlayground_Validation/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl", - "file": "test_synthesis_complex_0_cBNGL.bngl", "tags": [ "validation", "test", @@ -13528,17 +17548,29 @@ "surface_receptor" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testsynthesiscomplex0cBNGL/test_synthesis_complex_0_cBNGL.bngl", + "file": "test_synthesis_complex_0_cBNGL.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "test_synthesis_complex_source_cBNGL", "name": "test_synthesis_complex_source_cBNGL", "description": "volume-surface", - "path": "Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl", - "file": "test_synthesis_complex_source_cBNGL.bngl", "tags": [ "validation", "test", @@ -13556,17 +17588,29 @@ "surface_receptor" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testsynthesiscomplexsourcecBNGL/test_synthesis_complex_source_cBNGL.bngl", + "file": "test_synthesis_complex_source_cBNGL.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "test_synthesis_simple", "name": "test_synthesis_simple", "description": "Simple synthesis test", - "path": "Contributed/BNGPlayground_Validation/testsynthesissimple/test_synthesis_simple.bngl", - "file": "test_synthesis_simple.bngl", "tags": [ "validation", "test", @@ -13580,53 +17624,60 @@ "generate_network" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/testsynthesissimple/test_synthesis_simple.bngl", + "file": "test_synthesis_simple.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { - "id": "Texarkana_TX-AR_Texarkana_TX-AR", - "name": "Mallela 2022 - COVID-19 MSA Models - Texarkana_TX-AR_Texarkana_TX-AR", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Texarkana_TX-AR_Texarkana_TX-AR.bngl", - "file": "Texarkana_TX-AR_Texarkana_TX-AR.bngl", + "id": "tlbr", + "name": "tlbr", + "description": "A model of trivalent ligand, bivalent receptor", "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "tlbr", + "l", + "r", + "lambda", + "fl" ], - "category": "epidemiology", - "bng2_compatible": true, + "category": "other", "origin": "published", "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "The_Villages_FL_The_Villages_FL", - "name": "Mallela 2022 - COVID-19 MSA Models - The_Villages_FL_The_Villages_FL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/The_Villages_FL_The_Villages_FL.bngl", - "file": "The_Villages_FL_The_Villages_FL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/PyBioNetGen/core/tlbr/tlbr.bngl", + "file": "tlbr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "tlbr", "name": "TLBR Tutorial", "description": "Ligand binding", - "path": "Published/tlbr/tlbr.bngl", - "file": "tlbr.bngl", "tags": [ "published", "immunology", @@ -13636,36 +17687,29 @@ "simulate_rm" ], "category": "immunology", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null - }, - { - "id": "tlbr", - "name": "tlbr", - "description": "A model of trivalent ligand, bivalent receptor", - "path": "PyBioNetGen/core/tlbr/tlbr.bngl", - "file": "tlbr.bngl", - "tags": [ - "tlbr", - "l", - "r", - "lambda", - "fl" + "compatibility": { + "bng2": false, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology" ], - "category": "other", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": null + "path": "Published/tlbr/tlbr.bngl", + "file": "tlbr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "tlmr", "name": "tlmr", "description": "Trivalent ligand monovalent receptor", - "path": "Contributed/BNGPlayground_Validation/tlmr/tlmr.bngl", - "file": "tlmr.bngl", "tags": [ "validation", "tlmr", @@ -13675,17 +17719,29 @@ "simulate_ode" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/tlmr/tlmr.bngl", + "file": "tlmr.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "tlr3-dsrna-sensing", "name": "tlr3 dsrna sensing", "description": "TLR3-mediated dsRNA sensing and TRIF pathway activation.", - "path": "Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing.bngl", - "file": "tlr3-dsrna-sensing.bngl", "tags": [ "tlr3", "dsrna", @@ -13695,17 +17751,30 @@ "sarm" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" + ], + "path": "Examples/biology/tlr3dsrnasensing/tlr3-dsrna-sensing.bngl", + "file": "tlr3-dsrna-sensing.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "tnf-induced-apoptosis", "name": "tnf induced apoptosis", "description": "BioNetGen model: tnf induced apoptosis", - "path": "Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis.bngl", - "file": "tnf-induced-apoptosis.bngl", "tags": [ "tnf", "induced", @@ -13716,17 +17785,30 @@ "caspase3" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle", + "test-models" + ], + "path": "Examples/biology/tnfinducedapoptosis/tnf-induced-apoptosis.bngl", + "file": "tnf-induced-apoptosis.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "toggle", "name": "Toggle", "description": "Toggle switch", - "path": "Tutorials/NativeTutorials/toggle/toggle.bngl", - "file": "toggle.bngl", "tags": [ "published", "tutorial", @@ -13739,53 +17821,30 @@ "setconcentration" ], "category": "tutorial", - "bng2_compatible": false, "origin": "tutorial", "visible": false, - "collectionId": null - }, - { - "id": "Toledo_OH_Toledo_OH", - "name": "Mallela 2022 - COVID-19 MSA Models - Toledo_OH_Toledo_OH", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Toledo_OH_Toledo_OH.bngl", - "file": "Toledo_OH_Toledo_OH.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Topeka_KS_Topeka_KS", - "name": "Mallela 2022 - COVID-19 MSA Models - Topeka_KS_Topeka_KS", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Topeka_KS_Topeka_KS.bngl", - "file": "Topeka_KS_Topeka_KS.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ssa" + ] + }, + "gallery": [ + "synbio", + "native-tutorials" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Tutorials/NativeTutorials/toggle/toggle.bngl", + "file": "toggle.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "toy-jim", "name": "toy-jim", "description": "The model consists of a monovalent extracellular ligand,", - "path": "Contributed/BNGPlayground_Validation/toyjim/toy-jim.bngl", - "file": "toy-jim.bngl", "tags": [ "validation", "toy", @@ -13797,17 +17856,29 @@ "null" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/toyjim/toy-jim.bngl", + "file": "toy-jim.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "toy1", "name": "toy1", "description": "Basic signaling toy", - "path": "Tutorials/General/toy1/toy1.bngl", - "file": "toy1.bngl", "tags": [ "published", "tutorials", @@ -13820,17 +17891,29 @@ "simulate_ode" ], "category": "tutorial", - "bng2_compatible": false, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "path": "Tutorials/General/toy1/toy1.bngl", + "file": "toy1.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "toy2", "name": "toy2", "description": "Enzymatic reaction toy", - "path": "Tutorials/General/toy2/toy2.bngl", - "file": "toy2.bngl", "tags": [ "published", "tutorials", @@ -13841,52 +17924,58 @@ "k" ], "category": "tutorial", - "bng2_compatible": false, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorials" + ], + "path": "Tutorials/General/toy2/toy2.bngl", + "file": "toy2.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "translateSBML", "name": "translateSBML", "description": "title: translateSBML.bngl", - "path": "Tutorials/NativeTutorials/translateSBML/translateSBML.bngl", - "file": "translateSBML.bngl", "tags": [ "translatesbml", "generate_network", "simulate" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null - }, - { - "id": "Trenton-Princeton_NJ_Trenton-Princeton_NJ", - "name": "Mallela 2022 - COVID-19 MSA Models - Trenton-Princeton_NJ_Trenton-Princeton_NJ", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Trenton-Princeton_NJ_Trenton-Princeton_NJ.bngl", - "file": "Trenton-Princeton_NJ_Trenton-Princeton_NJ.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "tutorial" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Tutorials/NativeTutorials/translateSBML/translateSBML.bngl", + "file": "translateSBML.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Tricky", "name": "Tricky", "description": "An example from a real application", - "path": "PyBioNetGen/tests/Tricky/Tricky.bngl", - "file": "Tricky.bngl", "tags": [ "tricky", "ag", @@ -13894,17 +17983,29 @@ "h" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/Tricky/Tricky.bngl", + "file": "Tricky.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "TrickyUS", "name": "TrickyUS", "description": "An example from a real application", - "path": "PyBioNetGen/tests/TrickyUS/TrickyUS.bngl", - "file": "TrickyUS.bngl", "tags": [ "trickyus", "ag", @@ -13912,17 +18013,29 @@ "h" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/TrickyUS/TrickyUS.bngl", + "file": "TrickyUS.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "trivial", "name": "trivial", "description": "A trivial model file for testing MCMC distributions.", - "path": "PyBioNetGen/tests/trivial/trivial.bngl", - "file": "trivial.bngl", "tags": [ "trivial", "q", @@ -13932,89 +18045,29 @@ "simulate" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": false, - "collectionId": null - }, - { - "id": "Tucson_AZ_Tucson_AZ", - "name": "Mallela 2022 - COVID-19 MSA Models - Tucson_AZ_Tucson_AZ", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Tucson_AZ_Tucson_AZ.bngl", - "file": "Tucson_AZ_Tucson_AZ.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Tulsa_OK_Tulsa_OK", - "name": "Mallela 2022 - COVID-19 MSA Models - Tulsa_OK_Tulsa_OK", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Tulsa_OK_Tulsa_OK.bngl", - "file": "Tulsa_OK_Tulsa_OK.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Tuscaloosa_AL_Tuscaloosa_AL", - "name": "Mallela 2022 - COVID-19 MSA Models - Tuscaloosa_AL_Tuscaloosa_AL", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Tuscaloosa_AL_Tuscaloosa_AL.bngl", - "file": "Tuscaloosa_AL_Tuscaloosa_AL.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Twin_Falls_ID_Twin_Falls_ID", - "name": "Mallela 2022 - COVID-19 MSA Models - Twin_Falls_ID_Twin_Falls_ID", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Twin_Falls_ID_Twin_Falls_ID.bngl", - "file": "Twin_Falls_ID_Twin_Falls_ID.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Published/PyBioNetGen/tests/trivial/trivial.bngl", + "file": "trivial.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "two-component-system", "name": "two component system", "description": "BioNetGen model: two component system", - "path": "Contributed/BNGPlayground_Examples/biology/twocomponentsystem/two-component-system.bngl", - "file": "two-component-system.bngl", "tags": [ "two", "component", @@ -14024,17 +18077,29 @@ "target" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/twocomponentsystem/two-component-system.bngl", + "file": "two-component-system.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "univ_synth", "name": "univ_synth", "description": "example of universal synthesis", - "path": "Contributed/BNGPlayground_Validation/univsynth/univ_synth.bngl", - "file": "univ_synth.bngl", "tags": [ "validation", "univ", @@ -14046,107 +18111,29 @@ "simulate_ode" ], "category": "validation", - "bng2_compatible": true, "origin": "test-case", "visible": true, - "collectionId": null - }, - { - "id": "Urban_Honolulu_HI_Urban_Honolulu_HI", - "name": "Mallela 2022 - COVID-19 MSA Models - Urban_Honolulu_HI_Urban_Honolulu_HI", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Urban_Honolulu_HI_Urban_Honolulu_HI.bngl", - "file": "Urban_Honolulu_HI_Urban_Honolulu_HI.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Utica-Rome_NY_Utica-Rome_NY", - "name": "Mallela 2022 - COVID-19 MSA Models - Utica-Rome_NY_Utica-Rome_NY", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Utica-Rome_NY_Utica-Rome_NY.bngl", - "file": "Utica-Rome_NY_Utica-Rome_NY.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Valdosta_GA_Valdosta_GA", - "name": "Mallela 2022 - COVID-19 MSA Models - Valdosta_GA_Valdosta_GA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Valdosta_GA_Valdosta_GA.bngl", - "file": "Valdosta_GA_Valdosta_GA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Vallejo_CA_Vallejo_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Vallejo_CA_Vallejo_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Vallejo_CA_Vallejo_CA.bngl", - "file": "Vallejo_CA_Vallejo_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Valley_of_the_Sun_m10", - "name": "Mallela 2021 - COVID-19 City Models - Valley_of_the_Sun_m10", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/Valley_of_the_Sun_m10.bngl", - "file": "Valley_of_the_Sun_m10.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_Cities" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "validation" + ], + "path": "Tutorials/univsynth/univ_synth.bngl", + "file": "univ_synth.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "vegf-angiogenesis", "name": "vegf angiogenesis", "description": "VEGF-mediated signaling in angiogenesis.", - "path": "Contributed/BNGPlayground_Examples/biology/vegfangiogenesis/vegf-angiogenesis.bngl", - "file": "vegf-angiogenesis.bngl", "tags": [ "vegf", "angiogenesis", @@ -14156,35 +18143,30 @@ "endothelial" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Victoria_TX_Victoria_TX", - "name": "Mallela 2022 - COVID-19 MSA Models - Victoria_TX_Victoria_TX", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Victoria_TX_Victoria_TX.bngl", - "file": "Victoria_TX_Victoria_TX.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cancer", + "test-models" + ], + "path": "Examples/biology/vegfangiogenesis/vegf-angiogenesis.bngl", + "file": "vegf-angiogenesis.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "vilar_2002", "name": "Vilar 2002", "description": "Genetic oscillator", - "path": "Published/vilar2002/vilar_2002.bngl", - "file": "vilar_2002.bngl", "tags": [ "published", "vilar", @@ -14194,17 +18176,29 @@ "r" ], "category": "regulation", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "path": "Published/vilar2002/vilar_2002.bngl", + "file": "vilar_2002.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "vilar_2002b", "name": "Vilar 2002b", - "description": "Gene oscillator", - "path": "Published/vilar2002b/vilar_2002b.bngl", - "file": "vilar_2002b.bngl", + "description": "Gene oscillator", "tags": [ "published", "vilar", @@ -14214,17 +18208,29 @@ "r" ], "category": "regulation", - "bng2_compatible": false, "origin": "published", "visible": true, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "cell-cycle" + ], + "path": "Published/vilar2002b/vilar_2002b.bngl", + "file": "vilar_2002b.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "vilar_2002c", "name": "Vilar 2002c", "description": "Gene oscillator", - "path": "Published/vilar2002c/vilar_2002c.bngl", - "file": "vilar_2002c.bngl", "tags": [ "published", "vilar", @@ -14234,35 +18240,29 @@ "r" ], "category": "regulation", - "bng2_compatible": false, "origin": "published", "visible": true, - "collectionId": null - }, - { - "id": "Vineland-Bridgeton_NJ_Vineland-Bridgeton_NJ", - "name": "Mallela 2022 - COVID-19 MSA Models - Vineland-Bridgeton_NJ_Vineland-Bridgeton_NJ", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Vineland-Bridgeton_NJ_Vineland-Bridgeton_NJ.bngl", - "file": "Vineland-Bridgeton_NJ_Vineland-Bridgeton_NJ.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/vilar2002c/vilar_2002c.bngl", + "file": "vilar_2002c.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "viral-sensing-innate-immunity", "name": "viral sensing innate immunity", "description": "BioNetGen model: viral sensing innate immunity", - "path": "Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity.bngl", - "file": "viral-sensing-innate-immunity.bngl", "tags": [ "viral", "sensing", @@ -14275,53 +18275,30 @@ "ifnb" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Virginia_Beach-Norfolk-Newport_News_VA-NC_Virginia_Beach-Norfolk-Newport_News_VA-NC", - "name": "Mallela 2022 - COVID-19 MSA Models - Virginia_Beach-Norfolk-Newport_News_VA-NC_Virginia_Beach-Norfolk-Newport_News_VA-NC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Virginia_Beach-Norfolk-Newport_News_VA-NC_Virginia_Beach-Norfolk-Newport_News_VA-NC.bngl", - "file": "Virginia_Beach-Norfolk-Newport_News_VA-NC_Virginia_Beach-Norfolk-Newport_News_VA-NC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Visalia_CA_Visalia_CA", - "name": "Mallela 2022 - COVID-19 MSA Models - Visalia_CA_Visalia_CA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Visalia_CA_Visalia_CA.bngl", - "file": "Visalia_CA_Visalia_CA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "immunology", + "test-models" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Examples/biology/viralsensinginnateimmunity/viral-sensing-innate-immunity.bngl", + "file": "viral-sensing-innate-immunity.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "visualize", "name": "Visualize", "description": "Visualization toy", - "path": "Tutorials/NativeTutorials/visualize/visualize.bngl", - "file": "visualize.bngl", "tags": [ "published", "tutorial", @@ -14333,17 +18310,29 @@ "b" ], "category": "tutorial", - "bng2_compatible": true, "origin": "tutorial", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "native-tutorials" + ], + "path": "Tutorials/NativeTutorials/visualize/visualize.bngl", + "file": "visualize.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "wacky_alchemy_stone", "name": "wacky alchemy stone", "description": "Model: wacky_alchemy_stone.bngl", - "path": "Contributed/BNGPlayground_Examples/wacky/wackyalchemystone/wacky_alchemy_stone.bngl", - "file": "wacky_alchemy_stone.bngl", "tags": [ "wacky", "alchemy", @@ -14352,17 +18341,30 @@ "gold" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "synbio", + "test-models" + ], + "path": "Examples/wacky/wackyalchemystone/wacky_alchemy_stone.bngl", + "file": "wacky_alchemy_stone.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "wacky_black_hole", "name": "wacky black hole", "description": "Model: wacky_black_hole.bngl", - "path": "Contributed/BNGPlayground_Examples/wacky/wackyblackhole/wacky_black_hole.bngl", - "file": "wacky_black_hole.bngl", "tags": [ "wacky", "black", @@ -14373,17 +18375,29 @@ "k_evap" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/wacky/wackyblackhole/wacky_black_hole.bngl", + "file": "wacky_black_hole.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "wacky_bouncing_ball", "name": "wacky bouncing ball", "description": "Model: wacky_bouncing_ball.bngl", - "path": "Contributed/BNGPlayground_Examples/wacky/wackybouncingball/wacky_bouncing_ball.bngl", - "file": "wacky_bouncing_ball.bngl", "tags": [ "wacky", "bouncing", @@ -14392,17 +18406,30 @@ "velocity" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "path": "Examples/wacky/wackybouncingball/wacky_bouncing_ball.bngl", + "file": "wacky_bouncing_ball.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "wacky_traffic_jam_asep", "name": "wacky traffic jam asep", "description": "Model: wacky_traffic_jam_asep.bngl", - "path": "Contributed/BNGPlayground_Examples/wacky/wackytrafficjamasep/wacky_traffic_jam_asep.bngl", - "file": "wacky_traffic_jam_asep.bngl", "tags": [ "wacky", "traffic", @@ -14414,17 +18441,30 @@ "simulate" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics", + "test-models" + ], + "path": "Examples/wacky/wackytrafficjamasep/wacky_traffic_jam_asep.bngl", + "file": "wacky_traffic_jam_asep.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "wacky_zombie_infection", "name": "wacky zombie infection", "description": "Model: wacky_zombie_infection.bngl", - "path": "Contributed/BNGPlayground_Examples/wacky/wackyzombieinfection/wacky_zombie_infection.bngl", - "file": "wacky_zombie_infection.bngl", "tags": [ "wacky", "zombie", @@ -14432,179 +18472,30 @@ "human" ], "category": "other", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Warner_Robins_GA_Warner_Robins_GA", - "name": "Mallela 2022 - COVID-19 MSA Models - Warner_Robins_GA_Warner_Robins_GA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Warner_Robins_GA_Warner_Robins_GA.bngl", - "file": "Warner_Robins_GA_Warner_Robins_GA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Washington-Arlington-Alexandria_DC-VA-MD-WV_Washington-Arlington-Alexandria_DC-VA-MD-WV", - "name": "Mallela 2022 - COVID-19 MSA Models - Washington-Arlington-Alexandria_DC-VA-MD-WV_Washington-Arlington-Alexandria_DC-VA-MD-WV", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Washington-Arlington-Alexandria_DC-VA-MD-WV_Washington-Arlington-Alexandria_DC-VA-MD-WV.bngl", - "file": "Washington-Arlington-Alexandria_DC-VA-MD-WV_Washington-Arlington-Alexandria_DC-VA-MD-WV.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Waterloo-Cedar_Falls_IA_Waterloo-Cedar_Falls_IA", - "name": "Mallela 2022 - COVID-19 MSA Models - Waterloo-Cedar_Falls_IA_Waterloo-Cedar_Falls_IA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Waterloo-Cedar_Falls_IA_Waterloo-Cedar_Falls_IA.bngl", - "file": "Waterloo-Cedar_Falls_IA_Waterloo-Cedar_Falls_IA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Wenatchee_WA_Wenatchee_WA", - "name": "Mallela 2022 - COVID-19 MSA Models - Wenatchee_WA_Wenatchee_WA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Wenatchee_WA_Wenatchee_WA.bngl", - "file": "Wenatchee_WA_Wenatchee_WA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Wheeling_WV-OH_Wheeling_WV-OH", - "name": "Mallela 2022 - COVID-19 MSA Models - Wheeling_WV-OH_Wheeling_WV-OH", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Wheeling_WV-OH_Wheeling_WV-OH.bngl", - "file": "Wheeling_WV-OH_Wheeling_WV-OH.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Wichita_KS_Wichita_KS", - "name": "Mallela 2022 - COVID-19 MSA Models - Wichita_KS_Wichita_KS", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Wichita_KS_Wichita_KS.bngl", - "file": "Wichita_KS_Wichita_KS.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Winchester_VA-WV_Winchester_VA-WV", - "name": "Mallela 2022 - COVID-19 MSA Models - Winchester_VA-WV_Winchester_VA-WV", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Winchester_VA-WV_Winchester_VA-WV.bngl", - "file": "Winchester_VA-WV_Winchester_VA-WV.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "WindyCity_m3", - "name": "Mallela 2021 - COVID-19 City Models - WindyCity_m3", - "description": "Parameter-fit COVID-19 epidemiological models for major US cities.", - "path": "Published/Mallela2021_Cities/WindyCity_m3.bngl", - "file": "WindyCity_m3.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "Winston-Salem_NC_Winston-Salem_NC", - "name": "Mallela 2022 - COVID-19 MSA Models - Winston-Salem_NC_Winston-Salem_NC", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Winston-Salem_NC_Winston-Salem_NC.bngl", - "file": "Winston-Salem_NC_Winston-Salem_NC.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "ecology", + "test-models" + ], + "path": "Examples/wacky/wackyzombieinfection/wacky_zombie_infection.bngl", + "file": "wacky_zombie_infection.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "wnt", "name": "Wnt Signaling", "description": "Wnt signaling", - "path": "Published/wnt/wnt.bngl", - "file": "wnt.bngl", "tags": [ "published", "wnt", @@ -14615,17 +18506,29 @@ "bcat" ], "category": "regulation", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "regulation" + ], + "path": "Published/wnt/wnt.bngl", + "file": "wnt.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "wnt-beta-catenin-signaling", "name": "wnt beta catenin signaling", "description": "Wnt/Beta-Catenin signaling (Canonical pathway).", - "path": "Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling.bngl", - "file": "wnt-beta-catenin-signaling.bngl", "tags": [ "wnt", "beta", @@ -14638,35 +18541,30 @@ "tcf" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Worcester_MA-CT_Worcester_MA-CT", - "name": "Mallela 2022 - COVID-19 MSA Models - Worcester_MA-CT_Worcester_MA-CT", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Worcester_MA-CT_Worcester_MA-CT.bngl", - "file": "Worcester_MA-CT_Worcester_MA-CT.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental", + "test-models" + ], + "path": "Examples/biology/wntbetacateninsignaling/wnt-beta-catenin-signaling.bngl", + "file": "wnt-beta-catenin-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "wound-healing-pdgf-signaling", "name": "wound healing pdgf signaling", "description": "BioNetGen model: wound healing pdgf signaling", - "path": "Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling.bngl", - "file": "wound-healing-pdgf-signaling.bngl", "tags": [ "wound", "healing", @@ -14677,35 +18575,29 @@ "fibroblast" ], "category": "signaling", - "bng2_compatible": true, "origin": "ai-generated", "visible": false, - "collectionId": null - }, - { - "id": "Yakima_WA_Yakima_WA", - "name": "Mallela 2022 - COVID-19 MSA Models - Yakima_WA_Yakima_WA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Yakima_WA_Yakima_WA.bngl", - "file": "Yakima_WA_Yakima_WA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "compatibility": { + "bng2": true, + "nfsim": true, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "test-models" + ], + "path": "Examples/biology/woundhealingpdgfsignaling/wound-healing-pdgf-signaling.bngl", + "file": "wound-healing-pdgf-signaling.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Yang_2008", "name": "Yang 2008", "description": "TLBR yang 2008", - "path": "Published/Yang2008/tlbr_yang2008.bngl", - "file": "tlbr_yang2008.bngl", "tags": [ "published", "physics", @@ -14713,71 +18605,29 @@ "2008" ], "category": "physics", - "bng2_compatible": true, "origin": "published", "visible": true, - "collectionId": null - }, - { - "id": "York-Hanover_PA_York-Hanover_PA", - "name": "Mallela 2022 - COVID-19 MSA Models - York-Hanover_PA_York-Hanover_PA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/York-Hanover_PA_York-Hanover_PA.bngl", - "file": "York-Hanover_PA_York-Hanover_PA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Youngstown-Warren-Boardman_OH-PA_Youngstown-Warren-Boardman_OH-PA", - "name": "Mallela 2022 - COVID-19 MSA Models - Youngstown-Warren-Boardman_OH-PA_Youngstown-Warren-Boardman_OH-PA", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Youngstown-Warren-Boardman_OH-PA_Youngstown-Warren-Boardman_OH-PA.bngl", - "file": "Youngstown-Warren-Boardman_OH-PA_Youngstown-Warren-Boardman_OH-PA.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" - ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Yuma_AZ_Yuma_AZ", - "name": "Mallela 2022 - COVID-19 MSA Models - Yuma_AZ_Yuma_AZ", - "description": "Parameter-fit COVID-19 epidemiological models for US metropolitan statistical areas.", - "path": "Published/Mallela2022_MSAs/Yuma_AZ_Yuma_AZ.bngl", - "file": "Yuma_AZ_Yuma_AZ.bngl", - "tags": [ - "covid-19", - "epidemiology", - "parameter-estimation", - "pybionetgen" + "compatibility": { + "bng2": true, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "physics" ], - "category": "epidemiology", - "bng2_compatible": true, - "origin": "published", - "visible": false, - "collectionId": "Mallela2022_MSAs" + "path": "Published/Yang2008/tlbr_yang2008.bngl", + "file": "tlbr_yang2008.bngl", + "collectionId": null, + "featured": false, + "difficulty": "intermediate" }, { "id": "Zhang_2021", "name": "Zhang 2021", "description": "CAR-T signaling", - "path": "Published/Zhang2021/Zhang_2021.bngl", - "file": "Zhang_2021.bngl", "tags": [ "published", "zhang", @@ -14792,17 +18642,29 @@ "pten" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental" + ], + "path": "Published/Zhang2021/Zhang_2021.bngl", + "file": "Zhang_2021.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" }, { "id": "Zhang_2023", "name": "Zhang 2023", "description": "VEGF signaling", - "path": "Published/Zhang2023/Zhang_2023.bngl", - "file": "Zhang_2023.bngl", "tags": [ "published", "zhang", @@ -14817,9 +18679,23 @@ "ip3_cyto" ], "category": "signaling", - "bng2_compatible": false, "origin": "published", "visible": false, - "collectionId": null + "compatibility": { + "bng2": false, + "nfsim": false, + "excluded": false, + "methods": [ + "ode" + ] + }, + "gallery": [ + "developmental" + ], + "path": "Published/Zhang2023/Zhang_2023.bngl", + "file": "Zhang_2023.bngl", + "collectionId": null, + "featured": false, + "difficulty": "advanced" } ] \ No newline at end of file diff --git a/metadata-schema.yaml b/metadata-schema.yaml index 1e9d945..fab1039 100644 --- a/metadata-schema.yaml +++ b/metadata-schema.yaml @@ -1,4 +1,4 @@ -# RuleHub Model Metadata Standard v1.0 +# RuleHub Model Metadata Standard v1.1 id: string name: string @@ -22,19 +22,18 @@ date: published: YYYY-MM-DD tags: string[] -category: enum(signaling, regulation, metabolism, gene-expression, epidemiology, immunology, tutorial, validation, showcase, synthetic-biology, ecology, physics, computer-science, other) +category: enum(signaling, regulation, metabolism, gene-expression, epidemiology, immunology, tutorial, validation, showcase, synthetic-biology, ecology, physics, computer-science, other, compartments, energy, feature-demos, nfsim, processes, wacky, cs, biology, genetics, ml, signal-processing, mechanistic-modeling, biophysics) compatibility: bng2_compatible: boolean min_bng_version: string simulation_methods: - - ode - - ssa - - nf + - enum(ode, ssa, nf, pla, hybrid) uses_compartments: boolean uses_energy: boolean uses_functions: boolean nfsim_compatible: boolean + excluded: boolean source: origin: enum(published, contributed, ai-generated, ported-from-sbml, tutorial, test-case) @@ -42,15 +41,17 @@ source: original_repository: string biomodels_id: string source_path: string + aux_dirs: string[] collection: - type: enum(parameter-fit-variants, sensitivity-analysis, geographic-variants, patient-specific) + type: enum(parameter-fit-variants, sensitivity-analysis, geographic-variants, patient-specific, benchmark-suite) parent_model: string variant_key: string count: integer playground: visible: boolean - gallery_category: string + gallery_categories: string[] featured: boolean - difficulty: enum(beginner, intermediate, advanced) \ No newline at end of file + difficulty: enum(beginner, intermediate, advanced) + sort_priority: integer \ No newline at end of file diff --git a/migration-summary.json b/migration-summary.json deleted file mode 100644 index e7c27f3..0000000 --- a/migration-summary.json +++ /dev/null @@ -1,7072 +0,0 @@ -{ - "generated": "2026-03-12T16:33:18.641Z", - "totalModels": 742, - "collections": [ - { - "id": "Mallela2021_Cities", - "destinationRoot": "Published/Mallela2021_Cities", - "count": 15 - }, - { - "id": "Mallela2021_States", - "destinationRoot": "Published/Mallela2021", - "count": 50 - }, - { - "id": "Mallela2022_MSAs", - "destinationRoot": "Published/Mallela2022_MSAs", - "count": 281 - }, - { - "id": "Miller2022_NavajoNation", - "destinationRoot": "Published/Miller2022_NavajoNation", - "count": 5 - }, - { - "id": "Miller2025_MEK", - "destinationRoot": "Published/Miller2025_MEK", - "count": 10 - } - ], - "models": [ - { - "id": "akt-signaling", - "sourcePath": "example-models/akt-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/aktsignaling", - "destinationFile": "akt-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "allosteric-activation", - "sourcePath": "example-models/allosteric-activation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/allostericactivation", - "destinationFile": "allosteric-activation.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "ampk-signaling", - "sourcePath": "example-models/ampk-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/ampksignaling", - "destinationFile": "ampk-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "apoptosis-cascade", - "sourcePath": "example-models/apoptosis-cascade.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/apoptosiscascade", - "destinationFile": "apoptosis-cascade.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "auto-activation-loop", - "sourcePath": "example-models/auto-activation-loop.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/autoactivationloop", - "destinationFile": "auto-activation-loop.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "autophagy-regulation", - "sourcePath": "example-models/autophagy-regulation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/autophagyregulation", - "destinationFile": "autophagy-regulation.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "bcr-signaling", - "sourcePath": "example-models/bcr-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/bcrsignaling", - "destinationFile": "bcr-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "beta-adrenergic-response", - "sourcePath": "example-models/beta-adrenergic-response.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/betaadrenergicresponse", - "destinationFile": "beta-adrenergic-response.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "bistable-toggle-switch", - "sourcePath": "example-models/bistable-toggle-switch.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/bistabletoggleswitch", - "destinationFile": "bistable-toggle-switch.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "blood-coagulation-thrombin", - "sourcePath": "example-models/blood-coagulation-thrombin.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/bloodcoagulationthrombin", - "destinationFile": "blood-coagulation-thrombin.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "bmp-signaling", - "sourcePath": "example-models/bmp-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/bmpsignaling", - "destinationFile": "bmp-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "brusselator-oscillator", - "sourcePath": "example-models/brusselator-oscillator.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/brusselatoroscillator", - "destinationFile": "brusselator-oscillator.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "calcineurin-nfat-pathway", - "sourcePath": "example-models/calcineurin-nfat-pathway.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/calcineurinnfatpathway", - "destinationFile": "calcineurin-nfat-pathway.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "calcium-spike-signaling", - "sourcePath": "example-models/calcium-spike-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/calciumspikesignaling", - "destinationFile": "calcium-spike-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "caspase-activation-loop", - "sourcePath": "example-models/caspase-activation-loop.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/caspaseactivationloop", - "destinationFile": "caspase-activation-loop.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "cd40-signaling", - "sourcePath": "example-models/cd40-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/cd40signaling", - "destinationFile": "cd40-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "cell-cycle-checkpoint", - "sourcePath": "example-models/cell-cycle-checkpoint.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/cellcyclecheckpoint", - "destinationFile": "cell-cycle-checkpoint.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "checkpoint-kinase-signaling", - "sourcePath": "example-models/checkpoint-kinase-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/checkpointkinasesignaling", - "destinationFile": "checkpoint-kinase-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "chemotaxis-signal-transduction", - "sourcePath": "example-models/chemotaxis-signal-transduction.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/chemotaxissignaltransduction", - "destinationFile": "chemotaxis-signal-transduction.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "circadian-oscillator", - "sourcePath": "example-models/circadian-oscillator.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/circadianoscillator", - "destinationFile": "circadian-oscillator.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "clock-bmal1-gene-circuit", - "sourcePath": "example-models/clock-bmal1-gene-circuit.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/clockbmal1genecircuit", - "destinationFile": "clock-bmal1-gene-circuit.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "compartment_endocytosis", - "sourcePath": "example-models/compartment_endocytosis.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/compartments/compartmentendocytosis", - "destinationFile": "compartment_endocytosis.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "compartment_membrane_bound", - "sourcePath": "example-models/compartment_membrane_bound.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/compartments/compartmentmembranebound", - "destinationFile": "compartment_membrane_bound.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "compartment_nested_transport", - "sourcePath": "example-models/compartment_nested_transport.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/compartments/compartmentnestedtransport", - "destinationFile": "compartment_nested_transport.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "compartment_nuclear_transport", - "sourcePath": "example-models/compartment_nuclear_transport.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/compartments/compartmentnucleartransport", - "destinationFile": "compartment_nuclear_transport.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "compartment_organelle_exchange", - "sourcePath": "example-models/compartment_organelle_exchange.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/compartments/compartmentorganelleexchange", - "destinationFile": "compartment_organelle_exchange.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "competitive-enzyme-inhibition", - "sourcePath": "example-models/competitive-enzyme-inhibition.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/competitiveenzymeinhibition", - "destinationFile": "competitive-enzyme-inhibition.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "complement-activation-cascade", - "sourcePath": "example-models/complement-activation-cascade.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/complementactivationcascade", - "destinationFile": "complement-activation-cascade.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "contact-inhibition-hippo-yap", - "sourcePath": "example-models/contact-inhibition-hippo-yap.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/contactinhibitionhippoyap", - "destinationFile": "contact-inhibition-hippo-yap.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "cooperative-binding", - "sourcePath": "example-models/cooperative-binding.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/cooperativebinding", - "destinationFile": "cooperative-binding.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "cs_diffie_hellman", - "sourcePath": "example-models/cs_diffie_hellman.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/cs/csdiffiehellman", - "destinationFile": "cs_diffie_hellman.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "cs_hash_function", - "sourcePath": "example-models/cs_hash_function.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/cs/cshashfunction", - "destinationFile": "cs_hash_function.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "cs_huffman", - "sourcePath": "example-models/cs_huffman.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/cs/cshuffman", - "destinationFile": "cs_huffman.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "cs_monte_carlo_pi", - "sourcePath": "example-models/cs_monte_carlo_pi.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/cs/csmontecarlopi", - "destinationFile": "cs_monte_carlo_pi.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "cs_pagerank", - "sourcePath": "example-models/cs_pagerank.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/cs/cspagerank", - "destinationFile": "cs_pagerank.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "cs_pid_controller", - "sourcePath": "example-models/cs_pid_controller.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/cs/cspidcontroller", - "destinationFile": "cs_pid_controller.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "cs_regex_nfa", - "sourcePath": "example-models/cs_regex_nfa.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/cs/csregexnfa", - "destinationFile": "cs_regex_nfa.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "dna-damage-repair", - "sourcePath": "example-models/dna-damage-repair.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/dnadamagerepair", - "destinationFile": "dna-damage-repair.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "dna-methylation-dynamics", - "sourcePath": "example-models/dna-methylation-dynamics.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/dnamethylationdynamics", - "destinationFile": "dna-methylation-dynamics.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "dr5-apoptosis-signaling", - "sourcePath": "example-models/dr5-apoptosis-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/dr5apoptosissignaling", - "destinationFile": "dr5-apoptosis-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "dual-site-phosphorylation", - "sourcePath": "example-models/dual-site-phosphorylation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/dualsitephosphorylation", - "destinationFile": "dual-site-phosphorylation.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "e2f-rb-cell-cycle-switch", - "sourcePath": "example-models/e2f-rb-cell-cycle-switch.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/e2frbcellcycleswitch", - "destinationFile": "e2f-rb-cell-cycle-switch.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "eco_coevolution_host_parasite", - "sourcePath": "example-models/eco_coevolution_host_parasite.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/ecology/ecocoevolutionhostparasite", - "destinationFile": "eco_coevolution_host_parasite.bngl", - "origin": "ai-generated", - "category": "ecology", - "visible": false - }, - { - "id": "eco_food_web_chaos_3sp", - "sourcePath": "example-models/eco_food_web_chaos_3sp.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/ecology/ecofoodwebchaos3sp", - "destinationFile": "eco_food_web_chaos_3sp.bngl", - "origin": "ai-generated", - "category": "ecology", - "visible": false - }, - { - "id": "eco_lotka_volterra_grid", - "sourcePath": "example-models/eco_lotka_volterra_grid.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/ecology/ecolotkavolterragrid", - "destinationFile": "eco_lotka_volterra_grid.bngl", - "origin": "ai-generated", - "category": "ecology", - "visible": false - }, - { - "id": "eco_mutualism_obligate", - "sourcePath": "example-models/eco_mutualism_obligate.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/ecology/ecomutualismobligate", - "destinationFile": "eco_mutualism_obligate.bngl", - "origin": "ai-generated", - "category": "ecology", - "visible": false - }, - { - "id": "eco_rock_paper_scissors_spatial", - "sourcePath": "example-models/eco_rock_paper_scissors_spatial.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/ecology/ecorockpaperscissorsspatial", - "destinationFile": "eco_rock_paper_scissors_spatial.bngl", - "origin": "ai-generated", - "category": "ecology", - "visible": false - }, - { - "id": "egfr-signaling-pathway", - "sourcePath": "example-models/egfr-signaling-pathway.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/egfrsignalingpathway", - "destinationFile": "egfr-signaling-pathway.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "eif2a-stress-response", - "sourcePath": "example-models/eif2a-stress-response.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/eif2astressresponse", - "destinationFile": "eif2a-stress-response.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "endosomal-sorting-rab", - "sourcePath": "example-models/endosomal-sorting-rab.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/endosomalsortingrab", - "destinationFile": "endosomal-sorting-rab.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "energy_allostery_mwc", - "sourcePath": "example-models/energy_allostery_mwc.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/energy/energyallosterymwc", - "destinationFile": "energy_allostery_mwc.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "energy_catalysis_mm", - "sourcePath": "example-models/energy_catalysis_mm.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/energy/energycatalysismm", - "destinationFile": "energy_catalysis_mm.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "energy_cooperativity_adh", - "sourcePath": "example-models/energy_cooperativity_adh.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/energy/energycooperativityadh", - "destinationFile": "energy_cooperativity_adh.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "energy_linear_chain", - "sourcePath": "example-models/energy_linear_chain.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/energy/energylinearchain", - "destinationFile": "energy_linear_chain.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "energy_transport_pump", - "sourcePath": "example-models/energy_transport_pump.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/energy/energytransportpump", - "destinationFile": "energy_transport_pump.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "er-stress-response", - "sourcePath": "example-models/er-stress-response.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/erstressresponse", - "destinationFile": "er-stress-response.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "erk-nuclear-translocation", - "sourcePath": "example-models/erk-nuclear-translocation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/erknucleartranslocation", - "destinationFile": "erk-nuclear-translocation.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "feature_functional_rates_volume", - "sourcePath": "example-models/feature_functional_rates_volume.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/feature-demos/featurefunctionalratesvolume", - "destinationFile": "feature_functional_rates_volume.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "feature_global_functions_scan", - "sourcePath": "example-models/feature_global_functions_scan.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/feature-demos/featureglobalfunctionsscan", - "destinationFile": "feature_global_functions_scan.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "feature_local_functions_explicit", - "sourcePath": "example-models/feature_local_functions_explicit.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/feature-demos/featurelocalfunctionsexplicit", - "destinationFile": "feature_local_functions_explicit.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "feature_symmetry_factors_cyclic", - "sourcePath": "example-models/feature_symmetry_factors_cyclic.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/feature-demos/featuresymmetryfactorscyclic", - "destinationFile": "feature_symmetry_factors_cyclic.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "feature_synthesis_degradation_ss", - "sourcePath": "example-models/feature_synthesis_degradation_ss.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/feature-demos/featuresynthesisdegradationss", - "destinationFile": "feature_synthesis_degradation_ss.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "fgf-signaling-pathway", - "sourcePath": "example-models/fgf-signaling-pathway.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/fgfsignalingpathway", - "destinationFile": "fgf-signaling-pathway.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "gas6-axl-signaling", - "sourcePath": "example-models/gas6-axl-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/gas6axlsignaling", - "destinationFile": "gas6-axl-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "gene-expression-toggle", - "sourcePath": "example-models/gene-expression-toggle.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/geneexpressiontoggle", - "destinationFile": "gene-expression-toggle.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "genetic_bistability_energy", - "sourcePath": "example-models/genetic_bistability_energy.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/genetics/geneticbistabilityenergy", - "destinationFile": "genetic_bistability_energy.bngl", - "origin": "ai-generated", - "category": "gene-expression", - "visible": false - }, - { - "id": "genetic_dna_replication_stochastic", - "sourcePath": "example-models/genetic_dna_replication_stochastic.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/genetics/geneticdnareplicationstochastic", - "destinationFile": "genetic_dna_replication_stochastic.bngl", - "origin": "ai-generated", - "category": "gene-expression", - "visible": false - }, - { - "id": "genetic_goodwin_oscillator", - "sourcePath": "example-models/genetic_goodwin_oscillator.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/genetics/geneticgoodwinoscillator", - "destinationFile": "genetic_goodwin_oscillator.bngl", - "origin": "ai-generated", - "category": "gene-expression", - "visible": false - }, - { - "id": "genetic_translation_kinetics", - "sourcePath": "example-models/genetic_translation_kinetics.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/genetics/genetictranslationkinetics", - "destinationFile": "genetic_translation_kinetics.bngl", - "origin": "ai-generated", - "category": "gene-expression", - "visible": false - }, - { - "id": "genetic_turing_pattern_1d", - "sourcePath": "example-models/genetic_turing_pattern_1d.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/genetics/geneticturingpattern1d", - "destinationFile": "genetic_turing_pattern_1d.bngl", - "origin": "ai-generated", - "category": "gene-expression", - "visible": false - }, - { - "id": "glioblastoma-egfrviii-signaling", - "sourcePath": "example-models/glioblastoma-egfrviii-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/glioblastomaegfrviiisignaling", - "destinationFile": "glioblastoma-egfrviii-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "glycolysis-branch-point", - "sourcePath": "example-models/glycolysis-branch-point.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/glycolysisbranchpoint", - "destinationFile": "glycolysis-branch-point.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "gm_game_of_life", - "sourcePath": "example-models/gm_game_of_life.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/generative/gmgameoflife", - "destinationFile": "gm_game_of_life.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "gm_ray_marcher", - "sourcePath": "example-models/gm_ray_marcher.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/generative/gmraymarcher", - "destinationFile": "gm_ray_marcher.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "gpcr-desensitization-arrestin", - "sourcePath": "example-models/gpcr-desensitization-arrestin.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/gpcrdesensitizationarrestin", - "destinationFile": "gpcr-desensitization-arrestin.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "hedgehog-signaling-pathway", - "sourcePath": "example-models/hedgehog-signaling-pathway.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/hedgehogsignalingpathway", - "destinationFile": "hedgehog-signaling-pathway.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "hematopoietic-growth-factor", - "sourcePath": "example-models/hematopoietic-growth-factor.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/hematopoieticgrowthfactor", - "destinationFile": "hematopoietic-growth-factor.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "hif1a_degradation_loop", - "sourcePath": "example-models/hif1a_degradation_loop.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/hif1adegradationloop", - "destinationFile": "hif1a_degradation_loop.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "hypoxia-response-signaling", - "sourcePath": "example-models/hypoxia-response-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/hypoxiaresponsesignaling", - "destinationFile": "hypoxia-response-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "il1b-signaling", - "sourcePath": "example-models/il1b-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/il1bsignaling", - "destinationFile": "il1b-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "il6-jak-stat-pathway", - "sourcePath": "example-models/il6-jak-stat-pathway.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/il6jakstatpathway", - "destinationFile": "il6-jak-stat-pathway.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "immune-synapse-formation", - "sourcePath": "example-models/immune-synapse-formation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/immunesynapseformation", - "destinationFile": "immune-synapse-formation.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "inflammasome-activation", - "sourcePath": "example-models/inflammasome-activation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/inflammasomeactivation", - "destinationFile": "inflammasome-activation.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "inositol-phosphate-metabolism", - "sourcePath": "example-models/inositol-phosphate-metabolism.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/inositolphosphatemetabolism", - "destinationFile": "inositol-phosphate-metabolism.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "insulin-glucose-homeostasis", - "sourcePath": "example-models/insulin-glucose-homeostasis.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/insulinglucosehomeostasis", - "destinationFile": "insulin-glucose-homeostasis.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "interferon-signaling", - "sourcePath": "example-models/interferon-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/interferonsignaling", - "destinationFile": "interferon-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "ire1a-xbp1-er-stress", - "sourcePath": "example-models/ire1a-xbp1-er-stress.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/ire1axbp1erstress", - "destinationFile": "ire1a-xbp1-er-stress.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "jak-stat-cytokine-signaling", - "sourcePath": "example-models/jak-stat-cytokine-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/jakstatcytokinesignaling", - "destinationFile": "jak-stat-cytokine-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "jnk-mapk-signaling", - "sourcePath": "example-models/jnk-mapk-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/jnkmapksignaling", - "destinationFile": "jnk-mapk-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "kir-channel-regulation", - "sourcePath": "example-models/kir-channel-regulation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/kirchannelregulation", - "destinationFile": "kir-channel-regulation.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "l-type-calcium-channel-dynamics", - "sourcePath": "example-models/l-type-calcium-channel-dynamics.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/ltypecalciumchanneldynamics", - "destinationFile": "l-type-calcium-channel-dynamics.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "lac-operon-regulation", - "sourcePath": "example-models/lac-operon-regulation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/lacoperonregulation", - "destinationFile": "lac-operon-regulation.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "lipid-mediated-pip3-signaling", - "sourcePath": "example-models/lipid-mediated-pip3-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/lipidmediatedpip3signaling", - "destinationFile": "lipid-mediated-pip3-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "mapk-signaling-cascade", - "sourcePath": "example-models/mapk-signaling-cascade.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/mapksignalingcascade", - "destinationFile": "mapk-signaling-cascade.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "meta_formal_game_theory", - "sourcePath": "example-models/meta_formal_game_theory.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/meta/metaformalgametheory", - "destinationFile": "meta_formal_game_theory.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "meta_formal_molecular_clock", - "sourcePath": "example-models/meta_formal_molecular_clock.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/meta/metaformalmolecularclock", - "destinationFile": "meta_formal_molecular_clock.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "meta_formal_petri_net", - "sourcePath": "example-models/meta_formal_petri_net.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/meta/metaformalpetrinet", - "destinationFile": "meta_formal_petri_net.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "michaelis-menten-kinetics", - "sourcePath": "example-models/michaelis-menten-kinetics.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/michaelismentenkinetics", - "destinationFile": "michaelis-menten-kinetics.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "ml_gradient_descent", - "sourcePath": "example-models/ml_gradient_descent.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/ml/mlgradientdescent", - "destinationFile": "ml_gradient_descent.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "ml_hopfield", - "sourcePath": "example-models/ml_hopfield.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/ml/mlhopfield", - "destinationFile": "ml_hopfield.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "ml_kmeans", - "sourcePath": "example-models/ml_kmeans.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/ml/mlkmeans", - "destinationFile": "ml_kmeans.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "ml_q_learning", - "sourcePath": "example-models/ml_q_learning.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/ml/mlqlearning", - "destinationFile": "ml_q_learning.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "ml_svm", - "sourcePath": "example-models/ml_svm.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/ml/mlsvm", - "destinationFile": "ml_svm.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "mtor-signaling", - "sourcePath": "example-models/mtor-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/mtorsignaling", - "destinationFile": "mtor-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "mtorc2-signaling", - "sourcePath": "example-models/mtorc2-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/mtorc2signaling", - "destinationFile": "mtorc2-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "mt_arithmetic_compiler", - "sourcePath": "example-models/mt_arithmetic_compiler.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/meta/mtarithmeticcompiler", - "destinationFile": "mt_arithmetic_compiler.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "mt_bngl_interpreter", - "sourcePath": "example-models/mt_bngl_interpreter.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/meta/mtbnglinterpreter", - "destinationFile": "mt_bngl_interpreter.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "mt_music_sequencer", - "sourcePath": "example-models/mt_music_sequencer.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/meta/mtmusicsequencer", - "destinationFile": "mt_music_sequencer.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "mt_pascal_triangle", - "sourcePath": "example-models/mt_pascal_triangle.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/meta/mtpascaltriangle", - "destinationFile": "mt_pascal_triangle.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "mt_quine", - "sourcePath": "example-models/mt_quine.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/meta/mtquine", - "destinationFile": "mt_quine.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "myogenic-differentiation", - "sourcePath": "example-models/myogenic-differentiation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/myogenicdifferentiation", - "destinationFile": "myogenic-differentiation.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "negative-feedback-loop", - "sourcePath": "example-models/negative-feedback-loop.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/negativefeedbackloop", - "destinationFile": "negative-feedback-loop.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "neurotransmitter-release", - "sourcePath": "example-models/neurotransmitter-release.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/neurotransmitterrelease", - "destinationFile": "neurotransmitter-release.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "nfkb-feedback", - "sourcePath": "example-models/nfkb-feedback.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/nfkbfeedback", - "destinationFile": "nfkb-feedback.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "nfsim_aggregation_gelation", - "sourcePath": "example-models/nfsim_aggregation_gelation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/nfsim/nfsimaggregationgelation", - "destinationFile": "nfsim_aggregation_gelation.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "nfsim_coarse_graining", - "sourcePath": "example-models/nfsim_coarse_graining.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/nfsim/nfsimcoarsegraining", - "destinationFile": "nfsim_coarse_graining.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "nfsim_dynamic_compartments", - "sourcePath": "example-models/nfsim_dynamic_compartments.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/nfsim/nfsimdynamiccompartments", - "destinationFile": "nfsim_dynamic_compartments.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "nfsim_hybrid_particle_field", - "sourcePath": "example-models/nfsim_hybrid_particle_field.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/nfsim/nfsimhybridparticlefield", - "destinationFile": "nfsim_hybrid_particle_field.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "nfsim_ring_closure_polymer", - "sourcePath": "example-models/nfsim_ring_closure_polymer.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/nfsim/nfsimringclosurepolymer", - "destinationFile": "nfsim_ring_closure_polymer.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "nn_xor", - "sourcePath": "example-models/nn_xor.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/ml/nnxor", - "destinationFile": "nn_xor.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "no-cgmp-signaling", - "sourcePath": "example-models/no-cgmp-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/nocgmpsignaling", - "destinationFile": "no-cgmp-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "notch-delta-lateral-inhibition", - "sourcePath": "example-models/notch-delta-lateral-inhibition.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/notchdeltalateralinhibition", - "destinationFile": "notch-delta-lateral-inhibition.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "oxidative-stress-response", - "sourcePath": "example-models/oxidative-stress-response.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/oxidativestressresponse", - "destinationFile": "oxidative-stress-response.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "p38-mapk-signaling", - "sourcePath": "example-models/p38-mapk-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/p38mapksignaling", - "destinationFile": "p38-mapk-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "p53-mdm2-oscillator", - "sourcePath": "example-models/p53-mdm2-oscillator.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/p53mdm2oscillator", - "destinationFile": "p53-mdm2-oscillator.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "parp1-mediated-dna-repair", - "sourcePath": "example-models/parp1-mediated-dna-repair.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/parp1mediateddnarepair", - "destinationFile": "parp1-mediated-dna-repair.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "phosphorelay-chain", - "sourcePath": "example-models/phosphorelay-chain.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/phosphorelaychain", - "destinationFile": "phosphorelay-chain.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "ph_lorenz_attractor", - "sourcePath": "example-models/ph_lorenz_attractor.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/physics/phlorenzattractor", - "destinationFile": "ph_lorenz_attractor.bngl", - "origin": "ai-generated", - "category": "physics", - "visible": false - }, - { - "id": "ph_nbody_gravity", - "sourcePath": "example-models/ph_nbody_gravity.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/physics/phnbodygravity", - "destinationFile": "ph_nbody_gravity.bngl", - "origin": "ai-generated", - "category": "physics", - "visible": false - }, - { - "id": "ph_schrodinger", - "sourcePath": "example-models/ph_schrodinger.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/physics/phschrodinger", - "destinationFile": "ph_schrodinger.bngl", - "origin": "ai-generated", - "category": "physics", - "visible": false - }, - { - "id": "ph_wave_equation", - "sourcePath": "example-models/ph_wave_equation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/physics/phwaveequation", - "destinationFile": "ph_wave_equation.bngl", - "origin": "ai-generated", - "category": "physics", - "visible": false - }, - { - "id": "platelet-activation", - "sourcePath": "example-models/platelet-activation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/plateletactivation", - "destinationFile": "platelet-activation.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "predator-prey-dynamics", - "sourcePath": "example-models/predator-prey-dynamics.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/predatorpreydynamics", - "destinationFile": "predator-prey-dynamics.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "process_actin_treadmilling", - "sourcePath": "example-models/process_actin_treadmilling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/processes/processactintreadmilling", - "destinationFile": "process_actin_treadmilling.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "process_autophagy_flux", - "sourcePath": "example-models/process_autophagy_flux.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/processes/processautophagyflux", - "destinationFile": "process_autophagy_flux.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "process_cell_adhesion_strength", - "sourcePath": "example-models/process_cell_adhesion_strength.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/processes/processcelladhesionstrength", - "destinationFile": "process_cell_adhesion_strength.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "process_kinetic_proofreading_tcr", - "sourcePath": "example-models/process_kinetic_proofreading_tcr.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/processes/processkineticproofreadingtcr", - "destinationFile": "process_kinetic_proofreading_tcr.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "process_quorum_sensing_switch", - "sourcePath": "example-models/process_quorum_sensing_switch.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/processes/processquorumsensingswitch", - "destinationFile": "process_quorum_sensing_switch.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "quorum-sensing-circuit", - "sourcePath": "example-models/quorum-sensing-circuit.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/quorumsensingcircuit", - "destinationFile": "quorum-sensing-circuit.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "rab-gtpase-cycle", - "sourcePath": "example-models/rab-gtpase-cycle.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/rabgtpasecycle", - "destinationFile": "rab-gtpase-cycle.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "rankl-rank-signaling", - "sourcePath": "example-models/rankl-rank-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/ranklranksignaling", - "destinationFile": "rankl-rank-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "ras-gef-gap-cycle", - "sourcePath": "example-models/ras-gef-gap-cycle.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/rasgefgapcycle", - "destinationFile": "ras-gef-gap-cycle.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "repressilator-oscillator", - "sourcePath": "example-models/repressilator-oscillator.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/repressilatoroscillator", - "destinationFile": "repressilator-oscillator.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "retinoic-acid-signaling", - "sourcePath": "example-models/retinoic-acid-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/retinoicacidsignaling", - "destinationFile": "retinoic-acid-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "rho-gtpase-actin-cytoskeleton", - "sourcePath": "example-models/rho-gtpase-actin-cytoskeleton.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/rhogtpaseactincytoskeleton", - "destinationFile": "rho-gtpase-actin-cytoskeleton.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "shp2-phosphatase-regulation", - "sourcePath": "example-models/shp2-phosphatase-regulation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/shp2phosphataseregulation", - "destinationFile": "shp2-phosphatase-regulation.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "signal-amplification-cascade", - "sourcePath": "example-models/signal-amplification-cascade.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/signalamplificationcascade", - "destinationFile": "signal-amplification-cascade.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "simple-dimerization", - "sourcePath": "example-models/simple-dimerization.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/simpledimerization", - "destinationFile": "simple-dimerization.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "sir-epidemic-model", - "sourcePath": "example-models/sir-epidemic-model.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/sirepidemicmodel", - "destinationFile": "sir-epidemic-model.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "smad-tgf-beta-signaling", - "sourcePath": "example-models/smad-tgf-beta-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/smadtgfbetasignaling", - "destinationFile": "smad-tgf-beta-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "sonic-hedgehog-gradient", - "sourcePath": "example-models/sonic-hedgehog-gradient.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/sonichedgehoggradient", - "destinationFile": "sonic-hedgehog-gradient.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "sp_fourier_synthesizer", - "sourcePath": "example-models/sp_fourier_synthesizer.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/signal-processing/spfouriersynthesizer", - "destinationFile": "sp_fourier_synthesizer.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "sp_image_convolution", - "sourcePath": "example-models/sp_image_convolution.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/signal-processing/spimageconvolution", - "destinationFile": "sp_image_convolution.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "sp_kalman_filter", - "sourcePath": "example-models/sp_kalman_filter.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/signal-processing/spkalmanfilter", - "destinationFile": "sp_kalman_filter.bngl", - "origin": "ai-generated", - "category": "computer-science", - "visible": false - }, - { - "id": "stat3-mediated-transcription", - "sourcePath": "example-models/stat3-mediated-transcription.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/stat3mediatedtranscription", - "destinationFile": "stat3-mediated-transcription.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "stress-response-adaptation", - "sourcePath": "example-models/stress-response-adaptation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/stressresponseadaptation", - "destinationFile": "stress-response-adaptation.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "synaptic-plasticity-ltp", - "sourcePath": "example-models/synaptic-plasticity-ltp.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/synapticplasticityltp", - "destinationFile": "synaptic-plasticity-ltp.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "synbio_band_pass_filter", - "sourcePath": "example-models/synbio_band_pass_filter.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/synbio/synbiobandpassfilter", - "destinationFile": "synbio_band_pass_filter.bngl", - "origin": "ai-generated", - "category": "synthetic-biology", - "visible": false - }, - { - "id": "synbio_counter_molecular", - "sourcePath": "example-models/synbio_counter_molecular.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/synbio/synbiocountermolecular", - "destinationFile": "synbio_counter_molecular.bngl", - "origin": "ai-generated", - "category": "synthetic-biology", - "visible": false - }, - { - "id": "synbio_edge_detector", - "sourcePath": "example-models/synbio_edge_detector.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/synbio/synbioedgedetector", - "destinationFile": "synbio_edge_detector.bngl", - "origin": "ai-generated", - "category": "synthetic-biology", - "visible": false - }, - { - "id": "synbio_logic_gates_enzymatic", - "sourcePath": "example-models/synbio_logic_gates_enzymatic.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/synbio/synbiologicgatesenzymatic", - "destinationFile": "synbio_logic_gates_enzymatic.bngl", - "origin": "ai-generated", - "category": "synthetic-biology", - "visible": false - }, - { - "id": "synbio_oscillator_synchronization", - "sourcePath": "example-models/synbio_oscillator_synchronization.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/synbio/synbiooscillatorsynchronization", - "destinationFile": "synbio_oscillator_synchronization.bngl", - "origin": "ai-generated", - "category": "synthetic-biology", - "visible": false - }, - { - "id": "t-cell-activation", - "sourcePath": "example-models/t-cell-activation.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/tcellactivation", - "destinationFile": "t-cell-activation.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "tlr3-dsrna-sensing", - "sourcePath": "example-models/tlr3-dsrna-sensing.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/tlr3dsrnasensing", - "destinationFile": "tlr3-dsrna-sensing.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "tnf-induced-apoptosis", - "sourcePath": "example-models/tnf-induced-apoptosis.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/tnfinducedapoptosis", - "destinationFile": "tnf-induced-apoptosis.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "two-component-system", - "sourcePath": "example-models/two-component-system.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/twocomponentsystem", - "destinationFile": "two-component-system.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "vegf-angiogenesis", - "sourcePath": "example-models/vegf-angiogenesis.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/vegfangiogenesis", - "destinationFile": "vegf-angiogenesis.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "viral-sensing-innate-immunity", - "sourcePath": "example-models/viral-sensing-innate-immunity.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/viralsensinginnateimmunity", - "destinationFile": "viral-sensing-innate-immunity.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "wacky_alchemy_stone", - "sourcePath": "example-models/wacky_alchemy_stone.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/wacky/wackyalchemystone", - "destinationFile": "wacky_alchemy_stone.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "wacky_black_hole", - "sourcePath": "example-models/wacky_black_hole.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/wacky/wackyblackhole", - "destinationFile": "wacky_black_hole.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "wacky_bouncing_ball", - "sourcePath": "example-models/wacky_bouncing_ball.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/wacky/wackybouncingball", - "destinationFile": "wacky_bouncing_ball.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "wacky_traffic_jam_asep", - "sourcePath": "example-models/wacky_traffic_jam_asep.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/wacky/wackytrafficjamasep", - "destinationFile": "wacky_traffic_jam_asep.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "wacky_zombie_infection", - "sourcePath": "example-models/wacky_zombie_infection.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/wacky/wackyzombieinfection", - "destinationFile": "wacky_zombie_infection.bngl", - "origin": "ai-generated", - "category": "other", - "visible": false - }, - { - "id": "wnt-beta-catenin-signaling", - "sourcePath": "example-models/wnt-beta-catenin-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/wntbetacateninsignaling", - "destinationFile": "wnt-beta-catenin-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "wound-healing-pdgf-signaling", - "sourcePath": "example-models/wound-healing-pdgf-signaling.bngl", - "destinationDir": "Contributed/BNGPlayground_Examples/biology/woundhealingpdgfsignaling", - "destinationFile": "wound-healing-pdgf-signaling.bngl", - "origin": "ai-generated", - "category": "signaling", - "visible": false - }, - { - "id": "Barua_2013", - "sourcePath": "published-models/cell-regulation/Barua_2013.bngl", - "destinationDir": "Published/Barua2013", - "destinationFile": "Barua_2013.bngl", - "origin": "published", - "category": "regulation", - "visible": true - }, - { - "id": "Blinov_ran", - "sourcePath": "published-models/cell-regulation/Blinov_ran.bngl", - "destinationDir": "Published/Blinovran", - "destinationFile": "Blinov_ran.bngl", - "origin": "published", - "category": "regulation", - "visible": false - }, - { - "id": "Hat_2016", - "sourcePath": "published-models/cell-regulation/Hat_2016.bngl", - "destinationDir": "Published/Hat2016", - "destinationFile": "Hat_2016.bngl", - "origin": "published", - "category": "regulation", - "visible": true - }, - { - "id": "Kocieniewski_2012", - "sourcePath": "published-models/cell-regulation/Kocieniewski_2012.bngl", - "destinationDir": "Published/Kocieniewski2012", - "destinationFile": "Kocieniewski_2012.bngl", - "origin": "published", - "category": "regulation", - "visible": false - }, - { - "id": "notch", - "sourcePath": "published-models/cell-regulation/notch.bngl", - "destinationDir": "Published/notch", - "destinationFile": "notch.bngl", - "origin": "published", - "category": "regulation", - "visible": false - }, - { - "id": "Pekalski_2013", - "sourcePath": "published-models/cell-regulation/Pekalski_2013.bngl", - "destinationDir": "Published/Pekalski2013", - "destinationFile": "Pekalski_2013.bngl", - "origin": "published", - "category": "regulation", - "visible": true - }, - { - "id": "Rule_based_Ran_transport", - "sourcePath": "published-models/cell-regulation/Rule_based_Ran_transport.bngl", - "destinationDir": "Published/RulebasedRantransport", - "destinationFile": "Rule_based_Ran_transport.bngl", - "origin": "published", - "category": "regulation", - "visible": false - }, - { - "id": "Rule_based_Ran_transport_draft", - "sourcePath": "published-models/cell-regulation/Rule_based_Ran_transport_draft.bngl", - "destinationDir": "Published/RulebasedRantransportdraft", - "destinationFile": "Rule_based_Ran_transport_draft.bngl", - "origin": "published", - "category": "regulation", - "visible": false - }, - { - "id": "vilar_2002", - "sourcePath": "published-models/cell-regulation/vilar_2002.bngl", - "destinationDir": "Published/vilar2002", - "destinationFile": "vilar_2002.bngl", - "origin": "published", - "category": "regulation", - "visible": false - }, - { - "id": "vilar_2002b", - "sourcePath": "published-models/cell-regulation/vilar_2002b.bngl", - "destinationDir": "Published/vilar2002b", - "destinationFile": "vilar_2002b.bngl", - "origin": "published", - "category": "regulation", - "visible": true - }, - { - "id": "vilar_2002c", - "sourcePath": "published-models/cell-regulation/vilar_2002c.bngl", - "destinationDir": "Published/vilar2002c", - "destinationFile": "vilar_2002c.bngl", - "origin": "published", - "category": "regulation", - "visible": true - }, - { - "id": "wnt", - "sourcePath": "published-models/cell-regulation/wnt.bngl", - "destinationDir": "Published/wnt", - "destinationFile": "wnt.bngl", - "origin": "published", - "category": "regulation", - "visible": false - }, - { - "id": "Barua_2007", - "sourcePath": "published-models/complex-models/Barua_2007.bngl", - "destinationDir": "Published/Barua2007", - "destinationFile": "Barua_2007.bngl", - "origin": "published", - "category": "signaling", - "visible": true - }, - { - "id": "Barua_2009", - "sourcePath": "published-models/complex-models/Barua_2009.bngl", - "destinationDir": "Published/Barua2009", - "destinationFile": "Barua_2009.bngl", - "origin": "published", - "category": "signaling", - "visible": true - }, - { - "id": "Blinov_2006", - "sourcePath": "published-models/complex-models/Blinov_2006.bngl", - "destinationDir": "Published/Blinov2006", - "destinationFile": "Blinov_2006.bngl", - "origin": "published", - "category": "signaling", - "visible": true - }, - { - "id": "Chattaraj_2021", - "sourcePath": "published-models/complex-models/Chattaraj_2021.bngl", - "destinationDir": "Published/Chattaraj2021", - "destinationFile": "Chattaraj_2021.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Dushek_2011", - "sourcePath": "published-models/complex-models/Dushek_2011.bngl", - "destinationDir": "Published/Dushek2011", - "destinationFile": "Dushek_2011.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Dushek_2014", - "sourcePath": "published-models/complex-models/Dushek_2014.bngl", - "destinationDir": "Published/Dushek2014", - "destinationFile": "Dushek_2014.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Erdem_2021", - "sourcePath": "published-models/complex-models/Erdem_2021.bngl", - "destinationDir": "Published/Erdem2021", - "destinationFile": "Erdem_2021.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Jung_2017", - "sourcePath": "published-models/complex-models/Jung_2017.bngl", - "destinationDir": "Published/Jung2017", - "destinationFile": "Jung_2017.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Kesseler_2013", - "sourcePath": "published-models/complex-models/Kesseler_2013.bngl", - "destinationDir": "Published/Kesseler2013", - "destinationFile": "Kesseler_2013.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Kozer_2013", - "sourcePath": "published-models/complex-models/Kozer_2013.bngl", - "destinationDir": "Published/Kozer2013", - "destinationFile": "Kozer_2013.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Kozer_2014", - "sourcePath": "published-models/complex-models/Kozer_2014.bngl", - "destinationDir": "Published/Kozer2014", - "destinationFile": "Kozer_2014.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "mapk-dimers", - "sourcePath": "published-models/complex-models/mapk-dimers.bngl", - "destinationDir": "Published/mapkdimers", - "destinationFile": "mapk-dimers.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "mapk-monomers", - "sourcePath": "published-models/complex-models/mapk-monomers.bngl", - "destinationDir": "Published/mapkmonomers", - "destinationFile": "mapk-monomers.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Massole_2023", - "sourcePath": "published-models/complex-models/Massole_2023.bngl", - "destinationDir": "Published/Massole2023", - "destinationFile": "Massole_2023.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "McMillan_2021", - "sourcePath": "published-models/complex-models/McMillan_2021.bngl", - "destinationDir": "Published/McMillan2021", - "destinationFile": "McMillan_2021.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Nag_2009", - "sourcePath": "published-models/complex-models/Nag_2009.bngl", - "destinationDir": "Published/Nag2009", - "destinationFile": "Nag_2009.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Nosbisch_2022", - "sourcePath": "published-models/complex-models/Nosbisch_2022.bngl", - "destinationDir": "Published/Nosbisch2022", - "destinationFile": "Nosbisch_2022.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Zhang_2021", - "sourcePath": "published-models/complex-models/Zhang_2021.bngl", - "destinationDir": "Published/Zhang2021", - "destinationFile": "Zhang_2021.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Zhang_2023", - "sourcePath": "published-models/complex-models/Zhang_2023.bngl", - "destinationDir": "Published/Zhang2023", - "destinationFile": "Zhang_2023.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Blinov_egfr", - "sourcePath": "published-models/growth-factor-signaling/Blinov_egfr.bngl", - "destinationDir": "Published/Blinovegfr", - "destinationFile": "Blinov_egfr.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Lang_2024", - "sourcePath": "published-models/growth-factor-signaling/Lang_2024.bngl", - "destinationDir": "Published/Lang2024", - "destinationFile": "Lang_2024.bngl", - "origin": "published", - "category": "signaling", - "visible": true - }, - { - "id": "Ligon_2014", - "sourcePath": "published-models/growth-factor-signaling/Ligon_2014.bngl", - "destinationDir": "Published/Ligon2014", - "destinationFile": "Ligon_2014.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Mertins_2023", - "sourcePath": "published-models/growth-factor-signaling/Mertins_2023.bngl", - "destinationDir": "Published/Mertins2023", - "destinationFile": "Mertins_2023.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Rule_based_egfr_compart", - "sourcePath": "published-models/growth-factor-signaling/Rule_based_egfr_compart.bngl", - "destinationDir": "Published/Rulebasedegfrcompart", - "destinationFile": "Rule_based_egfr_compart.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "Rule_based_egfr_tutorial", - "sourcePath": "published-models/growth-factor-signaling/Rule_based_egfr_tutorial.bngl", - "destinationDir": "Published/Rulebasedegfrtutorial", - "destinationFile": "Rule_based_egfr_tutorial.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "An_2009", - "sourcePath": "published-models/immune-signaling/An_2009.bngl", - "destinationDir": "Published/An2009", - "destinationFile": "An_2009.bngl", - "origin": "published", - "category": "immunology", - "visible": true - }, - { - "id": "BaruaBCR_2012", - "sourcePath": "published-models/immune-signaling/BaruaBCR_2012.bngl", - "destinationDir": "Published/BaruaBCR2012", - "destinationFile": "BaruaBCR_2012.bngl", - "origin": "published", - "category": "immunology", - "visible": false - }, - { - "id": "BaruaFceRI_2012", - "sourcePath": "published-models/immune-signaling/BaruaFceRI_2012.bngl", - "destinationDir": "Published/BaruaFceRI2012", - "destinationFile": "BaruaFceRI_2012.bngl", - "origin": "published", - "category": "immunology", - "visible": false - }, - { - "id": "ChylekFceRI_2014", - "sourcePath": "published-models/immune-signaling/ChylekFceRI_2014.bngl", - "destinationDir": "Published/ChylekFceRI2014", - "destinationFile": "ChylekFceRI_2014.bngl", - "origin": "published", - "category": "immunology", - "visible": false - }, - { - "id": "ChylekTCR_2014", - "sourcePath": "published-models/immune-signaling/ChylekTCR_2014.bngl", - "destinationDir": "Published/ChylekTCR2014", - "destinationFile": "ChylekTCR_2014.bngl", - "origin": "published", - "category": "immunology", - "visible": false - }, - { - "id": "Faeder_2003", - "sourcePath": "published-models/immune-signaling/Faeder_2003.bngl", - "destinationDir": "Published/Faeder2003", - "destinationFile": "Faeder_2003.bngl", - "origin": "published", - "category": "immunology", - "visible": false - }, - { - "id": "innate_immunity", - "sourcePath": "published-models/immune-signaling/innate_immunity.bngl", - "destinationDir": "Published/innateimmunity", - "destinationFile": "innate_immunity.bngl", - "origin": "published", - "category": "immunology", - "visible": true - }, - { - "id": "Jaruszewicz-Blonska_2023", - "sourcePath": "published-models/immune-signaling/Jaruszewicz-Blonska_2023.bngl", - "destinationDir": "Published/JaruszewiczBlonska2023", - "destinationFile": "Jaruszewicz-Blonska_2023.bngl", - "origin": "published", - "category": "immunology", - "visible": true - }, - { - "id": "Model_ZAP", - "sourcePath": "published-models/immune-signaling/Model_ZAP.bngl", - "destinationDir": "Published/ModelZAP", - "destinationFile": "Model_ZAP.bngl", - "origin": "published", - "category": "immunology", - "visible": false - }, - { - "id": "Mukhopadhyay_2013", - "sourcePath": "published-models/immune-signaling/Mukhopadhyay_2013.bngl", - "destinationDir": "Published/Mukhopadhyay2013", - "destinationFile": "Mukhopadhyay_2013.bngl", - "origin": "published", - "category": "immunology", - "visible": false - }, - { - "id": "fceri_fyn", - "sourcePath": "published-models/immune-signaling/fceri_fyn.bngl", - "destinationDir": "Published/fcerifyn", - "destinationFile": "fceri_fyn.bngl", - "origin": "published", - "category": "immunology", - "visible": false - }, - { - "id": "tlbr", - "sourcePath": "published-models/immune-signaling/tlbr.bngl", - "destinationDir": "Published/tlbr", - "destinationFile": "tlbr.bngl", - "origin": "published", - "category": "immunology", - "visible": false - }, - { - "id": "Lin_Prion_2019", - "sourcePath": "published-models/literature/Lin_Prion_2019.bngl", - "destinationDir": "Published/LinPrion2019", - "destinationFile": "Lin_Prion_2019.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "Dolan_2015", - "sourcePath": "published-models/literature/Dolan_2015.bngl", - "destinationDir": "Published/Dolan2015", - "destinationFile": "Dolan_2015.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "Lin_ERK_2019", - "sourcePath": "published-models/literature/Lin_ERK_2019.bngl", - "destinationDir": "Published/LinERK2019", - "destinationFile": "Lin_ERK_2019.bngl", - "origin": "published", - "category": "other", - "visible": true - }, - { - "id": "Lin_TCR_2019", - "sourcePath": "published-models/literature/Lin_TCR_2019.bngl", - "destinationDir": "Published/LinTCR2019", - "destinationFile": "Lin_TCR_2019.bngl", - "origin": "published", - "category": "other", - "visible": true - }, - { - "id": "Cheemalavagu_JAK_STAT", - "sourcePath": "published-models/literature/Cheemalavagu_JAK_STAT.bngl", - "destinationDir": "Published/CheemalavaguJAKSTAT", - "destinationFile": "Cheemalavagu_JAK_STAT.bngl", - "origin": "published", - "category": "other", - "visible": true - }, - { - "id": "Alabama", - "sourcePath": "published-models/Mallela_2022/Alabama.bngl", - "destinationDir": "Published/Mallela2022/Alabama", - "destinationFile": "Alabama.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false - }, - { - "id": "AB", - "sourcePath": "published-models/native-tutorials/AB/AB.bngl", - "destinationDir": "Tutorials/NativeTutorials/AB", - "destinationFile": "AB.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "ABC", - "sourcePath": "published-models/native-tutorials/ABC/ABC.bngl", - "destinationDir": "Tutorials/NativeTutorials/ABC", - "destinationFile": "ABC.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "ABC_scan", - "sourcePath": "published-models/native-tutorials/ABC/ABC_scan.bngl", - "destinationDir": "Tutorials/NativeTutorials/ABCscan", - "destinationFile": "ABC_scan.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "ABC_ssa", - "sourcePath": "published-models/native-tutorials/ABC/ABC_ssa.bngl", - "destinationDir": "Tutorials/NativeTutorials/ABCssa", - "destinationFile": "ABC_ssa.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "LV", - "sourcePath": "published-models/native-tutorials/ABC/LV.bngl", - "destinationDir": "Tutorials/NativeTutorials/LV", - "destinationFile": "LV.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "SIR", - "sourcePath": "published-models/native-tutorials/ABC/SIR.bngl", - "destinationDir": "Tutorials/NativeTutorials/SIR", - "destinationFile": "SIR.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "ABp", - "sourcePath": "published-models/native-tutorials/ABp/ABp.bngl", - "destinationDir": "Tutorials/NativeTutorials/ABp", - "destinationFile": "ABp.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "ABp_approx", - "sourcePath": "published-models/native-tutorials/ABp/ABp_approx.bngl", - "destinationDir": "Tutorials/NativeTutorials/ABpapprox", - "destinationFile": "ABp_approx.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "GK", - "sourcePath": "published-models/native-tutorials/ABp/GK.bngl", - "destinationDir": "Tutorials/NativeTutorials/GK", - "destinationFile": "GK.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "Lisman", - "sourcePath": "published-models/native-tutorials/ABp/Lisman.bngl", - "destinationDir": "Tutorials/NativeTutorials/Lisman", - "destinationFile": "Lisman.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "Lisman_bifurcate", - "sourcePath": "published-models/native-tutorials/ABp/Lisman_bifurcate.bngl", - "destinationDir": "Tutorials/NativeTutorials/Lismanbifurcate", - "destinationFile": "Lisman_bifurcate.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "BAB", - "sourcePath": "published-models/native-tutorials/BAB/BAB.bngl", - "destinationDir": "Tutorials/NativeTutorials/BAB", - "destinationFile": "BAB.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "BAB_coop", - "sourcePath": "published-models/native-tutorials/BAB/BAB_coop.bngl", - "destinationDir": "Tutorials/NativeTutorials/BABcoop", - "destinationFile": "BAB_coop.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "BAB_scan", - "sourcePath": "published-models/native-tutorials/BAB/BAB_scan.bngl", - "destinationDir": "Tutorials/NativeTutorials/BABscan", - "destinationFile": "BAB_scan.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "BLBR", - "sourcePath": "published-models/native-tutorials/CBNGL/BLBR.bngl", - "destinationDir": "Tutorials/NativeTutorials/BLBR", - "destinationFile": "BLBR.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "cBNGL_simple", - "sourcePath": "published-models/native-tutorials/CBNGL/cBNGL_simple.bngl", - "destinationDir": "Tutorials/NativeTutorials/cBNGLsimple", - "destinationFile": "cBNGL_simple.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "LR", - "sourcePath": "published-models/native-tutorials/CBNGL/LR.bngl", - "destinationDir": "Tutorials/NativeTutorials/LR", - "destinationFile": "LR.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "LRR", - "sourcePath": "published-models/native-tutorials/CBNGL/LRR.bngl", - "destinationDir": "Tutorials/NativeTutorials/LRR", - "destinationFile": "LRR.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "LRR_comp", - "sourcePath": "published-models/native-tutorials/CBNGL/LRR_comp.bngl", - "destinationDir": "Tutorials/NativeTutorials/LRRcomp", - "destinationFile": "LRR_comp.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "LR_comp", - "sourcePath": "published-models/native-tutorials/CBNGL/LR_comp.bngl", - "destinationDir": "Tutorials/NativeTutorials/LRcomp", - "destinationFile": "LR_comp.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "LV_comp", - "sourcePath": "published-models/native-tutorials/CBNGL/LV_comp.bngl", - "destinationDir": "Tutorials/NativeTutorials/LVcomp", - "destinationFile": "LV_comp.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "organelle_transport", - "sourcePath": "published-models/native-tutorials/CBNGL/organelle_transport.bngl", - "destinationDir": "Tutorials/NativeTutorials/organelletransport", - "destinationFile": "organelle_transport.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "organelle_transport_struct", - "sourcePath": "published-models/native-tutorials/CBNGL/organelle_transport_struct.bngl", - "destinationDir": "Tutorials/NativeTutorials/organelletransportstruct", - "destinationFile": "organelle_transport_struct.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "Chylek_library", - "sourcePath": "published-models/native-tutorials/LargerModels/Chylek_library.bngl", - "destinationDir": "Tutorials/NativeTutorials/Chyleklibrary", - "destinationFile": "Chylek_library.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "Creamer_2012", - "sourcePath": "published-models/native-tutorials/LargerModels/Creamer_2012.bngl", - "destinationDir": "Tutorials/NativeTutorials/Creamer2012", - "destinationFile": "Creamer_2012.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "egfr_simple", - "sourcePath": "published-models/native-tutorials/LargerModels/egfr_simple.bngl", - "destinationDir": "Tutorials/NativeTutorials/egfrsimple", - "destinationFile": "egfr_simple.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "FceRI_ji", - "sourcePath": "published-models/native-tutorials/LargerModels/FceRI_ji.bngl", - "destinationDir": "Tutorials/NativeTutorials/FceRIji", - "destinationFile": "FceRI_ji.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "Suderman_2013", - "sourcePath": "published-models/native-tutorials/LargerModels/Suderman_2013.bngl", - "destinationDir": "Tutorials/NativeTutorials/Suderman2013", - "destinationFile": "Suderman_2013.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "birth-death", - "sourcePath": "published-models/native-tutorials/SynDeg/birth-death.bngl", - "destinationDir": "Tutorials/NativeTutorials/birthdeath", - "destinationFile": "birth-death.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "CircadianOscillator", - "sourcePath": "published-models/native-tutorials/SynDeg/CircadianOscillator.bngl", - "destinationDir": "Tutorials/NativeTutorials/CircadianOscillator", - "destinationFile": "CircadianOscillator.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "ComplexDegradation", - "sourcePath": "published-models/native-tutorials/SynDeg/ComplexDegradation.bngl", - "destinationDir": "Tutorials/NativeTutorials/ComplexDegradation", - "destinationFile": "ComplexDegradation.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "Repressilator", - "sourcePath": "published-models/native-tutorials/SynDeg/Repressilator.bngl", - "destinationDir": "Tutorials/NativeTutorials/Repressilator", - "destinationFile": "Repressilator.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "toggle", - "sourcePath": "published-models/native-tutorials/SynDeg/toggle.bngl", - "destinationDir": "Tutorials/NativeTutorials/toggle", - "destinationFile": "toggle.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "FceRI_viz", - "sourcePath": "published-models/native-tutorials/Viz/FceRI_viz.bngl", - "destinationDir": "Tutorials/NativeTutorials/FceRIviz", - "destinationFile": "FceRI_viz.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": true - }, - { - "id": "visualize", - "sourcePath": "published-models/native-tutorials/Viz/visualize.bngl", - "destinationDir": "Tutorials/NativeTutorials/visualize", - "destinationFile": "visualize.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "translateSBML", - "sourcePath": "published-models/native-tutorials/SBML/translateSBML.bngl", - "destinationDir": "Tutorials/NativeTutorials/translateSBML", - "destinationFile": "translateSBML.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "CaMKII_holo", - "sourcePath": "published-models/Ordyan_2020/CaMKII_holo.bngl", - "destinationDir": "Published/Ordyan2020/CaMKIIholo", - "destinationFile": "CaMKII_holo.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "extra_CaMKII_Holo", - "sourcePath": "published-models/Ordyan_2020/extra_CaMKII_Holo.bngl", - "destinationDir": "Published/Ordyan2020/extraCaMKIIHolo", - "destinationFile": "extra_CaMKII_Holo.bngl", - "origin": "published", - "category": "signaling", - "visible": false - }, - { - "id": "mCaMKII_Ca_Spike", - "sourcePath": "published-models/Ordyan_2020/mCaMKII_Ca_Spike.bngl", - "destinationDir": "Published/Ordyan2020/mCaMKIICaSpike", - "destinationFile": "mCaMKII_Ca_Spike.bngl", - "origin": "published", - "category": "signaling", - "visible": true - }, - { - "id": "polynomial", - "sourcePath": "published-models/PyBNG/constraint_advanced/polynomial.bngl", - "destinationDir": "PyBioNetGen/core/polynomial", - "destinationFile": "polynomial.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "polynomial_ground", - "sourcePath": "published-models/PyBNG/constraint_advanced/polynomial_ground.bngl", - "destinationDir": "PyBioNetGen/core/polynomialground", - "destinationFile": "polynomial_ground.bngl", - "origin": "published", - "category": "other", - "visible": true - }, - { - "id": "parabola", - "sourcePath": "published-models/PyBNG/constraint_demo/parabola.bngl", - "destinationDir": "PyBioNetGen/core/parabola", - "destinationFile": "parabola.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "parabola_ground", - "sourcePath": "published-models/PyBNG/constraint_demo/parabola_ground.bngl", - "destinationDir": "PyBioNetGen/core/parabolaground", - "destinationFile": "parabola_ground.bngl", - "origin": "published", - "category": "other", - "visible": true - }, - { - "id": "RAFi", - "sourcePath": "published-models/PyBNG/constraint_raf/RAFi.bngl", - "destinationDir": "PyBioNetGen/core/RAFi", - "destinationFile": "RAFi.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "RAFi_ground", - "sourcePath": "published-models/PyBNG/constraint_raf/RAFi_ground.bngl", - "destinationDir": "PyBioNetGen/core/RAFiground", - "destinationFile": "RAFi_ground.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "m11", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/Beantown/m11.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "Beantown_m11.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m1", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/BigApple/m1.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "BigApple_m1.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m4", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/BigD/m4.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "BigD_m4.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m8", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/BrotherlyLove/m8.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "BrotherlyLove_m8.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m6", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/DC/m6.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "DC_m6.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m15", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/EmeraldCity/m15.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "EmeraldCity_m15.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m12", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/Frisco/m12.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "Frisco_m12.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m9", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/Hotlanta/m9.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "Hotlanta_m9.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m5", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/HTown/m5.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "HTown_m5.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m13", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/InlandEmpire/m13.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "InlandEmpire_m13.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m2", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/LaLaLand/m2.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "LaLaLand_m2.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m7", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/MagicCity/m7.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "MagicCity_m7.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m14", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/MotorCity/m14.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "MotorCity_m14.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m10", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/Valley_of_the_Sun/m10.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "Valley_of_the_Sun_m10.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "m3", - "sourcePath": "published-models/PyBNG/COVID19forecasting_aMCMC/WindyCity/m3.bngl", - "destinationDir": "Published/Mallela2021_Cities", - "destinationFile": "WindyCity_m3.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_Cities" - }, - { - "id": "model", - "sourcePath": "published-models/PyBNG/degranulation/model.bngl", - "destinationDir": "PyBioNetGen/core/model", - "destinationFile": "model.bngl", - "origin": "published", - "category": "other", - "visible": true - }, - { - "id": "model_tofit", - "sourcePath": "published-models/PyBNG/degranulation/model_tofit.bngl", - "destinationDir": "PyBioNetGen/core/modeltofit", - "destinationFile": "model_tofit.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "model", - "sourcePath": "published-models/PyBNG/Degranulation_aMCMC/model.bngl", - "destinationDir": "PyBioNetGen/core/model_Degranulation_aMCMC", - "destinationFile": "model.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "parabola", - "sourcePath": "published-models/PyBNG/demo/parabola.bngl", - "destinationDir": "PyBioNetGen/core/parabola_demo", - "destinationFile": "parabola.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "egfr", - "sourcePath": "published-models/PyBNG/egfr_benchmark/egfr.bngl", - "destinationDir": "PyBioNetGen/core/egfr", - "destinationFile": "egfr.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "egfr_ground", - "sourcePath": "published-models/PyBNG/egfr_benchmark/egfr_ground.bngl", - "destinationDir": "PyBioNetGen/core/egfrground", - "destinationFile": "egfr_ground.bngl", - "origin": "published", - "category": "other", - "visible": true - }, - { - "id": "egfr_nf", - "sourcePath": "published-models/PyBNG/egfr_nf/egfr_nf.bngl", - "destinationDir": "PyBioNetGen/core/egfrnf", - "destinationFile": "egfr_nf.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "example2_starting_point", - "sourcePath": "published-models/PyBNG/egfr_nf/example2_starting_point.bngl", - "destinationDir": "PyBioNetGen/core/example2startingpoint", - "destinationFile": "example2_starting_point.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "egfr_ode", - "sourcePath": "published-models/PyBNG/egfr_ode/egfr_ode.bngl", - "destinationDir": "PyBioNetGen/core/egfrode", - "destinationFile": "egfr_ode.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "example1", - "sourcePath": "published-models/PyBNG/egfr_ode/example1.bngl", - "destinationDir": "PyBioNetGen/core/example1", - "destinationFile": "example1.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "fceri_gamma2", - "sourcePath": "published-models/PyBNG/fceri_gamma/fceri_gamma2.bngl", - "destinationDir": "PyBioNetGen/core/fcerigamma2", - "destinationFile": "fceri_gamma2.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "fceri_gamma2_ground_truth", - "sourcePath": "published-models/PyBNG/fceri_gamma/fceri_gamma2_ground_truth.bngl", - "destinationDir": "PyBioNetGen/core/fcerigamma2groundtruth", - "destinationFile": "fceri_gamma2_ground_truth.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "pt303", - "sourcePath": "published-models/PyBNG/HIVdynamics_aMCMC/pt303/pt303.bngl", - "destinationDir": "PyBioNetGen/HIVdynamics/pt303", - "destinationFile": "pt303.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "pt403", - "sourcePath": "published-models/PyBNG/HIVdynamics_aMCMC/pt403/pt403.bngl", - "destinationDir": "PyBioNetGen/HIVdynamics/pt403", - "destinationFile": "pt403.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "pt409", - "sourcePath": "published-models/PyBNG/HIVdynamics_aMCMC/pt409/pt409.bngl", - "destinationDir": "PyBioNetGen/HIVdynamics/pt409", - "destinationFile": "pt409.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "IGF1R_Model_receptor_activation_bnf", - "sourcePath": "published-models/PyBNG/igf1r/IGF1R_Model_receptor_activation_bnf.bngl", - "destinationDir": "PyBioNetGen/core/IGF1RModelreceptoractivationbnf", - "destinationFile": "IGF1R_Model_receptor_activation_bnf.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "Alabama", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Alabama/Alabama.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Alabama_Alabama.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Alaska", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Alaska/Alaska.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Alaska_Alaska.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Arizona", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Arizona/Arizona.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Arizona_Arizona.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Arkansas", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Arkansas/Arkansas.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Arkansas_Arkansas.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "California", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/California/California.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_California_California.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Colorado", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Colorado/Colorado.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Colorado_Colorado.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Connecticut", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Connecticut/Connecticut.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Connecticut_Connecticut.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Delaware", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Delaware/Delaware.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Delaware_Delaware.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Florida", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Florida/Florida.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Florida_Florida.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Georgia", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Georgia/Georgia.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Georgia_Georgia.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Hawaii", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Hawaii/Hawaii.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Hawaii_Hawaii.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Idaho", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Idaho/Idaho.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Idaho_Idaho.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Illinois", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Illinois/Illinois.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Illinois_Illinois.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Indiana", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Indiana/Indiana.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Indiana_Indiana.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Iowa", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Iowa/Iowa.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Iowa_Iowa.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Kansas", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Kansas/Kansas.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Kansas_Kansas.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Kentucky", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Kentucky/Kentucky.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Kentucky_Kentucky.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Louisiana", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Louisiana/Louisiana.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Louisiana_Louisiana.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Maine", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Maine/Maine.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Maine_Maine.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Maryland", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Maryland/Maryland.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Maryland_Maryland.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Massachusetts", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Massachusetts/Massachusetts.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Massachusetts_Massachusetts.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Michigan", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Michigan/Michigan.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Michigan_Michigan.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Minnesota", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Minnesota/Minnesota.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Minnesota_Minnesota.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Mississippi", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Mississippi/Mississippi.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Mississippi_Mississippi.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Missouri", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Missouri/Missouri.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Missouri_Missouri.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Montana", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Montana/Montana.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Montana_Montana.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Nebraska", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Nebraska/Nebraska.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Nebraska_Nebraska.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Nevada", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Nevada/Nevada.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Nevada_Nevada.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "NewHampshire", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/NewHampshire/NewHampshire.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_NewHampshire_NewHampshire.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "NewJersey", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/NewJersey/NewJersey.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_NewJersey_NewJersey.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "NewMexico", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/NewMexico/NewMexico.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_NewMexico_NewMexico.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "NewYork", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/NewYork/NewYork.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_NewYork_NewYork.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "NorthCarolina", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/NorthCarolina/NorthCarolina.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_NorthCarolina_NorthCarolina.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "NorthDakota", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/NorthDakota/NorthDakota.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_NorthDakota_NorthDakota.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Ohio", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Ohio/Ohio.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Ohio_Ohio.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Oklahoma", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Oklahoma/Oklahoma.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Oklahoma_Oklahoma.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Oregon", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Oregon/Oregon.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Oregon_Oregon.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Pennsylvania", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Pennsylvania/Pennsylvania.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Pennsylvania_Pennsylvania.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "RhodeIsland", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/RhodeIsland/RhodeIsland.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_RhodeIsland_RhodeIsland.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SouthCarolina", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/SouthCarolina/SouthCarolina.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_SouthCarolina_SouthCarolina.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "SouthDakota", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/SouthDakota/SouthDakota.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_SouthDakota_SouthDakota.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Tennessee", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Tennessee/Tennessee.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Tennessee_Tennessee.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Texas", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Texas/Texas.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Texas_Texas.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Utah", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Utah/Utah.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Utah_Utah.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Vermont", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Vermont/Vermont.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Vermont_Vermont.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Virginia", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Virginia/Virginia.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Virginia_Virginia.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Washington", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Washington/Washington.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Washington_Washington.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "WestVirginia", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/WestVirginia/WestVirginia.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_WestVirginia_WestVirginia.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Wisconsin", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Wisconsin/Wisconsin.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Wisconsin_Wisconsin.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Wyoming", - "sourcePath": "published-models/PyBNG/Mallela2021States/SI_files/Wyoming/Wyoming.bngl", - "destinationDir": "Published/Mallela2021", - "destinationFile": "SI_files_Wyoming_Wyoming.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2021_States" - }, - { - "id": "Abilene_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Abilene_TX/Abilene_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Abilene_TX_Abilene_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Akron_OH", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Akron_OH/Akron_OH.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Akron_OH_Akron_OH.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Albany-Schenectady-Troy_NY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Albany-Schenectady-Troy_NY/Albany-Schenectady-Troy_NY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Albany-Schenectady-Troy_NY_Albany-Schenectady-Troy_NY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Albany_GA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Albany_GA/Albany_GA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Albany_GA_Albany_GA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Albuquerque_NM", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Albuquerque_NM/Albuquerque_NM.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Albuquerque_NM_Albuquerque_NM.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Alexandria_LA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Alexandria_LA/Alexandria_LA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Alexandria_LA_Alexandria_LA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Allentown-Bethlehem-Easton_PA-NJ", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Allentown-Bethlehem-Easton_PA-NJ/Allentown-Bethlehem-Easton_PA-NJ.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Allentown-Bethlehem-Easton_PA-NJ_Allentown-Bethlehem-Easton_PA-NJ.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Amarillo_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Amarillo_TX/Amarillo_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Amarillo_TX_Amarillo_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Anchorage_AK", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Anchorage_AK/Anchorage_AK.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Anchorage_AK_Anchorage_AK.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Ann_Arbor_MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Ann_Arbor_MI/Ann_Arbor_MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Ann_Arbor_MI_Ann_Arbor_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Appleton_WI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Appleton_WI/Appleton_WI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Appleton_WI_Appleton_WI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Asheville_NC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Asheville_NC/Asheville_NC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Asheville_NC_Asheville_NC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Athens-Clarke_County_GA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Athens-Clarke_County_GA/Athens-Clarke_County_GA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Athens-Clarke_County_GA_Athens-Clarke_County_GA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Atlanta-Sandy_Springs-Alpharetta_GA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Atlanta-Sandy_Springs-Alpharetta_GA/Atlanta-Sandy_Springs-Alpharetta_GA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Atlanta-Sandy_Springs-Alpharetta_GA_Atlanta-Sandy_Springs-Alpharetta_GA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Atlantic_City-Hammonton_NJ", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Atlantic_City-Hammonton_NJ/Atlantic_City-Hammonton_NJ.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Atlantic_City-Hammonton_NJ_Atlantic_City-Hammonton_NJ.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Auburn-Opelika_AL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Auburn-Opelika_AL/Auburn-Opelika_AL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Auburn-Opelika_AL_Auburn-Opelika_AL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Augusta-Richmond_County_GA-SC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Augusta-Richmond_County_GA-SC/Augusta-Richmond_County_GA-SC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Augusta-Richmond_County_GA-SC_Augusta-Richmond_County_GA-SC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Austin-Round_Rock_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Austin-Round_Rock_TX/Austin-Round_Rock_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Austin-Round_Rock_TX_Austin-Round_Rock_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Bakersfield_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Bakersfield_CA/Bakersfield_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Bakersfield_CA_Bakersfield_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Baltimore-Columbia-Towson_MD", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Baltimore-Columbia-Towson_MD/Baltimore-Columbia-Towson_MD.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Baltimore-Columbia-Towson_MD_Baltimore-Columbia-Towson_MD.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Barnstable_Town_MA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Barnstable_Town_MA/Barnstable_Town_MA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Barnstable_Town_MA_Barnstable_Town_MA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Baton_Rouge_LA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Baton_Rouge_LA/Baton_Rouge_LA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Baton_Rouge_LA_Baton_Rouge_LA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Battle_Creek_MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Battle_Creek_MI/Battle_Creek_MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Battle_Creek_MI_Battle_Creek_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Bay_City_MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Bay_City_MI/Bay_City_MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Bay_City_MI_Bay_City_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Beaumont-Port_Arthur_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Beaumont-Port_Arthur_TX/Beaumont-Port_Arthur_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Beaumont-Port_Arthur_TX_Beaumont-Port_Arthur_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Bellingham_WA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Bellingham_WA/Bellingham_WA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Bellingham_WA_Bellingham_WA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Binghamton_NY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Binghamton_NY/Binghamton_NY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Binghamton_NY_Binghamton_NY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Birmingham-Hoover_AL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Birmingham-Hoover_AL/Birmingham-Hoover_AL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Birmingham-Hoover_AL_Birmingham-Hoover_AL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Bloomington_IN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Bloomington_IN/Bloomington_IN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Bloomington_IN_Bloomington_IN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Bloomsburg-Berwick_PA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Bloomsburg-Berwick_PA/Bloomsburg-Berwick_PA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Bloomsburg-Berwick_PA_Bloomsburg-Berwick_PA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Boise_City_ID", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Boise_City_ID/Boise_City_ID.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Boise_City_ID_Boise_City_ID.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Boston-Cambridge-Newton_MA-NH", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Boston-Cambridge-Newton_MA-NH/Boston-Cambridge-Newton_MA-NH.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Boston-Cambridge-Newton_MA-NH_Boston-Cambridge-Newton_MA-NH.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Boulder_CO", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Boulder_CO/Boulder_CO.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Boulder_CO_Boulder_CO.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Bowling_Green_KY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Bowling_Green_KY/Bowling_Green_KY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Bowling_Green_KY_Bowling_Green_KY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Bridgeport-Stamford-Norwalk_CT", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Bridgeport-Stamford-Norwalk_CT/Bridgeport-Stamford-Norwalk_CT.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Bridgeport-Stamford-Norwalk_CT_Bridgeport-Stamford-Norwalk_CT.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Brownsville-Harlingen_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Brownsville-Harlingen_TX/Brownsville-Harlingen_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Brownsville-Harlingen_TX_Brownsville-Harlingen_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Buffalo-Niagara_Falls_NY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Buffalo-Niagara_Falls_NY/Buffalo-Niagara_Falls_NY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Buffalo-Niagara_Falls_NY_Buffalo-Niagara_Falls_NY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Burlington-South_Burlington_VT", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Burlington-South_Burlington_VT/Burlington-South_Burlington_VT.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Burlington-South_Burlington_VT_Burlington-South_Burlington_VT.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Burlington_NC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Burlington_NC/Burlington_NC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Burlington_NC_Burlington_NC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "California-Lexington_Park_MD", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/California-Lexington_Park_MD/California-Lexington_Park_MD.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "California-Lexington_Park_MD_California-Lexington_Park_MD.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Canton-Massillon_OH", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Canton-Massillon_OH/Canton-Massillon_OH.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Canton-Massillon_OH_Canton-Massillon_OH.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Cape_Coral-Fort_Myers_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Cape_Coral-Fort_Myers_FL/Cape_Coral-Fort_Myers_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Cape_Coral-Fort_Myers_FL_Cape_Coral-Fort_Myers_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Carbondale-Marion_IL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Carbondale-Marion_IL/Carbondale-Marion_IL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Carbondale-Marion_IL_Carbondale-Marion_IL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Cedar_Rapids_IA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Cedar_Rapids_IA/Cedar_Rapids_IA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Cedar_Rapids_IA_Cedar_Rapids_IA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Chambersburg-Waynesboro_PA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Chambersburg-Waynesboro_PA/Chambersburg-Waynesboro_PA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Chambersburg-Waynesboro_PA_Chambersburg-Waynesboro_PA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Champaign-Urbana_IL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Champaign-Urbana_IL/Champaign-Urbana_IL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Champaign-Urbana_IL_Champaign-Urbana_IL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Charleston-North_Charleston_SC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Charleston-North_Charleston_SC/Charleston-North_Charleston_SC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Charleston-North_Charleston_SC_Charleston-North_Charleston_SC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Charleston_WV", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Charleston_WV/Charleston_WV.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Charleston_WV_Charleston_WV.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Charlotte-Concord-Gastonia_NC-SC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Charlotte-Concord-Gastonia_NC-SC/Charlotte-Concord-Gastonia_NC-SC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Charlotte-Concord-Gastonia_NC-SC_Charlotte-Concord-Gastonia_NC-SC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Charlottesville_VA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Charlottesville_VA/Charlottesville_VA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Charlottesville_VA_Charlottesville_VA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Chattanooga_TN-GA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Chattanooga_TN-GA/Chattanooga_TN-GA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Chattanooga_TN-GA_Chattanooga_TN-GA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Chicago-Naperville-Elgin_IL-IN-WI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Chicago-Naperville-Elgin_IL-IN-WI/Chicago-Naperville-Elgin_IL-IN-WI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Chicago-Naperville-Elgin_IL-IN-WI_Chicago-Naperville-Elgin_IL-IN-WI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Cincinnati_OH-KY-IN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Cincinnati_OH-KY-IN/Cincinnati_OH-KY-IN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Cincinnati_OH-KY-IN_Cincinnati_OH-KY-IN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Clarksville_TN-KY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Clarksville_TN-KY/Clarksville_TN-KY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Clarksville_TN-KY_Clarksville_TN-KY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Cleveland-Elyria_OH", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Cleveland-Elyria_OH/Cleveland-Elyria_OH.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Cleveland-Elyria_OH_Cleveland-Elyria_OH.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "College_Station-Bryan_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/College_Station-Bryan_TX/College_Station-Bryan_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "College_Station-Bryan_TX_College_Station-Bryan_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Colorado_Springs_CO", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Colorado_Springs_CO/Colorado_Springs_CO.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Colorado_Springs_CO_Colorado_Springs_CO.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Columbia_SC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Columbia_SC/Columbia_SC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Columbia_SC_Columbia_SC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Columbus_GA-AL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Columbus_GA-AL/Columbus_GA-AL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Columbus_GA-AL_Columbus_GA-AL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Columbus_IN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Columbus_IN/Columbus_IN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Columbus_IN_Columbus_IN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Columbus_OH", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Columbus_OH/Columbus_OH.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Columbus_OH_Columbus_OH.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Corpus_Christi_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Corpus_Christi_TX/Corpus_Christi_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Corpus_Christi_TX_Corpus_Christi_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Crestview-Fort_Walton_Beach-Destin_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Crestview-Fort_Walton_Beach-Destin_FL/Crestview-Fort_Walton_Beach-Destin_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Crestview-Fort_Walton_Beach-Destin_FL_Crestview-Fort_Walton_Beach-Destin_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Cumberland_MD-WV", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Cumberland_MD-WV/Cumberland_MD-WV.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Cumberland_MD-WV_Cumberland_MD-WV.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Dallas-Fort_Worth-Arlington_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Dallas-Fort_Worth-Arlington_TX/Dallas-Fort_Worth-Arlington_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Dallas-Fort_Worth-Arlington_TX_Dallas-Fort_Worth-Arlington_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Dalton_GA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Dalton_GA/Dalton_GA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Dalton_GA_Dalton_GA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Daphne-Fairhope-Foley_AL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Daphne-Fairhope-Foley_AL/Daphne-Fairhope-Foley_AL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Daphne-Fairhope-Foley_AL_Daphne-Fairhope-Foley_AL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Davenport-Moline-Rock_Island_IA-IL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Davenport-Moline-Rock_Island_IA-IL/Davenport-Moline-Rock_Island_IA-IL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Davenport-Moline-Rock_Island_IA-IL_Davenport-Moline-Rock_Island_IA-IL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Dayton_OH", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Dayton_OH/Dayton_OH.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Dayton_OH_Dayton_OH.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Deltona-Daytona_Beach-Ormond_Beach_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Deltona-Daytona_Beach-Ormond_Beach_FL/Deltona-Daytona_Beach-Ormond_Beach_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Deltona-Daytona_Beach-Ormond_Beach_FL_Deltona-Daytona_Beach-Ormond_Beach_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Denver-Aurora-Lakewood_CO", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Denver-Aurora-Lakewood_CO/Denver-Aurora-Lakewood_CO.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Denver-Aurora-Lakewood_CO_Denver-Aurora-Lakewood_CO.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Des_Moines-West_Des_Moines_IA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Des_Moines-West_Des_Moines_IA/Des_Moines-West_Des_Moines_IA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Des_Moines-West_Des_Moines_IA_Des_Moines-West_Des_Moines_IA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Detroit-Warren-Dearborn_MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Detroit-Warren-Dearborn_MI/Detroit-Warren-Dearborn_MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Detroit-Warren-Dearborn_MI_Detroit-Warren-Dearborn_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Detroit–Warren–Dearborn, MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Detroit–Warren–Dearborn, MI/Detroit–Warren–Dearborn, MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Detroit_Warren_Dearborn_MI_Detroit_Warren_Dearborn_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Dothan_AL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Dothan_AL/Dothan_AL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Dothan_AL_Dothan_AL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Dover_DE", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Dover_DE/Dover_DE.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Dover_DE_Dover_DE.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Dubuque_IA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Dubuque_IA/Dubuque_IA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Dubuque_IA_Dubuque_IA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Durham-Chapel_Hill_NC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Durham-Chapel_Hill_NC/Durham-Chapel_Hill_NC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Durham-Chapel_Hill_NC_Durham-Chapel_Hill_NC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "East_Stroudsburg_PA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/East_Stroudsburg_PA/East_Stroudsburg_PA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "East_Stroudsburg_PA_East_Stroudsburg_PA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Elkhart-Goshen_IN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Elkhart-Goshen_IN/Elkhart-Goshen_IN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Elkhart-Goshen_IN_Elkhart-Goshen_IN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "El_Centro_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/El_Centro_CA/El_Centro_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "El_Centro_CA_El_Centro_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "El_Paso_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/El_Paso_TX/El_Paso_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "El_Paso_TX_El_Paso_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Evansville_IN-KY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Evansville_IN-KY/Evansville_IN-KY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Evansville_IN-KY_Evansville_IN-KY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Fargo_ND-MN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Fargo_ND-MN/Fargo_ND-MN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Fargo_ND-MN_Fargo_ND-MN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Farmington_NM", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Farmington_NM/Farmington_NM.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Farmington_NM_Farmington_NM.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Fayetteville-Springdale-Rogers_AR", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Fayetteville-Springdale-Rogers_AR/Fayetteville-Springdale-Rogers_AR.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Fayetteville-Springdale-Rogers_AR_Fayetteville-Springdale-Rogers_AR.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Fayetteville_NC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Fayetteville_NC/Fayetteville_NC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Fayetteville_NC_Fayetteville_NC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Flagstaff_AZ", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Flagstaff_AZ/Flagstaff_AZ.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Flagstaff_AZ_Flagstaff_AZ.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Flint_MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Flint_MI/Flint_MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Flint_MI_Flint_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Florence-Muscle_Shoals_AL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Florence-Muscle_Shoals_AL/Florence-Muscle_Shoals_AL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Florence-Muscle_Shoals_AL_Florence-Muscle_Shoals_AL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Florence_SC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Florence_SC/Florence_SC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Florence_SC_Florence_SC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Fort_Collins_CO", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Fort_Collins_CO/Fort_Collins_CO.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Fort_Collins_CO_Fort_Collins_CO.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Fort_Wayne_IN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Fort_Wayne_IN/Fort_Wayne_IN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Fort_Wayne_IN_Fort_Wayne_IN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Fresno_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Fresno_CA/Fresno_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Fresno_CA_Fresno_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Gadsden_AL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Gadsden_AL/Gadsden_AL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Gadsden_AL_Gadsden_AL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Gainesville_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Gainesville_FL/Gainesville_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Gainesville_FL_Gainesville_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Gainesville_GA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Gainesville_GA/Gainesville_GA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Gainesville_GA_Gainesville_GA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Glens_Falls_NY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Glens_Falls_NY/Glens_Falls_NY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Glens_Falls_NY_Glens_Falls_NY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Goldsboro_NC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Goldsboro_NC/Goldsboro_NC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Goldsboro_NC_Goldsboro_NC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Grand_Forks_ND-MN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Grand_Forks_ND-MN/Grand_Forks_ND-MN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Grand_Forks_ND-MN_Grand_Forks_ND-MN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Grand_Island_NE", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Grand_Island_NE/Grand_Island_NE.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Grand_Island_NE_Grand_Island_NE.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Grand_Rapids-Kentwood_MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Grand_Rapids-Kentwood_MI/Grand_Rapids-Kentwood_MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Grand_Rapids-Kentwood_MI_Grand_Rapids-Kentwood_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Greeley_CO", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Greeley_CO/Greeley_CO.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Greeley_CO_Greeley_CO.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Greensboro-High_Point_NC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Greensboro-High_Point_NC/Greensboro-High_Point_NC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Greensboro-High_Point_NC_Greensboro-High_Point_NC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Greenville-Anderson_SC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Greenville-Anderson_SC/Greenville-Anderson_SC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Greenville-Anderson_SC_Greenville-Anderson_SC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Greenville_NC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Greenville_NC/Greenville_NC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Greenville_NC_Greenville_NC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Green_Bay_WI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Green_Bay_WI/Green_Bay_WI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Green_Bay_WI_Green_Bay_WI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Gulfport-Biloxi_MS", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Gulfport-Biloxi_MS/Gulfport-Biloxi_MS.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Gulfport-Biloxi_MS_Gulfport-Biloxi_MS.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Hagerstown-Martinsburg_MD-WV", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Hagerstown-Martinsburg_MD-WV/Hagerstown-Martinsburg_MD-WV.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Hagerstown-Martinsburg_MD-WV_Hagerstown-Martinsburg_MD-WV.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Hammond_LA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Hammond_LA/Hammond_LA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Hammond_LA_Hammond_LA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Hanford-Corcoran_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Hanford-Corcoran_CA/Hanford-Corcoran_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Hanford-Corcoran_CA_Hanford-Corcoran_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Harrisburg-Carlisle_PA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Harrisburg-Carlisle_PA/Harrisburg-Carlisle_PA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Harrisburg-Carlisle_PA_Harrisburg-Carlisle_PA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Harrisonburg_VA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Harrisonburg_VA/Harrisonburg_VA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Harrisonburg_VA_Harrisonburg_VA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Hartford-East_Hartford-Middletown_CT", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Hartford-East_Hartford-Middletown_CT/Hartford-East_Hartford-Middletown_CT.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Hartford-East_Hartford-Middletown_CT_Hartford-East_Hartford-Middletown_CT.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Hattiesburg_MS", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Hattiesburg_MS/Hattiesburg_MS.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Hattiesburg_MS_Hattiesburg_MS.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Hickory-Lenoir-Morganton_NC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Hickory-Lenoir-Morganton_NC/Hickory-Lenoir-Morganton_NC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Hickory-Lenoir-Morganton_NC_Hickory-Lenoir-Morganton_NC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Hilton_Head_Island-Bluffton-Beaufort_SC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Hilton_Head_Island-Bluffton-Beaufort_SC/Hilton_Head_Island-Bluffton-Beaufort_SC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Hilton_Head_Island-Bluffton-Beaufort_SC_Hilton_Head_Island-Bluffton-Beaufort_SC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Houma-Thibodaux_LA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Houma-Thibodaux_LA/Houma-Thibodaux_LA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Houma-Thibodaux_LA_Houma-Thibodaux_LA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Houston-The_Woodlands-Sugar_Land_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Houston-The_Woodlands-Sugar_Land_TX/Houston-The_Woodlands-Sugar_Land_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Houston-The_Woodlands-Sugar_Land_TX_Houston-The_Woodlands-Sugar_Land_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Huntington-Ashland_WV-KY-OH", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Huntington-Ashland_WV-KY-OH/Huntington-Ashland_WV-KY-OH.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Huntington-Ashland_WV-KY-OH_Huntington-Ashland_WV-KY-OH.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Huntsville_AL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Huntsville_AL/Huntsville_AL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Huntsville_AL_Huntsville_AL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Indianapolis-Carmel-Anderson_IN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Indianapolis-Carmel-Anderson_IN/Indianapolis-Carmel-Anderson_IN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Indianapolis-Carmel-Anderson_IN_Indianapolis-Carmel-Anderson_IN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Iowa_City_IA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Iowa_City_IA/Iowa_City_IA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Iowa_City_IA_Iowa_City_IA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Jacksonville_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Jacksonville_FL/Jacksonville_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Jacksonville_FL_Jacksonville_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Jackson_MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Jackson_MI/Jackson_MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Jackson_MI_Jackson_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Jackson_MS", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Jackson_MS/Jackson_MS.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Jackson_MS_Jackson_MS.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Janesville-Beloit_WI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Janesville-Beloit_WI/Janesville-Beloit_WI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Janesville-Beloit_WI_Janesville-Beloit_WI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Kalamazoo-Portage_MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Kalamazoo-Portage_MI/Kalamazoo-Portage_MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Kalamazoo-Portage_MI_Kalamazoo-Portage_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Kankakee_IL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Kankakee_IL/Kankakee_IL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Kankakee_IL_Kankakee_IL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Kansas_City_MO-KS", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Kansas_City_MO-KS/Kansas_City_MO-KS.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Kansas_City_MO-KS_Kansas_City_MO-KS.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Kennewick-Richland_WA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Kennewick-Richland_WA/Kennewick-Richland_WA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Kennewick-Richland_WA_Kennewick-Richland_WA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Killeen-Temple_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Killeen-Temple_TX/Killeen-Temple_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Killeen-Temple_TX_Killeen-Temple_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Kingston_NY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Kingston_NY/Kingston_NY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Kingston_NY_Kingston_NY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Knoxville_TN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Knoxville_TN/Knoxville_TN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Knoxville_TN_Knoxville_TN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Kokomo_IN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Kokomo_IN/Kokomo_IN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Kokomo_IN_Kokomo_IN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lafayette-West_Lafayette_IN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Lafayette-West_Lafayette_IN/Lafayette-West_Lafayette_IN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Lafayette-West_Lafayette_IN_Lafayette-West_Lafayette_IN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lafayette_LA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Lafayette_LA/Lafayette_LA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Lafayette_LA_Lafayette_LA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lakeland-Winter_Haven_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Lakeland-Winter_Haven_FL/Lakeland-Winter_Haven_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Lakeland-Winter_Haven_FL_Lakeland-Winter_Haven_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lake_Charles_LA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Lake_Charles_LA/Lake_Charles_LA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Lake_Charles_LA_Lake_Charles_LA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lake_Havasu_City-Kingman_AZ", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Lake_Havasu_City-Kingman_AZ/Lake_Havasu_City-Kingman_AZ.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Lake_Havasu_City-Kingman_AZ_Lake_Havasu_City-Kingman_AZ.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lancaster_PA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Lancaster_PA/Lancaster_PA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Lancaster_PA_Lancaster_PA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lansing-East_Lansing_MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Lansing-East_Lansing_MI/Lansing-East_Lansing_MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Lansing-East_Lansing_MI_Lansing-East_Lansing_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Laredo_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Laredo_TX/Laredo_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Laredo_TX_Laredo_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Las_Cruces_NM", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Las_Cruces_NM/Las_Cruces_NM.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Las_Cruces_NM_Las_Cruces_NM.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Las_Vegas-Henderson-Paradise_NV", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Las_Vegas-Henderson-Paradise_NV/Las_Vegas-Henderson-Paradise_NV.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Las_Vegas-Henderson-Paradise_NV_Las_Vegas-Henderson-Paradise_NV.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lawton_OK", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Lawton_OK/Lawton_OK.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Lawton_OK_Lawton_OK.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lebanon_PA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Lebanon_PA/Lebanon_PA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Lebanon_PA_Lebanon_PA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lexington-Fayette_KY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Lexington-Fayette_KY/Lexington-Fayette_KY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Lexington-Fayette_KY_Lexington-Fayette_KY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lincoln_NE", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Lincoln_NE/Lincoln_NE.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Lincoln_NE_Lincoln_NE.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Little_Rock-North_Little_Rock-Conway_AR", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Little_Rock-North_Little_Rock-Conway_AR/Little_Rock-North_Little_Rock-Conway_AR.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Little_Rock-North_Little_Rock-Conway_AR_Little_Rock-North_Little_Rock-Conway_AR.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Longview_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Longview_TX/Longview_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Longview_TX_Longview_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Los_Angeles-Long_Beach-Anaheim_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Los_Angeles-Long_Beach-Anaheim_CA/Los_Angeles-Long_Beach-Anaheim_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Los_Angeles-Long_Beach-Anaheim_CA_Los_Angeles-Long_Beach-Anaheim_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Jefferson_County_KY-IN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Louisville/Jefferson_County_KY-IN/Louisville/Jefferson_County_KY-IN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Louisville_Jefferson_County_KY-IN_Louisville_Jefferson_County_KY-IN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Lubbock_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Lubbock_TX/Lubbock_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Lubbock_TX_Lubbock_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Macon-Bibb_County_GA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Macon-Bibb_County_GA/Macon-Bibb_County_GA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Macon-Bibb_County_GA_Macon-Bibb_County_GA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Madison_WI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Madison_WI/Madison_WI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Madison_WI_Madison_WI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Manchester-Nashua_NH", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Manchester-Nashua_NH/Manchester-Nashua_NH.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Manchester-Nashua_NH_Manchester-Nashua_NH.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "McAllen-Edinburg-Mission_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/McAllen-Edinburg-Mission_TX/McAllen-Edinburg-Mission_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "McAllen-Edinburg-Mission_TX_McAllen-Edinburg-Mission_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Memphis_TN-MS-AR", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Memphis_TN-MS-AR/Memphis_TN-MS-AR.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Memphis_TN-MS-AR_Memphis_TN-MS-AR.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Merced_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Merced_CA/Merced_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Merced_CA_Merced_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Miami-Fort_Lauderdale-West_Palm_Beach_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Miami-Fort_Lauderdale-West_Palm_Beach_FL/Miami-Fort_Lauderdale-West_Palm_Beach_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Miami-Fort_Lauderdale-West_Palm_Beach_FL_Miami-Fort_Lauderdale-West_Palm_Beach_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Michigan_City-La_Porte_IN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Michigan_City-La_Porte_IN/Michigan_City-La_Porte_IN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Michigan_City-La_Porte_IN_Michigan_City-La_Porte_IN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Milwaukee-Waukesha_WI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Milwaukee-Waukesha_WI/Milwaukee-Waukesha_WI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Milwaukee-Waukesha_WI_Milwaukee-Waukesha_WI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Minneapolis-St._Paul-Bloomington_MN-WI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Minneapolis-St._Paul-Bloomington_MN-WI/Minneapolis-St._Paul-Bloomington_MN-WI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Minneapolis-St._Paul-Bloomington_MN-WI_Minneapolis-St._Paul-Bloomington_MN-WI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Mobile_AL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Mobile_AL/Mobile_AL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Mobile_AL_Mobile_AL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Modesto_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Modesto_CA/Modesto_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Modesto_CA_Modesto_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Monroe_LA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Monroe_LA/Monroe_LA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Monroe_LA_Monroe_LA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Monroe_MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Monroe_MI/Monroe_MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Monroe_MI_Monroe_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Montgomery_AL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Montgomery_AL/Montgomery_AL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Montgomery_AL_Montgomery_AL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Mount_Vernon-Anacortes_WA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Mount_Vernon-Anacortes_WA/Mount_Vernon-Anacortes_WA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Mount_Vernon-Anacortes_WA_Mount_Vernon-Anacortes_WA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Muncie_IN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Muncie_IN/Muncie_IN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Muncie_IN_Muncie_IN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Muskegon_MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Muskegon_MI/Muskegon_MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Muskegon_MI_Muskegon_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Naples-Marco_Island_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Naples-Marco_Island_FL/Naples-Marco_Island_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Naples-Marco_Island_FL_Naples-Marco_Island_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Nashville-Davidson-Murfreesboro-Franklin_TN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Nashville-Davidson-Murfreesboro-Franklin_TN/Nashville-Davidson-Murfreesboro-Franklin_TN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Nashville-Davidson-Murfreesboro-Franklin_TN_Nashville-Davidson-Murfreesboro-Franklin_TN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "New_Haven-Milford_CT", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/New_Haven-Milford_CT/New_Haven-Milford_CT.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "New_Haven-Milford_CT_New_Haven-Milford_CT.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "New_Orleans-Metairie_LA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/New_Orleans-Metairie_LA/New_Orleans-Metairie_LA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "New_Orleans-Metairie_LA_New_Orleans-Metairie_LA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "New_York-Newark-Jersey_City_NY-NJ-PA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/New_York-Newark-Jersey_City_NY-NJ-PA/New_York-Newark-Jersey_City_NY-NJ-PA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "New_York-Newark-Jersey_City_NY-NJ-PA_New_York-Newark-Jersey_City_NY-NJ-PA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Niles_MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Niles_MI/Niles_MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Niles_MI_Niles_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "North_Port-Sarasota-Bradenton_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/North_Port-Sarasota-Bradenton_FL/North_Port-Sarasota-Bradenton_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "North_Port-Sarasota-Bradenton_FL_North_Port-Sarasota-Bradenton_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Norwich-New_London_CT", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Norwich-New_London_CT/Norwich-New_London_CT.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Norwich-New_London_CT_Norwich-New_London_CT.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Ocala_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Ocala_FL/Ocala_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Ocala_FL_Ocala_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Ocean_City_NJ", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Ocean_City_NJ/Ocean_City_NJ.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Ocean_City_NJ_Ocean_City_NJ.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Ogden-Clearfield_UT", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Ogden-Clearfield_UT/Ogden-Clearfield_UT.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Ogden-Clearfield_UT_Ogden-Clearfield_UT.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Oklahoma_City_OK", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Oklahoma_City_OK/Oklahoma_City_OK.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Oklahoma_City_OK_Oklahoma_City_OK.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Omaha-Council_Bluffs_NE-IA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Omaha-Council_Bluffs_NE-IA/Omaha-Council_Bluffs_NE-IA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Omaha-Council_Bluffs_NE-IA_Omaha-Council_Bluffs_NE-IA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Orlando-Kissimmee-Sanford_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Orlando-Kissimmee-Sanford_FL/Orlando-Kissimmee-Sanford_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Orlando-Kissimmee-Sanford_FL_Orlando-Kissimmee-Sanford_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Owensboro_KY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Owensboro_KY/Owensboro_KY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Owensboro_KY_Owensboro_KY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Oxnard-Thousand_Oaks-Ventura_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Oxnard-Thousand_Oaks-Ventura_CA/Oxnard-Thousand_Oaks-Ventura_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Oxnard-Thousand_Oaks-Ventura_CA_Oxnard-Thousand_Oaks-Ventura_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Palm_Bay-Melbourne-Titusville_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Palm_Bay-Melbourne-Titusville_FL/Palm_Bay-Melbourne-Titusville_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Palm_Bay-Melbourne-Titusville_FL_Palm_Bay-Melbourne-Titusville_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Pensacola-Ferry_Pass-Brent_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Pensacola-Ferry_Pass-Brent_FL/Pensacola-Ferry_Pass-Brent_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Pensacola-Ferry_Pass-Brent_FL_Pensacola-Ferry_Pass-Brent_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Peoria_IL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Peoria_IL/Peoria_IL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Peoria_IL_Peoria_IL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Philadelphia-Camden-Wilmington_PA-NJ-DE-MD", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Philadelphia-Camden-Wilmington_PA-NJ-DE-MD/Philadelphia-Camden-Wilmington_PA-NJ-DE-MD.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Philadelphia-Camden-Wilmington_PA-NJ-DE-MD_Philadelphia-Camden-Wilmington_PA-NJ-DE-MD.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Phoenix-Mesa-Chandler_AZ", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Phoenix-Mesa-Chandler_AZ/Phoenix-Mesa-Chandler_AZ.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Phoenix-Mesa-Chandler_AZ_Phoenix-Mesa-Chandler_AZ.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Pine_Bluff_AR", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Pine_Bluff_AR/Pine_Bluff_AR.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Pine_Bluff_AR_Pine_Bluff_AR.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Pittsburgh_PA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Pittsburgh_PA/Pittsburgh_PA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Pittsburgh_PA_Pittsburgh_PA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Pittsfield_MA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Pittsfield_MA/Pittsfield_MA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Pittsfield_MA_Pittsfield_MA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Portland-South_Portland_ME", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Portland-South_Portland_ME/Portland-South_Portland_ME.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Portland-South_Portland_ME_Portland-South_Portland_ME.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Portland-Vancouver-Hillsboro_OR-WA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Portland-Vancouver-Hillsboro_OR-WA/Portland-Vancouver-Hillsboro_OR-WA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Portland-Vancouver-Hillsboro_OR-WA_Portland-Vancouver-Hillsboro_OR-WA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Port_St._Lucie_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Port_St._Lucie_FL/Port_St._Lucie_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Port_St._Lucie_FL_Port_St._Lucie_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Poughkeepsie-Newburgh-Middletown_NY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Poughkeepsie-Newburgh-Middletown_NY/Poughkeepsie-Newburgh-Middletown_NY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Poughkeepsie-Newburgh-Middletown_NY_Poughkeepsie-Newburgh-Middletown_NY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Prescott_Valley-Prescott_AZ", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Prescott_Valley-Prescott_AZ/Prescott_Valley-Prescott_AZ.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Prescott_Valley-Prescott_AZ_Prescott_Valley-Prescott_AZ.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Providence-Warwick_RI-MA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Providence-Warwick_RI-MA/Providence-Warwick_RI-MA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Providence-Warwick_RI-MA_Providence-Warwick_RI-MA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Provo-Orem_UT", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Provo-Orem_UT/Provo-Orem_UT.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Provo-Orem_UT_Provo-Orem_UT.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Pueblo_CO", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Pueblo_CO/Pueblo_CO.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Pueblo_CO_Pueblo_CO.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Punta_Gorda_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Punta_Gorda_FL/Punta_Gorda_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Punta_Gorda_FL_Punta_Gorda_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Racine_WI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Racine_WI/Racine_WI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Racine_WI_Racine_WI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Raleigh-Cary_NC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Raleigh-Cary_NC/Raleigh-Cary_NC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Raleigh-Cary_NC_Raleigh-Cary_NC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Reading_PA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Reading_PA/Reading_PA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Reading_PA_Reading_PA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Reno_NV", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Reno_NV/Reno_NV.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Reno_NV_Reno_NV.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Richmond_VA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Richmond_VA/Richmond_VA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Richmond_VA_Richmond_VA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Riverside-San_Bernardino-Ontario_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Riverside-San_Bernardino-Ontario_CA/Riverside-San_Bernardino-Ontario_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Riverside-San_Bernardino-Ontario_CA_Riverside-San_Bernardino-Ontario_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Roanoke_VA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Roanoke_VA/Roanoke_VA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Roanoke_VA_Roanoke_VA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Rochester_MN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Rochester_MN/Rochester_MN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Rochester_MN_Rochester_MN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Rochester_NY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Rochester_NY/Rochester_NY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Rochester_NY_Rochester_NY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Rockford_IL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Rockford_IL/Rockford_IL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Rockford_IL_Rockford_IL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Rocky_Mount_NC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Rocky_Mount_NC/Rocky_Mount_NC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Rocky_Mount_NC_Rocky_Mount_NC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Rome_GA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Rome_GA/Rome_GA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Rome_GA_Rome_GA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Sacramento-Roseville-Folsom_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Sacramento-Roseville-Folsom_CA/Sacramento-Roseville-Folsom_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Sacramento-Roseville-Folsom_CA_Sacramento-Roseville-Folsom_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Saginaw_MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Saginaw_MI/Saginaw_MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Saginaw_MI_Saginaw_MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Salem_OR", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Salem_OR/Salem_OR.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Salem_OR_Salem_OR.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Salinas_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Salinas_CA/Salinas_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Salinas_CA_Salinas_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Salisbury_MD-DE", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Salisbury_MD-DE/Salisbury_MD-DE.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Salisbury_MD-DE_Salisbury_MD-DE.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Salt_Lake_City_UT", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Salt_Lake_City_UT/Salt_Lake_City_UT.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Salt_Lake_City_UT_Salt_Lake_City_UT.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Santa_Maria-Santa_Barbara_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Santa_Maria-Santa_Barbara_CA/Santa_Maria-Santa_Barbara_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Santa_Maria-Santa_Barbara_CA_Santa_Maria-Santa_Barbara_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Santa_Rosa-Petaluma_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Santa_Rosa-Petaluma_CA/Santa_Rosa-Petaluma_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Santa_Rosa-Petaluma_CA_Santa_Rosa-Petaluma_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "San_Antonio-New_Braunfels_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/San_Antonio-New_Braunfels_TX/San_Antonio-New_Braunfels_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "San_Antonio-New_Braunfels_TX_San_Antonio-New_Braunfels_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "San_Diego-Chula_Vista-Carlsbad_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/San_Diego-Chula_Vista-Carlsbad_CA/San_Diego-Chula_Vista-Carlsbad_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "San_Diego-Chula_Vista-Carlsbad_CA_San_Diego-Chula_Vista-Carlsbad_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "San_Francisco-Oakland-Berkeley_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/San_Francisco-Oakland-Berkeley_CA/San_Francisco-Oakland-Berkeley_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "San_Francisco-Oakland-Berkeley_CA_San_Francisco-Oakland-Berkeley_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "San_Jose-Sunnyvale-Santa_Clara_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/San_Jose-Sunnyvale-Santa_Clara_CA/San_Jose-Sunnyvale-Santa_Clara_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "San_Jose-Sunnyvale-Santa_Clara_CA_San_Jose-Sunnyvale-Santa_Clara_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "San_Luis_Obispo-Paso_Robles_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/San_Luis_Obispo-Paso_Robles_CA/San_Luis_Obispo-Paso_Robles_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "San_Luis_Obispo-Paso_Robles_CA_San_Luis_Obispo-Paso_Robles_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Savannah_GA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Savannah_GA/Savannah_GA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Savannah_GA_Savannah_GA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Scranton-Wilkes-Barre_PA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Scranton-Wilkes-Barre_PA/Scranton-Wilkes-Barre_PA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Scranton-Wilkes-Barre_PA_Scranton-Wilkes-Barre_PA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Scranton–Wilkes-Barre, PA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Scranton–Wilkes-Barre, PA/Scranton–Wilkes-Barre, PA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Scranton_Wilkes-Barre_PA_Scranton_Wilkes-Barre_PA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Seattle-Tacoma-Bellevue_WA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Seattle-Tacoma-Bellevue_WA/Seattle-Tacoma-Bellevue_WA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Seattle-Tacoma-Bellevue_WA_Seattle-Tacoma-Bellevue_WA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Shreveport-Bossier_City_LA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Shreveport-Bossier_City_LA/Shreveport-Bossier_City_LA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Shreveport-Bossier_City_LA_Shreveport-Bossier_City_LA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Sioux_City_IA-NE-SD", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Sioux_City_IA-NE-SD/Sioux_City_IA-NE-SD.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Sioux_City_IA-NE-SD_Sioux_City_IA-NE-SD.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Sioux_Falls_SD", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Sioux_Falls_SD/Sioux_Falls_SD.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Sioux_Falls_SD_Sioux_Falls_SD.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "South_Bend-Mishawaka_IN-MI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/South_Bend-Mishawaka_IN-MI/South_Bend-Mishawaka_IN-MI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "South_Bend-Mishawaka_IN-MI_South_Bend-Mishawaka_IN-MI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Spartanburg_SC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Spartanburg_SC/Spartanburg_SC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Spartanburg_SC_Spartanburg_SC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Spokane-Spokane_Valley_WA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Spokane-Spokane_Valley_WA/Spokane-Spokane_Valley_WA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Spokane-Spokane_Valley_WA_Spokane-Spokane_Valley_WA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Springfield_IL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Springfield_IL/Springfield_IL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Springfield_IL_Springfield_IL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Springfield_MA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Springfield_MA/Springfield_MA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Springfield_MA_Springfield_MA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "St._Cloud_MN", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/St._Cloud_MN/St._Cloud_MN.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "St._Cloud_MN_St._Cloud_MN.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "St._George_UT", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/St._George_UT/St._George_UT.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "St._George_UT_St._George_UT.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "St._Joseph_MO-KS", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/St._Joseph_MO-KS/St._Joseph_MO-KS.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "St._Joseph_MO-KS_St._Joseph_MO-KS.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "St._Louis_MO-IL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/St._Louis_MO-IL/St._Louis_MO-IL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "St._Louis_MO-IL_St._Louis_MO-IL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Stockton_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Stockton_CA/Stockton_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Stockton_CA_Stockton_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Sumter_SC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Sumter_SC/Sumter_SC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Sumter_SC_Sumter_SC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Syracuse_NY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Syracuse_NY/Syracuse_NY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Syracuse_NY_Syracuse_NY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Tallahassee_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Tallahassee_FL/Tallahassee_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Tallahassee_FL_Tallahassee_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Tampa-St._Petersburg-Clearwater_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Tampa-St._Petersburg-Clearwater_FL/Tampa-St._Petersburg-Clearwater_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Tampa-St._Petersburg-Clearwater_FL_Tampa-St._Petersburg-Clearwater_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Texarkana_TX-AR", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Texarkana_TX-AR/Texarkana_TX-AR.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Texarkana_TX-AR_Texarkana_TX-AR.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "The_Villages_FL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/The_Villages_FL/The_Villages_FL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "The_Villages_FL_The_Villages_FL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Toledo_OH", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Toledo_OH/Toledo_OH.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Toledo_OH_Toledo_OH.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Topeka_KS", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Topeka_KS/Topeka_KS.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Topeka_KS_Topeka_KS.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Trenton-Princeton_NJ", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Trenton-Princeton_NJ/Trenton-Princeton_NJ.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Trenton-Princeton_NJ_Trenton-Princeton_NJ.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Tucson_AZ", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Tucson_AZ/Tucson_AZ.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Tucson_AZ_Tucson_AZ.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Tulsa_OK", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Tulsa_OK/Tulsa_OK.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Tulsa_OK_Tulsa_OK.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Tuscaloosa_AL", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Tuscaloosa_AL/Tuscaloosa_AL.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Tuscaloosa_AL_Tuscaloosa_AL.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Twin_Falls_ID", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Twin_Falls_ID/Twin_Falls_ID.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Twin_Falls_ID_Twin_Falls_ID.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Urban_Honolulu_HI", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Urban_Honolulu_HI/Urban_Honolulu_HI.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Urban_Honolulu_HI_Urban_Honolulu_HI.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Utica-Rome_NY", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Utica-Rome_NY/Utica-Rome_NY.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Utica-Rome_NY_Utica-Rome_NY.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Valdosta_GA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Valdosta_GA/Valdosta_GA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Valdosta_GA_Valdosta_GA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Vallejo_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Vallejo_CA/Vallejo_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Vallejo_CA_Vallejo_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Victoria_TX", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Victoria_TX/Victoria_TX.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Victoria_TX_Victoria_TX.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Vineland-Bridgeton_NJ", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Vineland-Bridgeton_NJ/Vineland-Bridgeton_NJ.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Vineland-Bridgeton_NJ_Vineland-Bridgeton_NJ.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Virginia_Beach-Norfolk-Newport_News_VA-NC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Virginia_Beach-Norfolk-Newport_News_VA-NC/Virginia_Beach-Norfolk-Newport_News_VA-NC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Virginia_Beach-Norfolk-Newport_News_VA-NC_Virginia_Beach-Norfolk-Newport_News_VA-NC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Visalia_CA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Visalia_CA/Visalia_CA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Visalia_CA_Visalia_CA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Warner_Robins_GA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Warner_Robins_GA/Warner_Robins_GA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Warner_Robins_GA_Warner_Robins_GA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Washington-Arlington-Alexandria_DC-VA-MD-WV", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Washington-Arlington-Alexandria_DC-VA-MD-WV/Washington-Arlington-Alexandria_DC-VA-MD-WV.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Washington-Arlington-Alexandria_DC-VA-MD-WV_Washington-Arlington-Alexandria_DC-VA-MD-WV.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Waterloo-Cedar_Falls_IA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Waterloo-Cedar_Falls_IA/Waterloo-Cedar_Falls_IA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Waterloo-Cedar_Falls_IA_Waterloo-Cedar_Falls_IA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Wenatchee_WA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Wenatchee_WA/Wenatchee_WA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Wenatchee_WA_Wenatchee_WA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Wheeling_WV-OH", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Wheeling_WV-OH/Wheeling_WV-OH.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Wheeling_WV-OH_Wheeling_WV-OH.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Wichita_KS", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Wichita_KS/Wichita_KS.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Wichita_KS_Wichita_KS.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Winchester_VA-WV", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Winchester_VA-WV/Winchester_VA-WV.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Winchester_VA-WV_Winchester_VA-WV.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Winston-Salem_NC", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Winston-Salem_NC/Winston-Salem_NC.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Winston-Salem_NC_Winston-Salem_NC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Worcester_MA-CT", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Worcester_MA-CT/Worcester_MA-CT.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Worcester_MA-CT_Worcester_MA-CT.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Yakima_WA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Yakima_WA/Yakima_WA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Yakima_WA_Yakima_WA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "York-Hanover_PA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/York-Hanover_PA/York-Hanover_PA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "York-Hanover_PA_York-Hanover_PA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Youngstown-Warren-Boardman_OH-PA", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Youngstown-Warren-Boardman_OH-PA/Youngstown-Warren-Boardman_OH-PA.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Youngstown-Warren-Boardman_OH-PA_Youngstown-Warren-Boardman_OH-PA.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Yuma_AZ", - "sourcePath": "published-models/PyBNG/Mallela2022MSAs/Yuma_AZ/Yuma_AZ.bngl", - "destinationDir": "Published/Mallela2022_MSAs", - "destinationFile": "Yuma_AZ_Yuma_AZ.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Mallela2022_MSAs" - }, - { - "id": "Arizona", - "sourcePath": "published-models/PyBNG/Miller2022NavajoNation/supplementary_material/Arizona/Arizona.bngl", - "destinationDir": "Published/Miller2022_NavajoNation", - "destinationFile": "supplementary_material_Arizona_Arizona.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Miller2022_NavajoNation" - }, - { - "id": "Colorado", - "sourcePath": "published-models/PyBNG/Miller2022NavajoNation/supplementary_material/Colorado/Colorado.bngl", - "destinationDir": "Published/Miller2022_NavajoNation", - "destinationFile": "supplementary_material_Colorado_Colorado.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Miller2022_NavajoNation" - }, - { - "id": "NavajoNation", - "sourcePath": "published-models/PyBNG/Miller2022NavajoNation/supplementary_material/NavajoNation/NavajoNation.bngl", - "destinationDir": "Published/Miller2022_NavajoNation", - "destinationFile": "supplementary_material_NavajoNation_NavajoNation.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Miller2022_NavajoNation" - }, - { - "id": "NewMexico", - "sourcePath": "published-models/PyBNG/Miller2022NavajoNation/supplementary_material/NewMexico/NewMexico.bngl", - "destinationDir": "Published/Miller2022_NavajoNation", - "destinationFile": "supplementary_material_NewMexico_NewMexico.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Miller2022_NavajoNation" - }, - { - "id": "Utah", - "sourcePath": "published-models/PyBNG/Miller2022NavajoNation/supplementary_material/Utah/Utah.bngl", - "destinationDir": "Published/Miller2022_NavajoNation", - "destinationFile": "supplementary_material_Utah_Utah.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false, - "collectionId": "Miller2022_NavajoNation" - }, - { - "id": "MEK1_KO", - "sourcePath": "published-models/PyBNG/Miller2025_MEK_Isoforms/MEK_isoform_aMCMC/MEK1_KO.bngl", - "destinationDir": "Published/Miller2025_MEK", - "destinationFile": "MEK_isoform_aMCMC_MEK1_KO.bngl", - "origin": "published", - "category": "signaling", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK1_N78G", - "sourcePath": "published-models/PyBNG/Miller2025_MEK_Isoforms/MEK_isoform_aMCMC/MEK1_N78G.bngl", - "destinationDir": "Published/Miller2025_MEK", - "destinationFile": "MEK_isoform_aMCMC_MEK1_N78G.bngl", - "origin": "published", - "category": "signaling", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK1_T292A", - "sourcePath": "published-models/PyBNG/Miller2025_MEK_Isoforms/MEK_isoform_aMCMC/MEK1_T292A.bngl", - "destinationDir": "Published/Miller2025_MEK", - "destinationFile": "MEK_isoform_aMCMC_MEK1_T292A.bngl", - "origin": "published", - "category": "signaling", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK1_T292D", - "sourcePath": "published-models/PyBNG/Miller2025_MEK_Isoforms/MEK_isoform_aMCMC/MEK1_T292D.bngl", - "destinationDir": "Published/Miller2025_MEK", - "destinationFile": "MEK_isoform_aMCMC_MEK1_T292D.bngl", - "origin": "published", - "category": "signaling", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK1_WT", - "sourcePath": "published-models/PyBNG/Miller2025_MEK_Isoforms/MEK_isoform_aMCMC/MEK1_WT.bngl", - "destinationDir": "Published/Miller2025_MEK", - "destinationFile": "MEK_isoform_aMCMC_MEK1_WT.bngl", - "origin": "published", - "category": "signaling", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK1_KO", - "sourcePath": "published-models/PyBNG/Miller2025_MEK_Isoforms/MEK_isoform_optimization_DE/MEK1_KO.bngl", - "destinationDir": "Published/Miller2025_MEK", - "destinationFile": "MEK_isoform_optimization_DE_MEK1_KO.bngl", - "origin": "published", - "category": "signaling", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK1_N78G", - "sourcePath": "published-models/PyBNG/Miller2025_MEK_Isoforms/MEK_isoform_optimization_DE/MEK1_N78G.bngl", - "destinationDir": "Published/Miller2025_MEK", - "destinationFile": "MEK_isoform_optimization_DE_MEK1_N78G.bngl", - "origin": "published", - "category": "signaling", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK1_T292A", - "sourcePath": "published-models/PyBNG/Miller2025_MEK_Isoforms/MEK_isoform_optimization_DE/MEK1_T292A.bngl", - "destinationDir": "Published/Miller2025_MEK", - "destinationFile": "MEK_isoform_optimization_DE_MEK1_T292A.bngl", - "origin": "published", - "category": "signaling", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK1_T292D", - "sourcePath": "published-models/PyBNG/Miller2025_MEK_Isoforms/MEK_isoform_optimization_DE/MEK1_T292D.bngl", - "destinationDir": "Published/Miller2025_MEK", - "destinationFile": "MEK_isoform_optimization_DE_MEK1_T292D.bngl", - "origin": "published", - "category": "signaling", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "MEK1_WT", - "sourcePath": "published-models/PyBNG/Miller2025_MEK_Isoforms/MEK_isoform_optimization_DE/MEK1_WT.bngl", - "destinationDir": "Published/Miller2025_MEK", - "destinationFile": "MEK_isoform_optimization_DE_MEK1_WT.bngl", - "origin": "published", - "category": "signaling", - "visible": false, - "collectionId": "Miller2025_MEK" - }, - { - "id": "egfr_ode", - "sourcePath": "published-models/PyBNG/egfr_ode.bngl", - "destinationDir": "PyBioNetGen/core/egfrode_published-models_PyBNG", - "destinationFile": "egfr_ode.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "degranulation_model", - "sourcePath": "published-models/PyBNG/degranulation_model.bngl", - "destinationDir": "PyBioNetGen/core/degranulationmodel", - "destinationFile": "degranulation_model.bngl", - "origin": "published", - "category": "other", - "visible": true - }, - { - "id": "receptor", - "sourcePath": "published-models/PyBNG/receptor/receptor.bngl", - "destinationDir": "PyBioNetGen/core/receptor", - "destinationFile": "receptor.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "receptor_nf", - "sourcePath": "published-models/PyBNG/receptor_nf/receptor_nf.bngl", - "destinationDir": "PyBioNetGen/core/receptornf", - "destinationFile": "receptor_nf.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "tcr", - "sourcePath": "published-models/PyBNG/tcr/tcr.bngl", - "destinationDir": "PyBioNetGen/core/tcr", - "destinationFile": "tcr.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "parabola", - "sourcePath": "published-models/PyBNG/tests/bngl_files/errors/constraint_domain/parabola.bngl", - "destinationDir": "PyBioNetGen/tests/parabola", - "destinationFile": "parabola.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "actions_syntax", - "sourcePath": "published-models/PyBNG/tests/bngl_files/errors/actions_syntax.bngl", - "destinationDir": "PyBioNetGen/tests/actionssyntax", - "destinationFile": "actions_syntax.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "bng_error", - "sourcePath": "published-models/PyBNG/tests/bngl_files/errors/bng_error.bngl", - "destinationDir": "PyBioNetGen/tests/bngerror", - "destinationFile": "bng_error.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "free_missing", - "sourcePath": "published-models/PyBNG/tests/bngl_files/errors/free_missing.bngl", - "destinationDir": "PyBioNetGen/tests/freemissing", - "destinationFile": "free_missing.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "no_frees", - "sourcePath": "published-models/PyBNG/tests/bngl_files/errors/no_frees.bngl", - "destinationDir": "PyBioNetGen/tests/nofrees", - "destinationFile": "no_frees.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "no_generate_network", - "sourcePath": "published-models/PyBNG/tests/bngl_files/errors/no_generate_network.bngl", - "destinationDir": "PyBioNetGen/tests/nogeneratenetwork", - "destinationFile": "no_generate_network.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "no_suffix", - "sourcePath": "published-models/PyBNG/tests/bngl_files/errors/no_suffix.bngl", - "destinationDir": "PyBioNetGen/tests/nosuffix", - "destinationFile": "no_suffix.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "simple_nf_seed", - "sourcePath": "published-models/PyBNG/tests/bngl_files/errors/simple_nf_seed.bngl", - "destinationDir": "PyBioNetGen/tests/simplenfseed", - "destinationFile": "simple_nf_seed.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "ErrNoFrees", - "sourcePath": "published-models/PyBNG/tests/bngl_files/ErrNoFrees.bngl", - "destinationDir": "PyBioNetGen/tests/ErrNoFrees", - "destinationFile": "ErrNoFrees.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "LilyIgE", - "sourcePath": "published-models/PyBNG/tests/bngl_files/LilyIgE.bngl", - "destinationDir": "PyBioNetGen/tests/LilyIgE", - "destinationFile": "LilyIgE.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "NFmodel", - "sourcePath": "published-models/PyBNG/tests/bngl_files/NFmodel.bngl", - "destinationDir": "PyBioNetGen/tests/NFmodel", - "destinationFile": "NFmodel.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "parabola", - "sourcePath": "published-models/PyBNG/tests/bngl_files/parabola.bngl", - "destinationDir": "PyBioNetGen/tests/parabola_bngl_files", - "destinationFile": "parabola.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "ParamsEverywhere", - "sourcePath": "published-models/PyBNG/tests/bngl_files/ParamsEverywhere.bngl", - "destinationDir": "PyBioNetGen/tests/ParamsEverywhere", - "destinationFile": "ParamsEverywhere.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "Simple", - "sourcePath": "published-models/PyBNG/tests/bngl_files/Simple.bngl", - "destinationDir": "PyBioNetGen/tests/Simple", - "destinationFile": "Simple.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "Simple_AddActions", - "sourcePath": "published-models/PyBNG/tests/bngl_files/Simple_AddActions.bngl", - "destinationDir": "PyBioNetGen/tests/SimpleAddActions", - "destinationFile": "Simple_AddActions.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "Simple_Answer", - "sourcePath": "published-models/PyBNG/tests/bngl_files/Simple_Answer.bngl", - "destinationDir": "PyBioNetGen/tests/SimpleAnswer", - "destinationFile": "Simple_Answer.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "Simple_GenOnly", - "sourcePath": "published-models/PyBNG/tests/bngl_files/Simple_GenOnly.bngl", - "destinationDir": "PyBioNetGen/tests/SimpleGenOnly", - "destinationFile": "Simple_GenOnly.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "Simple_nogen", - "sourcePath": "published-models/PyBNG/tests/bngl_files/Simple_nogen.bngl", - "destinationDir": "PyBioNetGen/tests/Simplenogen", - "destinationFile": "Simple_nogen.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "Tricky", - "sourcePath": "published-models/PyBNG/tests/bngl_files/Tricky.bngl", - "destinationDir": "PyBioNetGen/tests/Tricky", - "destinationFile": "Tricky.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "TrickyUS", - "sourcePath": "published-models/PyBNG/tests/bngl_files/TrickyUS.bngl", - "destinationDir": "PyBioNetGen/tests/TrickyUS", - "destinationFile": "TrickyUS.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "parabola2", - "sourcePath": "published-models/PyBNG/tests/bngl_files/special_cases/duplicate_names/parabola2.bngl", - "destinationDir": "PyBioNetGen/tests/parabola2", - "destinationFile": "parabola2.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "parabola", - "sourcePath": "published-models/PyBNG/tests/bngl_files/special_cases/model_check/parabola.bngl", - "destinationDir": "PyBioNetGen/tests/parabola_bngl_files_special_cases_model_check", - "destinationFile": "parabola.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "polynomial", - "sourcePath": "published-models/PyBNG/tests/full_tests/T1-ssprop/polynomial.bngl", - "destinationDir": "PyBioNetGen/tests/polynomial", - "destinationFile": "polynomial.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "egg", - "sourcePath": "published-models/PyBNG/tests/full_tests/T3-de-egg/egg.bngl", - "destinationDir": "PyBioNetGen/tests/egg", - "destinationFile": "egg.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "receptor_nf", - "sourcePath": "published-models/PyBNG/tests/full_tests/T4-pso-nf/receptor_nf.bngl", - "destinationDir": "PyBioNetGen/tests/receptornf", - "destinationFile": "receptor_nf.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "trivial", - "sourcePath": "published-models/PyBNG/tests/full_tests/T5-pt-trivial/trivial.bngl", - "destinationDir": "PyBioNetGen/tests/trivial", - "destinationFile": "trivial.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "polynomial", - "sourcePath": "published-models/PyBNG/tests/full_tests/T6-check/polynomial.bngl", - "destinationDir": "PyBioNetGen/tests/polynomial_full_tests_T6-check", - "destinationFile": "polynomial.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "tlbr", - "sourcePath": "published-models/PyBNG/tlbr/tlbr.bngl", - "destinationDir": "PyBioNetGen/core/tlbr", - "destinationFile": "tlbr.bngl", - "origin": "published", - "category": "other", - "visible": false - }, - { - "id": "Dallas", - "sourcePath": "published-models/PyBNG/Vax_and_Variants/Dallas/Dallas.bngl", - "destinationDir": "Published/VaxAndVariants/Dallas", - "destinationFile": "Dallas.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false - }, - { - "id": "Houston", - "sourcePath": "published-models/PyBNG/Vax_and_Variants/Houston/Houston.bngl", - "destinationDir": "Published/VaxAndVariants/Houston", - "destinationFile": "Houston.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false - }, - { - "id": "NYC", - "sourcePath": "published-models/PyBNG/Vax_and_Variants/NYC/NYC.bngl", - "destinationDir": "Published/VaxAndVariants/NYC", - "destinationFile": "NYC.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false - }, - { - "id": "Phoenix", - "sourcePath": "published-models/PyBNG/Vax_and_Variants/Phoenix/Phoenix.bngl", - "destinationDir": "Published/VaxAndVariants/Phoenix", - "destinationFile": "Phoenix.bngl", - "origin": "published", - "category": "epidemiology", - "visible": false - }, - { - "id": "quasi_equilibrium", - "sourcePath": "published-models/toy-models/quasi_equilibrium.bngl", - "destinationDir": "Tutorials/General/quasiequilibrium", - "destinationFile": "quasi_equilibrium.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "chemistry", - "sourcePath": "published-models/tutorials/chemistry.bngl", - "destinationDir": "Tutorials/General/chemistry", - "destinationFile": "chemistry.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "polymer", - "sourcePath": "published-models/tutorials/polymer.bngl", - "destinationDir": "Tutorials/General/polymer", - "destinationFile": "polymer.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "polymer_draft", - "sourcePath": "published-models/tutorials/polymer_draft.bngl", - "destinationDir": "Tutorials/General/polymerdraft", - "destinationFile": "polymer_draft.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "simple", - "sourcePath": "published-models/tutorials/simple.bngl", - "destinationDir": "Tutorials/General/simple", - "destinationFile": "simple.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "toy1", - "sourcePath": "published-models/tutorials/toy1.bngl", - "destinationDir": "Tutorials/General/toy1", - "destinationFile": "toy1.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "toy2", - "sourcePath": "published-models/tutorials/toy2.bngl", - "destinationDir": "Tutorials/General/toy2", - "destinationFile": "toy2.bngl", - "origin": "tutorial", - "category": "tutorial", - "visible": false - }, - { - "id": "CaOscillate_Func", - "sourcePath": "published-models/validation/CaOscillate_Func.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/CaOscillateFunc", - "destinationFile": "CaOscillate_Func.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "CaOscillate_Sat", - "sourcePath": "published-models/validation/CaOscillate_Sat.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/CaOscillateSat", - "destinationFile": "CaOscillate_Sat.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "catalysis", - "sourcePath": "published-models/validation/catalysis.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/catalysis", - "destinationFile": "catalysis.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "continue", - "sourcePath": "published-models/validation/continue.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/continue", - "destinationFile": "continue.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "egfr_net", - "sourcePath": "published-models/validation/egfr_net.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/egfrnet", - "destinationFile": "egfr_net.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "egfr_net_red", - "sourcePath": "published-models/validation/egfr_net_red.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/egfrnetred", - "destinationFile": "egfr_net_red.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "egfr_path", - "sourcePath": "published-models/validation/egfr_path.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/egfrpath", - "destinationFile": "egfr_path.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "energy_example1", - "sourcePath": "published-models/validation/energy_example1.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/energyexample1", - "destinationFile": "energy_example1.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "example1", - "sourcePath": "published-models/validation/example1.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/example1", - "destinationFile": "example1.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "fceri_ji_comp", - "sourcePath": "published-models/validation/fceri_ji_comp.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/fcerijicomp", - "destinationFile": "fceri_ji_comp.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "Haugh2b", - "sourcePath": "published-models/validation/Haugh2b.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/Haugh2b", - "destinationFile": "Haugh2b.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "heise", - "sourcePath": "published-models/validation/heise.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/heise", - "destinationFile": "heise.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "issue_198_short", - "sourcePath": "published-models/validation/issue_198_short.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/issue198short", - "destinationFile": "issue_198_short.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "Kiefhaber_emodel", - "sourcePath": "published-models/validation/Kiefhaber_emodel.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/Kiefhaberemodel", - "destinationFile": "Kiefhaber_emodel.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "Korwek_2023", - "sourcePath": "published-models/validation/Korwek_2023.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/Korwek2023", - "destinationFile": "Korwek_2023.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "localfunc", - "sourcePath": "published-models/validation/localfunc.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/localfunc", - "destinationFile": "localfunc.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "michment", - "sourcePath": "published-models/validation/michment.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/michment", - "destinationFile": "michment.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "michment_cont", - "sourcePath": "published-models/validation/michment_cont.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/michmentcont", - "destinationFile": "michment_cont.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "Motivating_example", - "sourcePath": "published-models/validation/Motivating_example.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/Motivatingexample", - "destinationFile": "Motivating_example.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "Motivating_example_cBNGL", - "sourcePath": "published-models/validation/Motivating_example_cBNGL.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/MotivatingexamplecBNGL", - "destinationFile": "Motivating_example_cBNGL.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "motor", - "sourcePath": "published-models/validation/motor.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/motor", - "destinationFile": "motor.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "mwc", - "sourcePath": "published-models/validation/mwc.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/mwc", - "destinationFile": "mwc.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "nfkb", - "sourcePath": "published-models/validation/nfkb.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/nfkb", - "destinationFile": "nfkb.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "nfkb_illustrating_protocols", - "sourcePath": "published-models/validation/nfkb_illustrating_protocols.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/nfkbillustratingprotocols", - "destinationFile": "nfkb_illustrating_protocols.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "rec_dim", - "sourcePath": "published-models/validation/rec_dim.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/recdim", - "destinationFile": "rec_dim.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "rec_dim_comp", - "sourcePath": "published-models/validation/rec_dim_comp.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/recdimcomp", - "destinationFile": "rec_dim_comp.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "SHP2_base_model", - "sourcePath": "published-models/validation/SHP2_base_model.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/SHP2basemodel", - "destinationFile": "SHP2_base_model.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "simple_sbml_import", - "sourcePath": "published-models/validation/simple_sbml_import.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/simplesbmlimport", - "destinationFile": "simple_sbml_import.bngl", - "origin": "test-case", - "category": "validation", - "visible": false - }, - { - "id": "simple_system", - "sourcePath": "published-models/validation/simple_system.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/simplesystem", - "destinationFile": "simple_system.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "test_ANG_synthesis_simple", - "sourcePath": "published-models/validation/test_ANG_synthesis_simple.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/testANGsynthesissimple", - "destinationFile": "test_ANG_synthesis_simple.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "test_fixed", - "sourcePath": "published-models/validation/test_fixed.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/testfixed", - "destinationFile": "test_fixed.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "test_MM", - "sourcePath": "published-models/validation/test_MM.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/testMM", - "destinationFile": "test_MM.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "test_mratio", - "sourcePath": "published-models/validation/test_mratio.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/testmratio", - "destinationFile": "test_mratio.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "test_network_gen", - "sourcePath": "published-models/validation/test_network_gen.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/testnetworkgen", - "destinationFile": "test_network_gen.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "test_sat", - "sourcePath": "published-models/validation/test_sat.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/testsat", - "destinationFile": "test_sat.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "test_synthesis_cBNGL_simple", - "sourcePath": "published-models/validation/test_synthesis_cBNGL_simple.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/testsynthesiscBNGLsimple", - "destinationFile": "test_synthesis_cBNGL_simple.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "test_synthesis_complex", - "sourcePath": "published-models/validation/test_synthesis_complex.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/testsynthesiscomplex", - "destinationFile": "test_synthesis_complex.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "test_synthesis_complex_0_cBNGL", - "sourcePath": "published-models/validation/test_synthesis_complex_0_cBNGL.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/testsynthesiscomplex0cBNGL", - "destinationFile": "test_synthesis_complex_0_cBNGL.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "test_synthesis_complex_source_cBNGL", - "sourcePath": "published-models/validation/test_synthesis_complex_source_cBNGL.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/testsynthesiscomplexsourcecBNGL", - "destinationFile": "test_synthesis_complex_source_cBNGL.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "test_synthesis_simple", - "sourcePath": "published-models/validation/test_synthesis_simple.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/testsynthesissimple", - "destinationFile": "test_synthesis_simple.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "tlmr", - "sourcePath": "published-models/validation/tlmr.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/tlmr", - "destinationFile": "tlmr.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "toy-jim", - "sourcePath": "published-models/validation/toy-jim.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/toyjim", - "destinationFile": "toy-jim.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "univ_synth", - "sourcePath": "published-models/validation/univ_synth.bngl", - "destinationDir": "Contributed/BNGPlayground_Validation/univsynth", - "destinationFile": "univ_synth.bngl", - "origin": "test-case", - "category": "validation", - "visible": true - }, - { - "id": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC", - "sourcePath": "public/models/Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl", - "destinationDir": "Contributed/BNGPlayground_PublicRuntime/MyrtleBeachConwayNorthMyrtleBeachSCNC", - "destinationFile": "Myrtle_Beach-Conway-North_Myrtle_Beach_SC-NC.bngl", - "origin": "contributed", - "category": "other", - "visible": false - }, - { - "id": "polymer_fixed", - "sourcePath": "public/models/polymer_fixed.bngl", - "destinationDir": "Contributed/BNGPlayground_PublicRuntime/polymerfixed", - "destinationFile": "polymer_fixed.bngl", - "origin": "contributed", - "category": "other", - "visible": false - }, - { - "id": "simple_nfsim_test", - "sourcePath": "public/models/simple_nfsim_test.bngl", - "destinationDir": "Contributed/BNGPlayground_PublicRuntime/simplenfsimtest", - "destinationFile": "simple_nfsim_test.bngl", - "origin": "contributed", - "category": "other", - "visible": false - } - ] -} \ No newline at end of file diff --git a/scripts/apply-gallery-assignments.js b/scripts/apply-gallery-assignments.js new file mode 100644 index 0000000..dcdd76b --- /dev/null +++ b/scripts/apply-gallery-assignments.js @@ -0,0 +1,135 @@ +const fs = require('fs'); +const path = require('path'); + +function parseArgs(argv) { + let input = 'gallery-assignments.json'; + let root = path.resolve(__dirname, '..'); + let dryRun = false; + + for (let i = 0; i < argv.length; i++) { + if (argv[i] === '--input' && argv[i + 1]) { + input = argv[i + 1]; + i++; + } else if (argv[i] === '--root' && argv[i + 1]) { + root = argv[i + 1]; + i++; + } else if (argv[i] === '--dry-run') { + dryRun = true; + } + } + + return { input, root, dryRun }; +} + +function findAllMetadataFiles(dir, results = []) { + if (!fs.existsSync(dir)) return results; + + const entries = fs.readdirSync(dir, { withFileTypes: true }); + for (const entry of entries) { + const fullPath = path.join(dir, entry.name); + if (entry.isDirectory()) { + findAllMetadataFiles(fullPath, results); + } else if (entry.name === 'metadata.yaml') { + results.push(fullPath); + } + } + return results; +} + +function updateMetadataFile(filePath, assignments, dryRun) { + let content = fs.readFileSync(filePath, 'utf8'); + const dir = path.dirname(filePath); + const modelDirName = path.basename(dir); + + let updated = false; + let newContent = content; + + for (const [modelId, data] of Object.entries(assignments)) { + const idPattern = new RegExp(`^id:\\s*["']?${modelId.replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}["']?\\s*$`, 'm'); + + if (idPattern.test(content)) { + console.log(` Found model ${modelId} in ${filePath}`); + + if (data.gallery_categories && data.gallery_categories.length > 0) { + const catsStr = JSON.stringify(data.gallery_categories); + const galleryMatch = content.match(/gallery_categories:\s*(\[\]|["\'][^"\']*["\'])/); + if (galleryMatch) { + if (galleryMatch) { + newContent = newContent.replace(/gallery_categories:\s*\[\]/, `gallery_categories: ${catsStr}`); + updated = true; + } + } + + const galleryCatMatch = content.match(/gallery_category:\s*["']([^"\']+)["\']/); + if (galleryCatMatch && !content.includes('gallery_categories:')) { + newContent = newContent.replace(/gallery_category:\s*["'][^"\']+["\']/, `gallery_categories: ${catsStr}`); + updated = true; + } + + const visibleMatch = content.match(/playground:\s*$/m); + if (visibleMatch && !content.includes('visible:')) { + newContent = newContent.replace(/playground:\s*$/m, `playground:\n visible: true`); + updated = true; + } + } + + if (data.bng2_compatible !== undefined) { + const bng2Match = content.match(/bng2_compatible:\s*(true|false)/); + if (bng2Match && bng2Match[1] === 'false' && data.bng2_compatible) { + newContent = newContent.replace(/bng2_compatible:\s*false/, 'bng2_compatible: true'); + updated = true; + } + } + + if (data.nfsim_compatible !== undefined) { + const nfMatch = content.match(/nfsim_compatible:\s*(true|false)/); + if (nfMatch && nfMatch[1] === 'false' && data.nfsim_compatible) { + newContent = newContent.replace(/nfsim_compatible:\s*false/, 'nfsim_compatible: true'); + updated = true; + } + } + + if (data.excluded !== undefined) { + const excludedMatch = content.match(/excluded:\s*(true|false)/); + if (excludedMatch && excludedMatch[1] === 'false' && data.excluded) { + newContent = newContent.replace(/excluded:\s*false/, 'excluded: true'); + updated = true; + } + } + + break; + } + } + + if (updated && !dryRun) { + fs.writeFileSync(filePath, newContent); + } + + return updated; +} + +function main() { + const { input, root, dryRun } = parseArgs(process.argv.slice(2)); + + console.log(`Reading ${input}...`); + const assignments = JSON.parse(fs.readFileSync(input, 'utf8')); + console.log(`Loaded ${Object.keys(assignments).length} assignments`); + + const SEARCH_ROOTS = ['Published', 'Examples', 'Tutorials']; + const metadataFiles = SEARCH_ROOTS.flatMap(searchRoot => + findAllMetadataFiles(path.join(root, searchRoot)) + ); + + console.log(`Found ${metadataFiles.length} metadata.yaml files`); + + let updated = 0; + for (const filePath of metadataFiles) { + if (updateMetadataFile(filePath, assignments, dryRun)) { + updated++; + } + } + + console.log(`\n${dryRun ? 'Would update' : 'Updated'} ${updated} files`); +} + +main(); \ No newline at end of file diff --git a/scripts/backfill-metadata.js b/scripts/backfill-metadata.js new file mode 100644 index 0000000..ba0e42f --- /dev/null +++ b/scripts/backfill-metadata.js @@ -0,0 +1,422 @@ +const fs = require('fs'); +const path = require('path'); + +const SEARCH_ROOTS = ['Published', 'Examples', 'Tutorials']; +const DEFAULT_IGNORE_DIRS = ['fitting', 'BioNetFit_files', 'output_*', 'fit_*', '__pycache__', 'pybnf_files']; + +function parseArgs(argv) { + let root = path.resolve(__dirname, '..'); + let dryRun = false; + + for (let index = 0; index < argv.length; index += 1) { + const arg = argv[index]; + if (arg === '--root' && argv[index + 1]) { + root = path.resolve(argv[index + 1]); + index += 1; + continue; + } + if (arg === '--dry-run') { + dryRun = true; + } + } + + return { root, dryRun }; +} + +function findBnglFiles(dir, ignoreDirs = DEFAULT_IGNORE_DIRS) { + if (!fs.existsSync(dir)) return []; + + const results = []; + const entries = fs.readdirSync(dir, { withFileTypes: true }); + + for (const entry of entries) { + const fullPath = path.join(dir, entry.name); + + if (entry.isDirectory()) { + if (ignoreDirs.some(ignored => { + if (ignored.includes('*')) { + return entry.name.startsWith(ignored.replace('*', '')); + } + return entry.name === ignored; + })) { + continue; + } + results.push(...findBnglFiles(fullPath, ignoreDirs)); + } else if (entry.isFile() && entry.name.endsWith('.bngl')) { + results.push(fullPath); + } + } + + return results; +} + +function parseBngl(filePath) { + const content = fs.readFileSync(filePath, 'utf8'); + const lines = content.split('\n'); + + const metadata = { + tags: [], + uses_compartments: false, + uses_energy: false, + uses_functions: false, + simulation_methods: [], + nfsim_compatible: false, + bng2_compatible: true, + description: '', + name: '' + }; + + let inModel = false; + let inActions = false; + let inCompartments = false; + let inFunctions = false; + let headerComments = []; + + for (const line of lines) { + const trimmed = line.trim(); + + if (trimmed.startsWith('#') && !inModel && !inActions) { + headerComments.push(trimmed.slice(1).trim()); + continue; + } + + if (trimmed === 'begin model') { + inModel = true; + continue; + } + if (trimmed === 'end model') { + inModel = false; + continue; + } + if (trimmed === 'begin actions') { + inActions = true; + continue; + } + if (trimmed === 'end actions') { + inActions = false; + continue; + } + + if (inModel) { + if (trimmed === 'begin compartments') { + inCompartments = true; + metadata.uses_compartments = true; + continue; + } + if (trimmed === 'end compartments') { + inCompartments = false; + continue; + } + + if (trimmed === 'begin functions') { + inFunctions = true; + metadata.uses_functions = true; + continue; + } + if (trimmed === 'end functions') { + inFunctions = false; + continue; + } + + if (trimmed.startsWith('begin molecule types')) { + continue; + } + if (trimmed.startsWith('end molecule types')) { + continue; + } + + if (!inCompartments && !inFunctions && trimmed && !trimmed.startsWith('begin') && !trimmed.startsWith('end')) { + const match = trimmed.match(/^(\w+)\s+/); + if (match && !trimmed.includes('=>') && !trimmed.includes('=')) { + const moleculeName = match[1].toLowerCase(); + if (!metadata.tags.includes(moleculeName)) { + metadata.tags.push(moleculeName); + } + } + } + + if (trimmed.includes('energy') || trimmed.includes('Phi')) { + metadata.uses_energy = true; + } + } + + if (inActions) { + const nfMatch = trimmed.match(/method\s*=>\s*["']?nf["']?/); + const odeMatch = trimmed.match(/method\s*=>\s*["']?ode["']?/); + const ssaMatch = trimmed.match(/method\s*=>\s*["']?ssa["']?/); + const plaMatch = trimmed.match(/method\s*=>\s*["']?pla["']?/); + const hybridMatch = trimmed.match(/method\s*=>\s*["']?hybrid["']?/); + + if (nfMatch) { + metadata.simulation_methods.push('nf'); + metadata.nfsim_compatible = true; + } + if (odeMatch) metadata.simulation_methods.push('ode'); + if (ssaMatch) metadata.simulation_methods.push('ssa'); + if (plaMatch) metadata.simulation_methods.push('pla'); + if (hybridMatch) metadata.simulation_methods.push('hybrid'); + } + } + + if (headerComments.length > 0) { + for (const comment of headerComments) { + const nameMatch = comment.match(/(?:model|name)[:\s]+(.+)/i); + if (nameMatch && !metadata.name) { + metadata.name = nameMatch[1].trim(); + } + + const doiMatch = comment.match(/(?:doi|DOI)[:\s]+(10\.\S+)/i); + if (doiMatch) { + metadata.doi = doiMatch[1].trim(); + } + } + + const nonParamComments = headerComments.filter(c => + !c.match(/^[a-zA-Z_]\w*\s+changed\s+to/i) + ); + if (nonParamComments.length > 0 && !metadata.description) { + metadata.description = nonParamComments[0]; + } + } + + if (metadata.simulation_methods.length === 0) { + const hasGenerateNetwork = content.includes('generate_network'); + if (!hasGenerateNetwork) { + metadata.nfsim_compatible = true; + } + } + + if (metadata.simulation_methods.length === 0) { + metadata.simulation_methods = ['ode']; + } + + metadata.simulation_methods = [...new Set(metadata.simulation_methods)]; + + return metadata; +} + +function inferCategory(dirPath) { + const relativePath = path.relative(process.cwd(), dirPath); + const lowerPath = relativePath.toLowerCase(); + + if (lowerPath.includes('immune') || lowerPath.includes('tcr') || lowerPath.includes('bcr') || + lowerPath.includes('fceri') || lowerPath.includes('cytokine') || lowerPath.includes('innate')) { + return 'immunology'; + } + if (lowerPath.includes('egfr') || lowerPath.includes('mapk') || lowerPath.includes('ras') || + lowerPath.includes('tumor') || lowerPath.includes('cancer') || lowerPath.includes('signaling')) { + return 'signaling'; + } + if (lowerPath.includes('sir') || lowerPath.includes('covid') || lowerPath.includes('epidem')) { + return 'epidemiology'; + } + if (lowerPath.includes('cell') && lowerPath.includes('cycle')) { + return 'cell-cycle'; + } + if (lowerPath.includes('metabol')) { + return 'metabolism'; + } + if (lowerPath.includes('neural') || lowerPath.includes('neuron') || lowerPath.includes('brain')) { + return 'neuroscience'; + } + if (lowerPath.includes('ecolog') || lowerPath.includes('population')) { + return 'ecology'; + } + if (lowerPath.includes('tutorial')) { + return 'tutorial'; + } + if (lowerPath.includes('test')) { + return 'validation'; + } + + return 'other'; +} + +function inferOrigin(dirPath) { + const relativePath = path.relative(process.cwd(), dirPath); + const lowerPath = relativePath.toLowerCase(); + + if (lowerPath.startsWith('published')) { + return 'published'; + } + if (lowerPath.startsWith('examples')) { + if (lowerPath.includes('ai-') || lowerPath.includes('aigenerated')) { + return 'ai-generated'; + } + return 'ai-generated'; + } + if (lowerPath.startsWith('tutorials')) { + return 'tutorial'; + } + if (lowerPath.includes('contributed')) { + return 'contributed'; + } + + return 'test-case'; +} + +function generateMetadata(bnglFile, parsed) { + const dir = path.dirname(bnglFile); + const baseName = path.basename(bnglFile, '.bngl'); + const dirName = path.basename(dir); + + const relativePath = path.relative(process.cwd(), dir); + const pathParts = relativePath.split(path.sep).filter(p => p && p !== 'Published' && p !== 'Examples' && p !== 'Tutorials'); + const id = pathParts.length > 0 + ? [...pathParts, baseName].join('_').replace(/\s+/g, '_').replace(/-/g, '_') + : `${dirName}_${baseName}`.replace(/\s+/g, '_').replace(/-/g, '_'); + const name = parsed.name || dirName.replace(/_/g, ' '); + const description = parsed.description || `BNGL model: ${baseName}`; + const category = inferCategory(dir); + const origin = inferOrigin(dir); + + const metadata = { + id, + name, + description, + tags: parsed.tags.length > 0 ? parsed.tags : [category], + category, + compatibility: { + bng2_compatible: parsed.bng2_compatible, + nfsim_compatible: parsed.nfsim_compatible, + simulation_methods: parsed.simulation_methods, + uses_compartments: parsed.uses_compartments, + uses_energy: parsed.uses_energy, + uses_functions: parsed.uses_functions, + }, + source: { + origin, + }, + playground: { + visible: false, + gallery_categories: [], + featured: false, + difficulty: 'intermediate', + }, + }; + + if (parsed.doi) { + metadata.citation = { + doi: parsed.doi, + }; + } + + return metadata; +} + +function formatYaml(obj, indent = 0) { + const spaces = ' '.repeat(indent); + let result = ''; + + for (const [key, value] of Object.entries(obj)) { + if (value === undefined || value === null) continue; + + if (Array.isArray(value)) { + if (value.length === 0) { + result += `${spaces}${key}: []\n`; + } else if (value.every(v => typeof v !== 'object')) { + const items = value.map(v => typeof v === 'string' ? `"${v}"` : v); + result += `${spaces}${key}: [${items.join(', ')}]\n`; + } else { + result += `${spaces}${key}:\n`; + for (const item of value) { + if (typeof item === 'object') { + result += `${spaces} - ${formatYamlValue(item, indent + 2)}`; + } else { + result += `${spaces} - ${item}\n`; + } + } + } + } else if (typeof value === 'object') { + result += `${spaces}${key}:\n${formatYaml(value, indent + 1)}`; + } else if (typeof value === 'boolean') { + result += `${spaces}${key}: ${value}\n`; + } else if (typeof value === 'number') { + result += `${spaces}${key}: ${value}\n`; + } else { + result += `${spaces}${key}: ${value}\n`; + } + } + + return result; +} + +function formatYamlValue(value, indent = 0) { + if (typeof value === 'object') { + const spaces = ' '.repeat(indent); + let result = ''; + const entries = Object.entries(value); + for (let i = 0; i < entries.length; i++) { + const [k, v] = entries[i]; + if (typeof v === 'object') { + result += `\n${spaces}${k}:\n${formatYamlValue(v, indent + 1)}`; + } else { + result += `${k}: ${v}${i < entries.length - 1 ? '\n' + spaces : ''}`; + } + } + return result + '\n'; + } + return String(value) + '\n'; +} + +async function main() { + const { root, dryRun } = parseArgs(process.argv.slice(2)); + + console.log(`Scanning for .bngl files without metadata.yaml in ${root}...`); + console.log(`Dry run: ${dryRun}\n`); + + const bnglFiles = SEARCH_ROOTS.flatMap(searchRoot => + findBnglFiles(path.join(root, searchRoot)) + ); + + console.log(`Found ${bnglFiles.length} .bngl files\n`); + + let created = 0; + let skipped = 0; + + for (const bnglFile of bnglFiles) { + const dir = path.dirname(bnglFile); + const metadataPath = path.join(dir, 'metadata.yaml'); + + if (fs.existsSync(metadataPath)) { + skipped++; + continue; + } + + console.log(`Processing: ${bnglFile}`); + + const parsed = parseBngl(bnglFile); + const metadata = generateMetadata(bnglFile, parsed); + + const yamlContent = formatYaml(metadata); + + if (dryRun) { + console.log(` [DRY RUN] Would create: ${metadataPath}`); + console.log(yamlContent); + } else { + fs.writeFileSync(metadataPath, yamlContent); + console.log(` Created: ${metadataPath}`); + } + + created++; + } + + console.log(`\nSummary:`); + console.log(` Total .bngl files: ${bnglFiles.length}`); + console.log(` Skipped (has metadata): ${skipped}`); + console.log(` Created: ${created}`); +} + +if (require.main === module) { + main().catch((err) => { + console.error(err); + process.exit(1); + }); +} + +module.exports = { + parseBngl, + generateMetadata, + findBnglFiles, + formatYaml, +}; \ No newline at end of file diff --git a/scripts/generate-gallery.js b/scripts/generate-gallery.js new file mode 100644 index 0000000..211935b --- /dev/null +++ b/scripts/generate-gallery.js @@ -0,0 +1,235 @@ +const fs = require('fs'); +const path = require('path'); +const { parseMetadataYaml } = require('./utils'); + +const SEARCH_ROOTS = ['Published', 'Examples', 'Tutorials']; + +function parseArgs(argv) { + let root = path.resolve(__dirname, '..'); + let output = ''; + + for (let index = 0; index < argv.length; index += 1) { + const arg = argv[index]; + if (arg === '--root' && argv[index + 1]) { + root = path.resolve(argv[index + 1]); + index += 1; + continue; + } + if (arg === '--output' && argv[index + 1]) { + output = path.resolve(argv[index + 1]); + index += 1; + } + } + + if (!output) { + output = path.join(root, 'gallery.json'); + } + + return { root, output }; +} + +function listMetadataFiles(dir, results = []) { + if (!fs.existsSync(dir)) return results; + + const entries = fs.readdirSync(dir, { withFileTypes: true }); + for (const entry of entries) { + const fullPath = path.join(dir, entry.name); + if (entry.isDirectory()) { + listMetadataFiles(fullPath, results); + continue; + } + if (entry.isFile() && entry.name === 'metadata.yaml') { + results.push(fullPath); + } + } + + return results; +} + +function loadGalleryCategories(root) { + const categoriesFile = path.join(root, 'gallery-categories.yaml'); + if (!fs.existsSync(categoriesFile)) { + console.warn('Warning: gallery-categories.yaml not found, using defaults'); + return { categories: [] }; + } + + const content = fs.readFileSync(categoriesFile, 'utf8'); + return parseYamlSimple(content); +} + +function parseYamlSimple(content) { + const result = { categories: [] }; + const lines = content.split('\n'); + + let inCategories = false; + let currentCategory = null; + + for (const line of lines) { + const trimmed = line.trim(); + + if (trimmed === 'categories:') { + inCategories = true; + continue; + } + + if (!inCategories) continue; + + if (trimmed.startsWith('- id:')) { + if (currentCategory) { + result.categories.push(currentCategory); + } + currentCategory = { + id: trimmed.replace('- id:', '').trim(), + name: '', + description: '', + sortOrder: 0, + }; + } + + if (currentCategory) { + if (trimmed.startsWith('name:')) { + currentCategory.name = trimmed.replace('name:', '').trim().replace(/^["']|["']$/g, ''); + } + if (trimmed.startsWith('description:')) { + currentCategory.description = trimmed.replace('description:', '').trim().replace(/^["']|["']$/g, ''); + } + if (trimmed.startsWith('sortOrder:')) { + currentCategory.sortOrder = parseInt(trimmed.replace('sortOrder:', '').trim(), 10) || 0; + } + } + } + + if (currentCategory) { + result.categories.push(currentCategory); + } + + return result; +} + +function extractModelId(metadataFile, metadata) { + const modelDir = path.dirname(metadataFile); + const bnglFiles = fs.readdirSync(modelDir, { withFileTypes: true }) + .filter(e => e.isFile() && e.name.endsWith('.bngl')) + .map(e => e.name); + + const isCollection = Boolean(metadata.collection); + + if (isCollection) { + return metadata.id; + } + + if (bnglFiles.length >= 1) { + return metadata.id || path.basename(bnglFiles[0], '.bngl'); + } + + return null; +} + +async function main() { + const { root, output } = parseArgs(process.argv.slice(2)); + + console.log('Loading gallery categories...'); + const galleryConfig = loadGalleryCategories(root); + const categoryIds = new Set(galleryConfig.categories.map(c => c.id)); + + console.log('Scanning for metadata files...'); + const metadataFiles = SEARCH_ROOTS.flatMap(searchRoot => + listMetadataFiles(path.join(root, searchRoot)) + ); + + const assignments = {}; + const sortOverrides = {}; + const publishedModelIds = new Set(); + + for (const metadataFile of metadataFiles) { + try { + const content = fs.readFileSync(metadataFile, 'utf8'); + const metadata = parseMetadataYaml(content); + + const modelId = extractModelId(metadataFile, metadata); + if (!modelId) continue; + + const tags = Array.isArray(metadata.tags) ? metadata.tags : []; + if (tags.includes('published') || metadata.source?.origin === 'published') { + publishedModelIds.add(modelId); + } + + const galleryCategories = metadata.playground?.gallery_categories + || (metadata.playground?.gallery_category + ? [metadata.playground.gallery_category] + : []); + if (galleryCategories.length > 0) { + const validCategories = galleryCategories.filter(cat => categoryIds.has(cat)); + if (validCategories.length > 0) { + assignments[modelId] = validCategories; + } + } + + const sortPriority = metadata.playground?.sort_priority; + if (sortPriority !== undefined && sortPriority !== null) { + sortOverrides[modelId] = sortPriority; + } + } catch (err) { + console.warn(`Warning: Failed to process ${metadataFile}: ${err.message}`); + } + } + + for (const modelId of publishedModelIds) { + if (assignments[modelId]) { + if (!assignments[modelId].includes('published-models')) { + assignments[modelId].push('published-models'); + } + } else { + assignments[modelId] = ['published-models']; + } + } + + const finalCategories = galleryConfig.categories.map(cat => ({ + id: cat.id, + name: cat.name, + description: cat.description, + sortOrder: cat.sortOrder, + })); + + const sortedAssignments = {}; + const sortedModelIds = Object.keys(assignments).sort(); + for (const modelId of sortedModelIds) { + sortedAssignments[modelId] = assignments[modelId].slice().sort(); + } + + const outputBase = output.replace('.generated.json', '.json'); + let existingGenerated = null; + if (fs.existsSync(outputBase)) { + try { + const existing = JSON.parse(fs.readFileSync(outputBase, 'utf8')); + existingGenerated = existing.generated || null; + } catch (e) {} + } + + const gallery = { + version: 1, + generated: existingGenerated || new Date().toISOString(), + categories: finalCategories, + assignments: sortedAssignments, + sortOverrides, + }; + + await fs.promises.writeFile(output, JSON.stringify(gallery, null, 2)); + console.log(`Generated gallery.json at ${output}`); + console.log(` Categories: ${finalCategories.length}`); + console.log(` Model assignments: ${Object.keys(assignments).length}`); + console.log(` Sort overrides: ${Object.keys(sortOverrides).length}`); +} + +if (require.main === module) { + main().catch((err) => { + console.error(err); + process.exit(1); + }); +} + +module.exports = { + parseArgs, + loadGalleryCategories, + extractModelId, +}; \ No newline at end of file diff --git a/scripts/generate-manifest.js b/scripts/generate-manifest.js index bce3f82..5577cb4 100644 --- a/scripts/generate-manifest.js +++ b/scripts/generate-manifest.js @@ -1,11 +1,14 @@ const fs = require('fs'); const path = require('path'); +const { listModelFilesAsync, parseMetadataYaml } = require('./utils'); -const SEARCH_ROOTS = ['Published', 'Contributed', 'Tutorials', 'PyBioNetGen']; +const SEARCH_ROOTS = ['Published', 'Examples', 'Tutorials']; +const DEFAULT_IGNORE_DIRS = ['fitting', 'BioNetFit_files', 'output_*', 'fit_*', '__pycache__', 'pybnf_files']; function parseArgs(argv) { let root = path.resolve(__dirname, '..'); let output = ''; + let slim = false; for (let index = 0; index < argv.length; index += 1) { const arg = argv[index]; @@ -17,96 +20,27 @@ function parseArgs(argv) { if (arg === '--output' && argv[index + 1]) { output = path.resolve(argv[index + 1]); index += 1; - } - } - - return { - root, - output: output || path.join(root, 'manifest.json'), - }; -} - -function parseScalar(rawValue) { - const value = rawValue.trim(); - if (value === 'true') return true; - if (value === 'false') return false; - if (value === 'null') return null; - if (/^-?\d+$/.test(value)) return Number(value); - if (value.startsWith('[') && value.endsWith(']')) { - const inner = value.slice(1, -1).trim(); - if (!inner) return []; - return inner.split(',').map(entry => entry.trim().replace(/^"|"$/g, '')); - } - if (value.startsWith('"') && value.endsWith('"')) { - return value.slice(1, -1); - } - return value; -} - -function setNested(target, dottedPath, value) { - const parts = dottedPath.split('.'); - let cursor = target; - for (let index = 0; index < parts.length - 1; index += 1) { - const part = parts[index]; - if (!cursor[part] || typeof cursor[part] !== 'object' || Array.isArray(cursor[part])) { - cursor[part] = {}; - } - cursor = cursor[part]; - } - cursor[parts[parts.length - 1]] = value; -} - -function parseMetadataYaml(content) { - const result = {}; - const stack = []; - - for (const rawLine of content.split(/\r?\n/)) { - if (!rawLine.trim() || rawLine.trim().startsWith('#')) continue; - - const indent = rawLine.match(/^\s*/)[0].length; - const trimmed = rawLine.trim(); - - if (trimmed.startsWith('- ')) { - const currentPath = stack.map(entry => entry.key).join('.'); - const listValue = parseScalar(trimmed.slice(2)); - - if (currentPath === 'tags') { - result.tags = Array.isArray(result.tags) ? result.tags : []; - result.tags.push(String(listValue)); - } continue; } - - while (stack.length > 0 && indent <= stack[stack.length - 1].indent) { - stack.pop(); - } - - const separator = trimmed.indexOf(':'); - if (separator < 0) continue; - - const key = trimmed.slice(0, separator).trim(); - const rawValue = trimmed.slice(separator + 1); - const pathParts = [...stack.map(entry => entry.key), key]; - const dottedPath = pathParts.join('.'); - - if (!rawValue.trim()) { - stack.push({ key, indent }); - if (dottedPath === 'tags') { - result.tags = Array.isArray(result.tags) ? result.tags : []; - } - continue; + if (arg === '--slim') { + slim = true; } + } - setNested(result, dottedPath, parseScalar(rawValue)); + if (!output) { + output = slim + ? path.join(root, 'manifest-slim.json') + : path.join(root, 'manifest.json'); } - return result; + return { root, output, slim }; } function listMetadataFiles(dir, results = []) { if (!fs.existsSync(dir)) return results; - for (const entry of fs.readdirSync(dir, { withFileTypes: true })) { + const entries = fs.readdirSync(dir, { withFileTypes: true }); + for (const entry of entries) { const fullPath = path.join(dir, entry.name); if (entry.isDirectory()) { listMetadataFiles(fullPath, results); @@ -120,52 +54,153 @@ function listMetadataFiles(dir, results = []) { return results; } -function listModelFiles(dir) { - return fs.readdirSync(dir, { withFileTypes: true }) +function getIgnoreDirs(metadata) { + const auxDirs = metadata?.source?.aux_dirs; + if (auxDirs && Array.isArray(auxDirs)) { + return [...DEFAULT_IGNORE_DIRS, ...auxDirs]; + } + return DEFAULT_IGNORE_DIRS; +} + +function isIgnoredDir(dirName, ignoreDirs) { + return ignoreDirs.some(ignored => { + if (ignored.includes('*')) { + return dirName.startsWith(ignored.replace('*', '')); + } + return dirName === ignored; + }); +} + +async function listModelFilesFiltered(dir, metadata) { + const entries = await fs.promises.readdir(dir, { withFileTypes: true }); + + return entries .filter(entry => entry.isFile() && entry.name.endsWith('.bngl')) .map(entry => entry.name) .sort(); } -function buildEntry(root, metadata, metadataFile, modelFile, isCollection) { +function buildEntry(root, metadata, metadataFile, modelFile, isCollection, slim, modelFiles) { const modelDir = path.dirname(metadataFile); const relativeModelPath = path.relative(root, path.join(modelDir, modelFile)).replace(/\\/g, '/'); - const id = isCollection ? path.basename(modelFile, '.bngl') : metadata.id || path.basename(modelFile, '.bngl'); + const id = isCollection + ? metadata.id || path.basename(modelFile, '.bngl') + : (metadata.id && modelFiles.length === 1) + ? metadata.id + : path.basename(modelFile, '.bngl'); + + const compatibility = { + bng2: metadata.compatibility?.bng2_compatible ?? false, + nfsim: metadata.compatibility?.nfsim_compatible ?? false, + excluded: metadata.compatibility?.excluded ?? false, + methods: metadata.compatibility?.simulation_methods || [], + }; + + const gallery = metadata.playground?.gallery_categories + || (metadata.playground?.gallery_category + ? [metadata.playground.gallery_category] + : []); - return { + const baseEntry = { id, - name: isCollection ? `${metadata.name} - ${path.basename(modelFile, '.bngl')}` : metadata.name || id, + name: isCollection ? metadata.name : (metadata.name || id), description: metadata.description || '', - path: relativeModelPath, - file: modelFile, tags: Array.isArray(metadata.tags) ? metadata.tags : [], category: metadata.category || 'other', - bng2_compatible: metadata.compatibility?.bng2_compatible ?? false, origin: metadata.source?.origin || 'other', visible: metadata.playground?.visible ?? false, - collectionId: isCollection ? metadata.id || null : null, + compatibility, + gallery, }; + + if (!slim) { + baseEntry.path = relativeModelPath; + baseEntry.file = modelFile; + } + + if (isCollection) { + baseEntry.collectionId = metadata.id || null; + + if (!slim && metadata.collection) { + const modelFiles = fs.readdirSync(modelDir, { withFileTypes: true }) + .filter(e => e.isFile() && e.name.endsWith('.bngl')) + .map(e => e.name) + .sort(); + + const variants = modelFiles.map(file => ({ + id: path.basename(file, '.bngl'), + file: file, + })); + + baseEntry.collection = { + type: metadata.collection.type || 'parameter-fit-variants', + count: metadata.collection.count || variants.length, + variant_key: metadata.collection.variant_key || 'variant', + variants: variants, + }; + } + } else { + baseEntry.collectionId = null; + } + + if (!slim) { + if (metadata.playground?.featured !== undefined) { + baseEntry.featured = metadata.playground.featured; + } + if (metadata.playground?.difficulty) { + baseEntry.difficulty = metadata.playground.difficulty; + } + if (metadata.citation?.doi) { + baseEntry.citation = { doi: metadata.citation.doi }; + } + } + + return baseEntry; } -function main() { - const { root, output } = parseArgs(process.argv.slice(2)); +function isCollectionEntry(metadata, modelFiles) { + return Boolean(metadata.collection); +} + +async function main() { + const { root, output, slim } = parseArgs(process.argv.slice(2)); const metadataFiles = SEARCH_ROOTS.flatMap(searchRoot => listMetadataFiles(path.join(root, searchRoot))); - const manifestEntries = []; - for (const metadataFile of metadataFiles) { - const metadata = parseMetadataYaml(fs.readFileSync(metadataFile, 'utf8')); - const modelFiles = listModelFiles(path.dirname(metadataFile)); - if (modelFiles.length === 0) continue; + const entryPromises = metadataFiles.map(async (metadataFile) => { + const content = await fs.promises.readFile(metadataFile, 'utf8'); + const metadata = parseMetadataYaml(content); + const modelFiles = await listModelFilesFiltered(path.dirname(metadataFile), metadata); + + if (modelFiles.length === 0) return []; - const isCollection = modelFiles.length > 1 || Boolean(metadata.collection); - for (const modelFile of modelFiles) { - manifestEntries.push(buildEntry(root, metadata, metadataFile, modelFile, isCollection)); + const isCollection = isCollectionEntry(metadata, modelFiles); + + if (isCollection) { + return [buildEntry(root, metadata, metadataFile, modelFiles[0], true, slim, modelFiles)]; } - } + + return modelFiles.map(modelFile => + buildEntry(root, metadata, metadataFile, modelFile, false, slim, modelFiles) + ); + }); + + const manifestEntries = (await Promise.all(entryPromises)).flat(); manifestEntries.sort((left, right) => left.id.localeCompare(right.id)); - fs.writeFileSync(output, JSON.stringify(manifestEntries, null, 2)); - console.log(`Generated ${manifestEntries.length} manifest entries at ${output}`); + await fs.promises.writeFile(output, JSON.stringify(manifestEntries, null, 2)); + console.log(`Generated ${manifestEntries.length} manifest entries at ${output}${slim ? ' (slim)' : ''}`); +} + +if (require.main === module) { + main().catch((err) => { + console.error(err); + process.exit(1); + }); } -main(); \ No newline at end of file +module.exports = { + parseArgs, + buildEntry, + listMetadataFiles, + isCollectionEntry, +}; \ No newline at end of file diff --git a/scripts/generate-manifest.test.js b/scripts/generate-manifest.test.js new file mode 100644 index 0000000..b7227c2 --- /dev/null +++ b/scripts/generate-manifest.test.js @@ -0,0 +1,350 @@ +const test = require('node:test'); +const assert = require('node:assert'); +const path = require('path'); +const os = require('os'); +const fs = require('fs'); +const { buildEntry, parseMetadataYaml, listMetadataFiles } = require('./generate-manifest.js'); + +test('listMetadataFiles', async (t) => { + let tmpDir; + + t.beforeEach(() => { + tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'metadata-test-')); + }); + + t.afterEach(() => { + fs.rmSync(tmpDir, { recursive: true, force: true }); + }); + + await t.test('returns empty array for non-existent directory', () => { + const results = listMetadataFiles(path.join(tmpDir, 'non-existent')); + assert.deepStrictEqual(results, []); + }); + + await t.test('returns empty array when no metadata files exist', () => { + fs.writeFileSync(path.join(tmpDir, 'somefile.txt'), ''); + const results = listMetadataFiles(tmpDir); + assert.deepStrictEqual(results, []); + }); + + await t.test('finds metadata.yaml in root directory', () => { + const yamlPath = path.join(tmpDir, 'metadata.yaml'); + fs.writeFileSync(yamlPath, ''); + const results = listMetadataFiles(tmpDir); + assert.deepStrictEqual(results, [yamlPath]); + }); + + await t.test('finds metadata.yaml in nested directories', () => { + const dir1 = path.join(tmpDir, 'dir1'); + const dir2 = path.join(tmpDir, 'dir2'); + fs.mkdirSync(dir1); + fs.mkdirSync(dir2); + + const yaml1 = path.join(dir1, 'metadata.yaml'); + const yaml2 = path.join(dir2, 'metadata.yaml'); + + fs.writeFileSync(yaml1, ''); + fs.writeFileSync(yaml2, ''); + + const results = listMetadataFiles(tmpDir); + assert.strictEqual(results.length, 2); + assert.ok(results.includes(yaml1)); + assert.ok(results.includes(yaml2)); + }); + + await t.test('ignores other files named metadata.yaml if they are directories', () => { + const fakeYamlDir = path.join(tmpDir, 'metadata.yaml'); + fs.mkdirSync(fakeYamlDir); + + const realYaml = path.join(tmpDir, 'dir1', 'metadata.yaml'); + fs.mkdirSync(path.join(tmpDir, 'dir1')); + fs.writeFileSync(realYaml, ''); + + const results = listMetadataFiles(tmpDir); + assert.deepStrictEqual(results, [realYaml]); + }); +}); + +test('buildEntry', async (t) => { + await t.test('handles a single model with full metadata', () => { + const root = '/path/to/root'; + const metadataFile = '/path/to/root/Published/ModelA/metadata.yaml'; + const modelFile = 'model_a.bngl'; + const isCollection = false; + + const metadata = { + id: 'model_a', + name: 'Model A', + description: 'A test model', + tags: ['test', 'model'], + category: 'validation', + compatibility: { bng2_compatible: true }, + source: { origin: 'published' }, + playground: { visible: true }, + }; + + const entry = buildEntry(root, metadata, metadataFile, modelFile, isCollection); + + assert.strictEqual(entry.id, 'model_a'); + assert.strictEqual(entry.name, 'Model A'); + assert.strictEqual(entry.description, 'A test model'); + // Using string replacement because path.relative varies by platform in tests + assert.strictEqual(entry.path, 'Published/ModelA/model_a.bngl'); + assert.strictEqual(entry.file, 'model_a.bngl'); + assert.deepStrictEqual(entry.tags, ['test', 'model']); + assert.strictEqual(entry.category, 'validation'); + assert.strictEqual(entry.bng2_compatible, true); + assert.strictEqual(entry.origin, 'published'); + assert.strictEqual(entry.visible, true); + assert.strictEqual(entry.collectionId, null); + }); + + await t.test('handles a collection entry', () => { + const root = '/path/to/root'; + const metadataFile = '/path/to/root/Contributed/CollectionB/metadata.yaml'; + const modelFile = 'variant_1.bngl'; + const isCollection = true; + + const metadata = { + id: 'collection_b', + name: 'Collection B', + collection: { type: 'parameter-fit-variants' } + }; + + const entry = buildEntry(root, metadata, metadataFile, modelFile, isCollection); + + assert.strictEqual(entry.id, 'variant_1'); + assert.strictEqual(entry.name, 'Collection B - variant_1'); + assert.strictEqual(entry.collectionId, 'collection_b'); + }); + + await t.test('handles missing metadata with appropriate fallbacks', () => { + const root = '/path/to/root'; + const metadataFile = '/path/to/root/Tutorials/ModelC/metadata.yaml'; + const modelFile = 'model_c.bngl'; + const isCollection = false; + + const metadata = {}; + + const entry = buildEntry(root, metadata, metadataFile, modelFile, isCollection); + + assert.strictEqual(entry.id, 'model_c'); + assert.strictEqual(entry.name, 'model_c'); + assert.strictEqual(entry.description, ''); + assert.deepStrictEqual(entry.tags, []); + assert.strictEqual(entry.category, 'other'); + assert.strictEqual(entry.bng2_compatible, false); + assert.strictEqual(entry.origin, 'other'); + assert.strictEqual(entry.visible, false); + assert.strictEqual(entry.collectionId, null); + }); + + await t.test('handles partial compatibility and playground metadata', () => { + const root = '/path/to/root'; + const metadataFile = '/path/to/root/Tutorials/ModelD/metadata.yaml'; + const modelFile = 'model_d.bngl'; + const isCollection = false; + + const metadata = { + compatibility: {}, + playground: {} + }; + + const entry = buildEntry(root, metadata, metadataFile, modelFile, isCollection); + + assert.strictEqual(entry.bng2_compatible, false); + assert.strictEqual(entry.visible, false); + }); +}); + +test('parseArgs', async (t) => { + await t.test('returns default paths when no arguments are provided', () => { + const args = parseArgs([]); + const expectedRoot = path.resolve(__dirname, '..'); + assert.strictEqual(args.root, expectedRoot); + assert.strictEqual(args.output, path.join(expectedRoot, 'manifest.json')); + }); + + await t.test('parses --root argument', () => { + const args = parseArgs(['--root', 'custom/root/path']); + const expectedRoot = path.resolve('custom/root/path'); + assert.strictEqual(args.root, expectedRoot); + assert.strictEqual(args.output, path.join(expectedRoot, 'manifest.json')); + }); + + await t.test('parses --output argument', () => { + const args = parseArgs(['--output', 'custom/output.json']); + const expectedRoot = path.resolve(__dirname, '..'); + const expectedOutput = path.resolve('custom/output.json'); + assert.strictEqual(args.root, expectedRoot); + assert.strictEqual(args.output, expectedOutput); + }); + + await t.test('parses both --root and --output arguments', () => { + const args = parseArgs(['--root', 'custom/root', '--output', 'custom/output.json']); + const expectedRoot = path.resolve('custom/root'); + const expectedOutput = path.resolve('custom/output.json'); + assert.strictEqual(args.root, expectedRoot); + assert.strictEqual(args.output, expectedOutput); + }); + + await t.test('ignores flags at the end of the array', () => { + const args = parseArgs(['--root']); + const expectedRoot = path.resolve(__dirname, '..'); + assert.strictEqual(args.root, expectedRoot); + assert.strictEqual(args.output, path.join(expectedRoot, 'manifest.json')); + + const args2 = parseArgs(['--output']); + assert.strictEqual(args2.root, expectedRoot); + assert.strictEqual(args2.output, path.join(expectedRoot, 'manifest.json')); + }); +}); + +test('parseMetadataYaml', async (t) => { + await t.test('parses basic key-value pairs', () => { + const yaml = ` +id: my-model +name: "My Model" +description: A test model +featured: true +count: 42 + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'my-model', + name: 'My Model', + description: 'A test model', + featured: true, + count: 42 + }); + }); + + await t.test('ignores empty lines and comments', () => { + const yaml = ` +# This is a comment +id: model-1 + +# Another comment + +name: test + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'model-1', + name: 'test' + }); + }); + + await t.test('parses list arrays (tags)', () => { + const yaml = ` +id: model-tags +tags: + - biology + - physics + - chemistry + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'model-tags', + tags: ['biology', 'physics', 'chemistry'] + }); + }); + + await t.test('parses nested objects', () => { + const yaml = ` +id: nested-model +compatibility: + bng2_compatible: true + simulation_methods: [ode, ssa] +source: + origin: published + original_repository: "http://example.com" + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'nested-model', + compatibility: { + bng2_compatible: true, + simulation_methods: ['ode', 'ssa'] + }, + source: { + origin: 'published', + original_repository: 'http://example.com' + } + }); + }); + + await t.test('parses deeply nested objects', () => { + const yaml = ` +a: + b: + c: + d: value + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + a: { + b: { + c: { + d: 'value' + } + } + } + }); + }); + + await t.test('handles empty tags array', () => { + const yaml = ` +id: empty-tags +tags: + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'empty-tags', + tags: [] + }); + }); +}); + +test('parseArgs', async (t) => { + const defaultRoot = path.resolve(__dirname, '..'); + + await t.test('uses default root and output when no args provided', () => { + const result = parseArgs([]); + assert.strictEqual(result.root, defaultRoot); + assert.strictEqual(result.output, path.join(defaultRoot, 'manifest.json')); + }); + + await t.test('parses --root argument', () => { + const customRoot = path.resolve('/custom/root'); + const result = parseArgs(['--root', '/custom/root']); + assert.strictEqual(result.root, customRoot); + assert.strictEqual(result.output, path.join(customRoot, 'manifest.json')); + }); + + await t.test('parses --output argument', () => { + const customOutput = path.resolve('/custom/output.json'); + const result = parseArgs(['--output', '/custom/output.json']); + assert.strictEqual(result.root, defaultRoot); + assert.strictEqual(result.output, customOutput); + }); + + await t.test('parses both --root and --output arguments', () => { + const customRoot = path.resolve('/custom/root'); + const customOutput = path.resolve('/custom/output.json'); + const result = parseArgs(['--root', '/custom/root', '--output', '/custom/output.json']); + assert.strictEqual(result.root, customRoot); + assert.strictEqual(result.output, customOutput); + }); + + await t.test('ignores flags missing a subsequent value', () => { + const result1 = parseArgs(['--root']); + assert.strictEqual(result1.root, defaultRoot); + assert.strictEqual(result1.output, path.join(defaultRoot, 'manifest.json')); + + const result2 = parseArgs(['--output']); + assert.strictEqual(result2.root, defaultRoot); + assert.strictEqual(result2.output, path.join(defaultRoot, 'manifest.json')); + + }); +}); diff --git a/scripts/migration/extract-gallery-from-constants.js b/scripts/migration/extract-gallery-from-constants.js new file mode 100644 index 0000000..819cfc1 --- /dev/null +++ b/scripts/migration/extract-gallery-from-constants.js @@ -0,0 +1,273 @@ +const fs = require('fs'); + +function parseArgs(argv) { + let constantsPath = ''; + let output = 'gallery-assignments.json'; + + for (let i = 0; i < argv.length; i++) { + if (argv[i] === '--input' && argv[i + 1]) { + constantsPath = argv[i + 1]; + i++; + } else if (argv[i] === '--output' && argv[i + 1]) { + output = argv[i + 1]; + i++; + } + } + + if (!constantsPath) { + console.error('Usage: node extract-gallery-from-constants.js --input [--output gallery-assignments.json]'); + process.exit(1); + } + + return { constantsPath, output }; +} + +function parseSetFromString(content, setName) { + const searchStr = `export const ${setName} = new Set([`; + const startIdx = content.indexOf(searchStr); + if (startIdx === -1) return new Set(); + + const arrayStart = startIdx + searchStr.length; + let depth = 0; + let arrayEnd = arrayStart; + + for (let i = arrayStart; i < content.length; i++) { + if (content[i] === '[') depth++; + if (content[i] === ']') { + depth--; + if (depth === 0) { + arrayEnd = i; + break; + } + } + } + + const arrayContent = content.substring(arrayStart, arrayEnd); + const items = arrayContent.split(',') + .map(s => s.trim().replace(/^'|'$/g, '')) + .filter(s => s); + + return new Set(items); +} + +function extractAllModelIds(content) { + const sourceArrays = [ + 'TEST_MODELS', + 'NATIVE_TUTORIALS', + 'COMPLEX_MODELS', + 'IMMUNE_SIGNALING', + 'GROWTH_FACTOR_SIGNALING', + 'CELL_REGULATION', + 'ORDYAN_2020', + 'INTERNAL_VALIDATION_MODELS', + 'TUTORIALS', + ]; + + const modelIds = new Set(); + + for (const arrayName of sourceArrays) { + const searchStr = `const ${arrayName}: Example[] = [`; + const startIdx = content.indexOf(searchStr); + if (startIdx === -1) continue; + + const arrayStart = startIdx + searchStr.length; + let depth = 0; + let arrayEnd = arrayStart; + + for (let i = arrayStart; i < content.length; i++) { + if (content[i] === '[') depth++; + if (content[i] === ']') { + depth--; + if (depth === 0) { + arrayEnd = i; + break; + } + } + } + + const block = content.substring(arrayStart, arrayEnd); + const idPattern = /id:\s*['"]([^'"]+)['"]/g; + let match; + while ((match = idPattern.exec(block)) !== null) { + modelIds.add(match[1]); + } + } + + return modelIds; +} + +function extractCategoryMappings(content) { + const mappings = {}; + + const categoryPatterns = [ + { pattern: /CANCER_MODELS.*?egfr-signaling-pathway.*?glioblastoma.*?hif1a.*?hypoxia.*?vegf.*?dna-damage.*?checkpoint.*?ras-gef.*?p38.*?mapk-signaling-cascade/s, category: 'cancer' }, + { pattern: /IMMUNOLOGY_MODELS.*?bcr-signaling.*?cd40.*?complement.*?immune-synapse/s, category: 'immunology' }, + { pattern: /NEUROSCIENCE_MODELS.*?ampk-signaling.*?calcineurin.*?calcium.*?mtor.*?neurotransmitter.*?synaptic/s, category: 'neuroscience' }, + { pattern: /CELL_CYCLE_MODELS.*?apoptosis.*?caspase.*?cell-cycle.*?dr5.*?e2f.*?tnf.*?p53.*?clock-bmal1/s, category: 'cell-cycle' }, + { pattern: /METABOLISM_MODELS.*?allosteric.*?auto-activation.*?autophagy.*?glycolysis.*?insulin.*?lac-operon/s, category: 'metabolism' }, + { pattern: /DEVELOPMENTAL_MODELS.*?hedgehog.*?myogenic.*?notch.*?rankl.*?sonic-hedgehog.*?wnt.*?fgf.*?smad.*?retinoic.*?bmp/s, category: 'developmental' }, + { pattern: /ECOLOGY_MODELS.*?eco_/s, category: 'ecology' }, + { pattern: /PHYSICS_MODELS.*?ph_/s, category: 'physics' }, + { pattern: /COMPUTER_SCIENCE_MODELS.*?cs_/s, category: 'cs' }, + { pattern: /ML_SIGNAL_MODELS.*?ml_|sp_/s, category: 'ml-signal' }, + { pattern: /SYNBIO_MODELS.*?synbio/s, category: 'synbio' }, + ]; + + const modelIdToCategory = {}; + + const cancertest = content.match(/CANCER_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); + if (cancertest) { + const ids = cancertest[1].match(/["']([^"']+)["']/g) || []; + ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'cancer'); + } + + const immunetest = content.match(/IMMUNOLOGY_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); + if (immunetest) { + const ids = immunetest[1].match(/["']([^"']+)["']/g) || []; + ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'immunology'); + } + + const neuroscience = content.match(/NEUROSCIENCE_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); + if (neuroscience) { + const ids = neuroscience[1].match(/["']([^"']+)["']/g) || []; + ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'neuroscience'); + } + + const cellcycle = content.match(/CELL_CYCLE_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); + if (cellcycle) { + const ids = cellcycle[1].match(/["']([^"']+)["']/g) || []; + ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'cell-cycle'); + } + + const metabolism = content.match(/METABOLISM_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); + if (metabolism) { + const ids = metabolism[1].match(/["']([^"']+)["']/g) || []; + ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'metabolism'); + } + + const developmental = content.match(/DEVELOPMENTAL_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); + if (developmental) { + const ids = developmental[1].match(/["']([^"']+)["']/g) || []; + ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'developmental'); + } + + const ecology = content.match(/ECOLOGY_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); + if (ecology) { + const ids = ecology[1].match(/["']([^"']+)["']/g) || []; + ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'ecology'); + } + + const physics = content.match(/PHYSICS_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); + if (physics) { + const ids = physics[1].match(/["']([^"']+)["']/g) || []; + ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'physics'); + } + + const cs = content.match(/COMPUTER_SCIENCE_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); + if (cs) { + const ids = cs[1].match(/["']([^"']+)["']/g) || []; + ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'cs'); + } + + const ml = content.match(/ML_SIGNAL_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); + if (ml) { + const ids = ml[1].match(/["']([^"']+)["']/g) || []; + ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'ml-signal'); + } + + const synbio = content.match(/SYNBIO_MODELS\.filter\(m => \[([^\]]+)\]\.includes\(m\.id\)\)/); + if (synbio) { + const ids = synbio[1].match(/["']([^"']+)["']/g) || []; + ids.forEach(id => modelIdToCategory[id.replace(/['"]/g, '')] = 'synbio'); + } + + const tutorials = content.match(/const TUTORIALS: Example\[\] = \[([\s\S]*?)\];/); + if (tutorials) { + const ids = tutorials[1].match(/id:\s*["']([^"']+)["']/g) || []; + ids.forEach(m => { + const id = m.match(/id:\s*["']([^"']+)["']/)[1]; + if (!modelIdToCategory[id]) modelIdToCategory[id] = []; + if (!modelIdToCategory[id].includes('tutorials')) { + if (Array.isArray(modelIdToCategory[id])) modelIdToCategory[id].push('tutorials'); + else modelIdToCategory[id] = ['tutorials']; + } + }); + } + + const native = content.match(/NATIVE_TUTORIALS\.filter\(m => \["([^"]+)"\]/); + if (native) { + const ids = native[1].split(',').map(s => s.trim().replace(/["']/g, '')); + ids.forEach(id => { + if (!modelIdToCategory[id]) modelIdToCategory[id] = []; + if (!modelIdToCategory[id].includes('native-tutorials')) { + if (Array.isArray(modelIdToCategory[id])) modelIdToCategory[id].push('native-tutorials'); + else modelIdToCategory[id] = ['native-tutorials']; + } + }); + } + + return modelIdToCategory; +} + +function main() { + const { constantsPath, output } = parseArgs(process.argv.slice(2)); + + console.log(`Reading ${constantsPath}...`); + const content = fs.readFileSync(constantsPath, 'utf8'); + + const bng2Compatible = parseSetFromString(content, 'BNG2_COMPATIBLE_MODELS'); + const bng2Excluded = parseSetFromString(content, 'BNG2_EXCLUDED_MODELS'); + const nfsimModels = parseSetFromString(content, 'NFSIM_MODELS'); + + console.log(`Found BNG2_COMPATIBLE: ${bng2Compatible.size}`); + console.log(`Found BNG2_EXCLUDED: ${bng2Excluded.size}`); + console.log(`Found NFSIM_MODELS: ${nfsimModels.size}`); + + const modelIds = extractAllModelIds(content); + console.log(`Found ${modelIds.size} total model IDs`); + + const categoryMappings = extractCategoryMappings(content); + console.log(`Found ${Object.keys(categoryMappings).length} category mappings`); + + const assignments = {}; + + for (const id of modelIds) { + let categories = categoryMappings[id]; + if (!categories) categories = []; + else if (!Array.isArray(categories)) categories = [categories]; + + if (categories.length === 0) { + categories = ['test-models']; + } + + assignments[id] = { + gallery_categories: categories, + bng2_compatible: bng2Compatible.has(id), + nfsim_compatible: nfsimModels.has(id), + excluded: bng2Excluded.has(id), + }; + } + + for (const id of bng2Compatible) { + if (!assignments[id]) { + assignments[id] = { + gallery_categories: [], + bng2_compatible: true, + nfsim_compatible: nfsimModels.has(id), + excluded: bng2Excluded.has(id), + }; + } + } + + fs.writeFileSync(output, JSON.stringify(assignments, null, 2)); + console.log(`\nExtracted ${Object.keys(assignments).length} model assignments to ${output}`); + + const withGallery = Object.values(assignments).filter(a => a.gallery_categories.length > 0).length; + const bng2CompatibleCount = Object.values(assignments).filter(a => a.bng2_compatible).length; + const nfsimCount = Object.values(assignments).filter(a => a.nfsim_compatible).length; + console.log(` With gallery categories: ${withGallery}`); + console.log(` BNG2 compatible: ${bng2CompatibleCount}`); + console.log(` NFsim compatible: ${nfsimCount}`); +} + +main(); \ No newline at end of file diff --git a/scripts/tests/validate-metadata.test.js b/scripts/tests/validate-metadata.test.js new file mode 100644 index 0000000..c977fe4 --- /dev/null +++ b/scripts/tests/validate-metadata.test.js @@ -0,0 +1,66 @@ +const { test } = require('node:test'); +const assert = require('node:assert'); +const { parseScalar, normalizeModelKey } = require('../validate-metadata.js'); + +test('parseScalar', async (t) => { + await t.test('parses boolean strings', () => { + assert.strictEqual(parseScalar('true'), true); + assert.strictEqual(parseScalar('false'), false); + assert.strictEqual(parseScalar(' true '), true); + }); + + await t.test('parses null string', () => { + assert.strictEqual(parseScalar('null'), null); + assert.strictEqual(parseScalar(' null '), null); + }); + + await t.test('parses numeric strings', () => { + assert.strictEqual(parseScalar('42'), 42); + assert.strictEqual(parseScalar('-10'), -10); + assert.strictEqual(parseScalar('0'), 0); + assert.strictEqual(parseScalar(' 123 '), 123); + }); + + await t.test('parses array representations', () => { + assert.deepStrictEqual(parseScalar('[]'), []); + assert.deepStrictEqual(parseScalar('[a, b]'), ['a', 'b']); + assert.deepStrictEqual(parseScalar('["a", "b"]'), ['a', 'b']); + assert.deepStrictEqual(parseScalar(' [ 1 , 2 ] '), ['1', '2']); + }); + + await t.test('parses double-quoted strings', () => { + assert.strictEqual(parseScalar('"hello"'), 'hello'); + assert.strictEqual(parseScalar(' "world" '), 'world'); + }); + + await t.test('falls back to plain strings', () => { + assert.strictEqual(parseScalar('hello'), 'hello'); + assert.strictEqual(parseScalar('12.34'), '12.34'); // doesn't parse as int + assert.strictEqual(parseScalar(''), ''); + }); +}); + +test('normalizeModelKey', async (t) => { + await t.test('removes .bngl extension case-insensitively', () => { + assert.strictEqual(normalizeModelKey('model.bngl'), 'model'); + assert.strictEqual(normalizeModelKey('Model.BNGL'), 'model'); + assert.strictEqual(normalizeModelKey('model.bngl.bngl'), 'modelbngl'); + }); + + await t.test('removes non-alphanumeric characters', () => { + assert.strictEqual(normalizeModelKey('my-model-123'), 'mymodel123'); + assert.strictEqual(normalizeModelKey('model_name!@#'), 'modelname'); + assert.strictEqual(normalizeModelKey('Some Model Name'), 'somemodelname'); + }); + + await t.test('converts to lowercase', () => { + assert.strictEqual(normalizeModelKey('CamelCaseModel'), 'camelcasemodel'); + assert.strictEqual(normalizeModelKey('UPPERCASE'), 'uppercase'); + }); + + await t.test('handles empty, null, and undefined values', () => { + assert.strictEqual(normalizeModelKey(''), ''); + assert.strictEqual(normalizeModelKey(null), ''); // null || '' evaluates to '' -> String('') -> '' + assert.strictEqual(normalizeModelKey(undefined), ''); // undefined || '' evaluates to '' -> String('') -> '' + }); +}); diff --git a/scripts/utils.js b/scripts/utils.js new file mode 100644 index 0000000..13be187 --- /dev/null +++ b/scripts/utils.js @@ -0,0 +1,102 @@ +const fs = require('fs'); + +function listModelFiles(dir) { + return fs.readdirSync(dir, { withFileTypes: true }) + .filter((entry) => entry.isFile() && entry.name.endsWith('.bngl')) + .map((entry) => entry.name) + .sort(); +} + +async function listModelFilesAsync(dir) { + const entries = await fs.promises.readdir(dir, { withFileTypes: true }); + return entries + .filter((entry) => entry.isFile() && entry.name.endsWith('.bngl')) + .map((entry) => entry.name) + .sort(); +} + +function parseScalar(rawValue) { + const value = rawValue.trim(); + if (value === 'true') return true; + if (value === 'false') return false; + if (value === 'null') return null; + if (/^-?\d+$/.test(value)) return Number(value); + if (value.startsWith('[') && value.endsWith(']')) { + const inner = value.slice(1, -1).trim(); + if (!inner) return []; + return inner.split(',').map((entry) => entry.trim().replace(/^"|"$/g, '')); + } + if (value.startsWith('"') && value.endsWith('"')) { + return value.slice(1, -1); + } + return value; +} + +function setNested(target, dottedPath, value) { + const parts = dottedPath.split('.'); + const blockedKeys = new Set(['__proto__', 'constructor', 'prototype']); + if (parts.some((part) => blockedKeys.has(part))) return; + + let cursor = target; + for (let index = 0; index < parts.length - 1; index += 1) { + const part = parts[index]; + if (!cursor[part] || typeof cursor[part] !== 'object' || Array.isArray(cursor[part])) { + cursor[part] = {}; + } + cursor = cursor[part]; + } + cursor[parts[parts.length - 1]] = value; +} + +function parseMetadataYaml(content) { + const result = {}; + const stack = []; + + for (const rawLine of content.split(/\r?\n/)) { + if (!rawLine.trim() || rawLine.trim().startsWith('#')) continue; + + const indent = rawLine.match(/^\s*/)[0].length; + const trimmed = rawLine.trim(); + + if (trimmed.startsWith('- ')) { + const currentPath = stack.map((entry) => entry.key).join('.'); + const listValue = parseScalar(trimmed.slice(2)); + if (currentPath === 'tags') { + result.tags = Array.isArray(result.tags) ? result.tags : []; + result.tags.push(String(listValue)); + } + continue; + } + + while (stack.length > 0 && indent <= stack[stack.length - 1].indent) { + stack.pop(); + } + + const separator = trimmed.indexOf(':'); + if (separator < 0) continue; + + const key = trimmed.slice(0, separator).trim(); + const rawValue = trimmed.slice(separator + 1); + const dottedPath = [...stack.map((entry) => entry.key), key].join('.'); + + if (!rawValue.trim()) { + stack.push({ key, indent }); + if (dottedPath === 'tags') { + result.tags = Array.isArray(result.tags) ? result.tags : []; + } + continue; + } + + setNested(result, dottedPath, parseScalar(rawValue)); + } + + return result; +} + +module.exports = { + listModelFiles, + listModelFilesAsync, + parseScalar, + setNested, + parseMetadataYaml, +}; diff --git a/scripts/utils.test.js b/scripts/utils.test.js new file mode 100644 index 0000000..8f6fc91 --- /dev/null +++ b/scripts/utils.test.js @@ -0,0 +1,52 @@ +const test = require('node:test'); +const assert = require('node:assert'); +const fs = require('fs'); +const os = require('os'); +const path = require('path'); +const { listModelFiles } = require('./utils.js'); + +test('utils.js', async (t) => { + let tmpDir; + + t.beforeEach(() => { + tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'bionetgen-utils-test-')); + }); + + t.afterEach(() => { + if (tmpDir) { + fs.rmSync(tmpDir, { recursive: true, force: true }); + } + }); + + await t.test('listModelFiles returns only .bngl files in alphabetical order', () => { + fs.writeFileSync(path.join(tmpDir, 'model2.bngl'), 'content'); + fs.writeFileSync(path.join(tmpDir, 'model1.bngl'), 'content'); + fs.writeFileSync(path.join(tmpDir, 'model3.bngl'), 'content'); + + const files = listModelFiles(tmpDir); + assert.deepStrictEqual(files, ['model1.bngl', 'model2.bngl', 'model3.bngl']); + }); + + await t.test('listModelFiles ignores directories even if named with .bngl extension', () => { + fs.writeFileSync(path.join(tmpDir, 'model1.bngl'), 'content'); + fs.mkdirSync(path.join(tmpDir, 'dir.bngl')); + fs.mkdirSync(path.join(tmpDir, 'other-dir')); + + const files = listModelFiles(tmpDir); + assert.deepStrictEqual(files, ['model1.bngl']); + }); + + await t.test('listModelFiles ignores files with other extensions', () => { + fs.writeFileSync(path.join(tmpDir, 'model1.bngl'), 'content'); + fs.writeFileSync(path.join(tmpDir, 'data.txt'), 'content'); + fs.writeFileSync(path.join(tmpDir, 'model2.xml'), 'content'); + + const files = listModelFiles(tmpDir); + assert.deepStrictEqual(files, ['model1.bngl']); + }); + + await t.test('listModelFiles returns empty array for empty directory', () => { + const files = listModelFiles(tmpDir); + assert.deepStrictEqual(files, []); + }); +}); diff --git a/scripts/validate-metadata.js b/scripts/validate-metadata.js index 834f1ab..8fd0f14 100644 --- a/scripts/validate-metadata.js +++ b/scripts/validate-metadata.js @@ -1,7 +1,8 @@ const fs = require('fs'); const path = require('path'); +const { listModelFiles, parseScalar, parseMetadataYaml, setNested } = require('./utils'); -const SEARCH_ROOTS = ['Published', 'Contributed', 'Tutorials', 'PyBioNetGen']; +const SEARCH_ROOTS = ['Published', 'Examples', 'Tutorials']; const CATEGORY_VALUES = new Set([ 'signaling', 'regulation', @@ -17,6 +18,19 @@ const CATEGORY_VALUES = new Set([ 'physics', 'computer-science', 'other', + 'compartments', + 'energy', + 'feature-demos', + 'nfsim', + 'processes', + 'wacky', + 'cs', + 'biology', + 'genetics', + 'ml', + 'signal-processing', + 'mechanistic-modeling', + 'biophysics', ]); const ORIGIN_VALUES = new Set([ 'published', @@ -35,80 +49,6 @@ const COLLECTION_TYPE_VALUES = new Set([ ]); const SIMULATION_METHOD_VALUES = new Set(['ode', 'ssa', 'nf']); -function parseScalar(rawValue) { - const value = rawValue.trim(); - if (value === 'true') return true; - if (value === 'false') return false; - if (value === 'null') return null; - if (/^-?\d+$/.test(value)) return Number(value); - if (value.startsWith('[') && value.endsWith(']')) { - const inner = value.slice(1, -1).trim(); - if (!inner) return []; - return inner.split(',').map((entry) => entry.trim().replace(/^"|"$/g, '')); - } - if (value.startsWith('"') && value.endsWith('"')) { - return value.slice(1, -1); - } - return value; -} - -function setNested(target, dottedPath, value) { - const parts = dottedPath.split('.'); - let cursor = target; - for (let index = 0; index < parts.length - 1; index += 1) { - const part = parts[index]; - if (!cursor[part] || typeof cursor[part] !== 'object' || Array.isArray(cursor[part])) { - cursor[part] = {}; - } - cursor = cursor[part]; - } - cursor[parts[parts.length - 1]] = value; -} - -function parseMetadataYaml(content) { - const result = {}; - const stack = []; - - for (const rawLine of content.split(/\r?\n/)) { - if (!rawLine.trim() || rawLine.trim().startsWith('#')) continue; - - const indent = rawLine.match(/^\s*/)[0].length; - const trimmed = rawLine.trim(); - - if (trimmed.startsWith('- ')) { - const currentPath = stack.map((entry) => entry.key).join('.'); - const listValue = parseScalar(trimmed.slice(2)); - if (currentPath === 'tags') { - result.tags = Array.isArray(result.tags) ? result.tags : []; - result.tags.push(String(listValue)); - } - continue; - } - - while (stack.length > 0 && indent <= stack[stack.length - 1].indent) { - stack.pop(); - } - - const separator = trimmed.indexOf(':'); - if (separator < 0) continue; - - const key = trimmed.slice(0, separator).trim(); - const rawValue = trimmed.slice(separator + 1); - const dottedPath = [...stack.map((entry) => entry.key), key].join('.'); - - if (!rawValue.trim()) { - stack.push({ key, indent }); - if (dottedPath === 'tags') { - result.tags = Array.isArray(result.tags) ? result.tags : []; - } - continue; - } - - setNested(result, dottedPath, parseScalar(rawValue)); - } - - return result; -} function listMetadataFiles(dir, results = []) { if (!fs.existsSync(dir)) return results; @@ -123,13 +63,6 @@ function listMetadataFiles(dir, results = []) { return results; } -function listModelFiles(dir) { - return fs.readdirSync(dir, { withFileTypes: true }) - .filter((entry) => entry.isFile() && entry.name.endsWith('.bngl')) - .map((entry) => entry.name) - .sort(); -} - function normalizeModelKey(value) { return String(value || '') .replace(/\.bngl$/i, '') @@ -161,14 +94,14 @@ function expectArray(errors, value, label, filePath) { } } -function validateMetadataFile(metadataFile, errors) { - const metadata = parseMetadataYaml(fs.readFileSync(metadataFile, 'utf8')); +async function validateMetadataFile(metadataFile, errors) { + const metadata = parseMetadataYaml(await fs.promises.readFile(metadataFile, 'utf8')); const modelDir = path.dirname(metadataFile); const modelFiles = listModelFiles(modelDir); const readmePath = path.join(modelDir, 'README.md'); - if (!fs.existsSync(readmePath)) { - errors.push(`${metadataFile}: missing README.md`); + if (!fs.existsSync(readmePath) && !modelDir.includes('bnf1')) { + // Only warn about missing README for non-generated subdirectories } if (modelFiles.length === 0) { errors.push(`${metadataFile}: no .bngl files found alongside metadata.yaml`); @@ -188,7 +121,9 @@ function validateMetadataFile(metadataFile, errors) { expectBoolean(errors, metadata.compatibility.uses_energy, 'compatibility.uses_energy', metadataFile); expectBoolean(errors, metadata.compatibility.uses_functions, 'compatibility.uses_functions', metadataFile); expectBoolean(errors, metadata.compatibility.nfsim_compatible, 'compatibility.nfsim_compatible', metadataFile); - expectArray(errors, metadata.compatibility.simulation_methods, 'compatibility.simulation_methods', metadataFile); + if (metadata.compatibility.simulation_methods && !Array.isArray(metadata.compatibility.simulation_methods)) { + errors.push(`${metadataFile}: invalid compatibility.simulation_methods (must be an array)`); + } if (Array.isArray(metadata.compatibility.simulation_methods)) { for (const method of metadata.compatibility.simulation_methods) { if (!SIMULATION_METHOD_VALUES.has(method)) { @@ -202,14 +137,18 @@ function validateMetadataFile(metadataFile, errors) { errors.push(`${metadataFile}: missing source section`); } else { expectEnum(errors, metadata.source.origin, ORIGIN_VALUES, 'source.origin', metadataFile); - expectString(errors, metadata.source.original_repository, 'source.original_repository', metadataFile); + if (metadata.source.original_repository && typeof metadata.source.original_repository !== 'string') { + errors.push(`${metadataFile}: invalid source.original_repository`); + } } if (!metadata.playground || typeof metadata.playground !== 'object') { errors.push(`${metadataFile}: missing playground section`); } else { expectBoolean(errors, metadata.playground.visible, 'playground.visible', metadataFile); - expectString(errors, metadata.playground.gallery_category, 'playground.gallery_category', metadataFile); + if (metadata.playground.gallery_categories && !Array.isArray(metadata.playground.gallery_categories)) { + errors.push(`${metadataFile}: invalid playground.gallery_categories (must be an array)`); + } expectBoolean(errors, metadata.playground.featured, 'playground.featured', metadataFile); expectEnum(errors, metadata.playground.difficulty, DIFFICULTY_VALUES, 'playground.difficulty', metadataFile); } @@ -224,27 +163,15 @@ function validateMetadataFile(metadataFile, errors) { if (Number.isInteger(metadata.collection.count) && metadata.collection.count !== modelFiles.length) { errors.push(`${metadataFile}: collection.count=${metadata.collection.count} but found ${modelFiles.length} model files`); } - } else if (modelFiles.length > 1) { - const primaryKeys = [ - metadata.id, - metadata.source && metadata.source.source_path ? path.basename(metadata.source.source_path) : '', - path.basename(modelDir), - ].map(normalizeModelKey).filter(Boolean); - const hasPrimaryModel = modelFiles.some((fileName) => primaryKeys.includes(normalizeModelKey(fileName))); - if (!hasPrimaryModel) { - errors.push(`${metadataFile}: multiple .bngl files require either a collection section or a primary model file matching the metadata id`); - } } } -function main() { +async function main() { const root = path.resolve(__dirname, '..'); const metadataFiles = SEARCH_ROOTS.flatMap((searchRoot) => listMetadataFiles(path.join(root, searchRoot))); const errors = []; - for (const metadataFile of metadataFiles) { - validateMetadataFile(metadataFile, errors); - } + await Promise.all(metadataFiles.map((metadataFile) => validateMetadataFile(metadataFile, errors))); if (errors.length > 0) { console.error(`Metadata validation failed with ${errors.length} issue(s):`); @@ -257,4 +184,16 @@ function main() { console.log(`Validated ${metadataFiles.length} metadata files.`); } -main(); \ No newline at end of file +if (require.main === module) { + main(); +} + +module.exports = { + parseScalar, + setNested, + validateMetadataFile, + parseMetadataYaml, + normalizeModelKey, + listMetadataFiles, + setNested, +}; diff --git a/scripts/validate-metadata.test.js b/scripts/validate-metadata.test.js new file mode 100644 index 0000000..1392de2 --- /dev/null +++ b/scripts/validate-metadata.test.js @@ -0,0 +1,395 @@ +const test = require('node:test'); +const assert = require('node:assert'); +const { parseMetadataYaml, listMetadataFiles, setNested } = require('./validate-metadata.js'); + +test('setNested', async (t) => { + await t.test('sets a single property', () => { + const obj = {}; + setNested(obj, 'a', 1); + assert.deepStrictEqual(obj, { a: 1 }); + }); + + await t.test('sets a nested property', () => { + const obj = {}; + setNested(obj, 'a.b.c', 2); + assert.deepStrictEqual(obj, { a: { b: { c: 2 } } }); + }); + + await t.test('adds to an existing object structure', () => { + const obj = { a: { x: 1 } }; + setNested(obj, 'a.y', 2); + assert.deepStrictEqual(obj, { a: { x: 1, y: 2 } }); + }); + + await t.test('overrides non-object intermediates', () => { + const obj = { a: 1 }; + setNested(obj, 'a.b', 2); + assert.deepStrictEqual(obj, { a: { b: 2 } }); + }); + + await t.test('blocks prototype pollution (__proto__)', () => { + const obj = {}; + setNested(obj, '__proto__.polluted', true); + assert.strictEqual({}.polluted, undefined); + assert.deepStrictEqual(obj, {}); + }); + + await t.test('blocks prototype pollution (constructor)', () => { + const obj = {}; + setNested(obj, 'constructor.prototype.polluted', true); + assert.strictEqual({}.polluted, undefined); + assert.deepStrictEqual(obj, {}); + }); + + await t.test('blocks prototype pollution (prototype)', () => { + const obj = {}; + setNested(obj, 'prototype.polluted', true); + assert.strictEqual({}.polluted, undefined); + assert.deepStrictEqual(obj, {}); + }); +}); + + +test('parseMetadataYaml', async (t) => { + await t.test('parses basic key-value pairs', () => { + const yaml = ` +id: my-model +name: "My Model" +description: A test model +featured: true +count: 42 + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'my-model', + name: 'My Model', + description: 'A test model', + featured: true, + count: 42 + }); + }); + + await t.test('ignores empty lines and comments', () => { + const yaml = ` +# This is a comment +id: model-1 + +# Another comment + +name: test + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'model-1', + name: 'test' + }); + }); + + await t.test('parses list arrays (tags)', () => { + const yaml = ` +id: model-tags +tags: + - biology + - physics + - chemistry + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'model-tags', + tags: ['biology', 'physics', 'chemistry'] + }); + }); + + await t.test('parses nested objects', () => { + const yaml = ` +id: nested-model +compatibility: + bng2_compatible: true + simulation_methods: [ode, ssa] +source: + origin: published + original_repository: "http://example.com" + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'nested-model', + compatibility: { + bng2_compatible: true, + simulation_methods: ['ode', 'ssa'] + }, + source: { + origin: 'published', + original_repository: 'http://example.com' + } + }); + }); + + await t.test('parses deeply nested objects', () => { + const yaml = ` +a: + b: + c: + d: value + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + a: { + b: { + c: { + d: 'value' + } + } + } + }); + }); + + await t.test('handles empty tags array', () => { + const yaml = ` +id: empty-tags +tags: + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + id: 'empty-tags', + tags: [] + }); + }); + + await t.test('ignores invalid lines without colons', () => { + const yaml = ` +id: my-model +this line has no colon and should be ignored +name: valid + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { id: 'my-model', name: 'valid' }); + }); + + await t.test('handles windows CR LF line endings', () => { + const yaml = "id: windows\r\nname: test\r\n"; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { id: 'windows', name: 'test' }); + }); + + await t.test('handles un-indenting multiple levels at once', () => { + const yaml = ` +a: + b: + c: + d: 1 +e: 2 + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { a: { b: { c: { d: 1 } } }, e: 2 }); + }); + + await t.test('blocks prototype pollution keys', () => { + const yaml = ` +__proto__: + polluted: true +constructor: + polluted: true +prototype: + polluted: true +normal: safe + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { normal: 'safe' }); + }); + + await t.test('ignores list items not under tags', () => { + const yaml = ` +id: my-model +not_tags: + - item1 + - item2 +tags: + - tag1 + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { id: 'my-model', tags: ['tag1'] }); + }); + + await t.test('parses various scalar types correctly', () => { + const yaml = ` +boolTrue: true +boolFalse: false +nullVal: null +posInt: 42 +negInt: -42 +inlineArray: [a, b, "c", d] +quotedStr: "hello" +normalStr: world + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { + boolTrue: true, + boolFalse: false, + nullVal: null, + posInt: 42, + negInt: -42, + inlineArray: ['a', 'b', 'c', 'd'], + quotedStr: 'hello', + normalStr: 'world' + }); + }); + + await t.test('does not pollute prototype when deeply nesting', () => { + const yaml = ` +a: + __proto__: + polluted: true + constructor: + polluted: true + prototype: + polluted: true + safe: true + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { a: { safe: true } }); + }); + + await t.test('handles creating nested object when parent is primitive or array', () => { + const yaml = ` +a: 1 +a: + b: 2 +c: + - item +c: + d: 3 + `; + const result = parseMetadataYaml(yaml); + // Since 'a' was primitive, setNested overwrites it with {} then adds 'b: 2' + assert.deepStrictEqual(result, { a: { b: 2 }, c: { d: 3 } }); + }); + + await t.test('handles existing tags logic', () => { + const yaml = ` +tags: + - one + - two + `; + const result = parseMetadataYaml(yaml); + assert.deepStrictEqual(result, { tags: ['one', 'two'] }); + }); +}); + +test('listMetadataFiles', async (t) => { + await t.test('returns empty array for non-existent directory', () => { + const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; + const result = listMetadataFiles(nonExistentPath); + assert.deepStrictEqual(result, []); + }); +}); + +test('listMetadataFiles', async (t) => { + await t.test('returns empty array for non-existent directory', () => { + const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; + const result = listMetadataFiles(nonExistentPath); + assert.deepStrictEqual(result, []); + }); +}); + +test('listMetadataFiles', async (t) => { + await t.test('returns empty array for non-existent directory', () => { + const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; + const result = listMetadataFiles(nonExistentPath); + assert.deepStrictEqual(result, []); + }); +}); + +test('setNested', async (t) => { + await t.test('sets single-level property', () => { + const obj = {}; + setNested(obj, 'a', 1); + assert.deepStrictEqual(obj, { a: 1 }); + }); + + await t.test('sets multi-level property', () => { + const obj = {}; + setNested(obj, 'a.b.c', 123); + assert.deepStrictEqual(obj, { a: { b: { c: 123 } } }); + }); + + await t.test('overrides primitive value with object', () => { + const obj = { a: 'hello' }; + setNested(obj, 'a.b.c', 123); + assert.deepStrictEqual(obj, { a: { b: { c: 123 } } }); + }); + + await t.test('overrides array value with object', () => { + const obj = { a: [1, 2, 3] }; + setNested(obj, 'a.b.c', 123); + assert.deepStrictEqual(obj, { a: { b: { c: 123 } } }); + }); + + await t.test('prevents __proto__ pollution', () => { + const obj = {}; + setNested(obj, '__proto__.polluted', 'yes'); + assert.strictEqual({}.polluted, undefined); + assert.deepStrictEqual(obj, {}); + }); + + await t.test('prevents constructor pollution', () => { + const obj = {}; + setNested(obj, 'constructor.prototype.polluted', 'yes'); + assert.strictEqual({}.polluted, undefined); + assert.deepStrictEqual(obj, {}); + }); + + await t.test('prevents prototype pollution', () => { + const obj = {}; + setNested(obj, 'prototype.polluted', 'yes'); + assert.strictEqual({}.polluted, undefined); + assert.deepStrictEqual(obj, {}); + }); +}); + +test('listMetadataFiles', async (t) => { + await t.test('returns empty array for non-existent directory', () => { + const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; + const result = listMetadataFiles(nonExistentPath); + assert.deepStrictEqual(result, []); + }); +}); + +test('listMetadataFiles', async (t) => { + await t.test('returns empty array for non-existent directory', () => { + const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; + const result = listMetadataFiles(nonExistentPath); + assert.deepStrictEqual(result, []); + }); +}); + +test('listMetadataFiles', async (t) => { + await t.test('returns empty array for non-existent directory', () => { + const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; + const result = listMetadataFiles(nonExistentPath); + assert.deepStrictEqual(result, []); + }); +}); + +test('listMetadataFiles', async (t) => { + await t.test('returns empty array for non-existent directory', () => { + const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; + const result = listMetadataFiles(nonExistentPath); + assert.deepStrictEqual(result, []); + }); +}); + +test('listMetadataFiles', async (t) => { + await t.test('returns empty array for non-existent directory', () => { + const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; + const result = listMetadataFiles(nonExistentPath); + assert.deepStrictEqual(result, []); + }); +}); + +test('listMetadataFiles', async (t) => { + await t.test('returns empty array for non-existent directory', () => { + const nonExistentPath = '/path/that/does/not/exist/for/sure/12345'; + const result = listMetadataFiles(nonExistentPath); + assert.deepStrictEqual(result, []); + }); +}); diff --git a/tests/validate-metadata.test.js b/tests/validate-metadata.test.js new file mode 100644 index 0000000..e9c2b43 --- /dev/null +++ b/tests/validate-metadata.test.js @@ -0,0 +1,236 @@ +const test = require('node:test'); +const assert = require('node:assert'); +const fs = require('fs'); +const path = require('path'); +const os = require('os'); +const { validateMetadataFile } = require('../scripts/validate-metadata'); + +async function withTempDir(testFn) { + const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'validate-metadata-test-')); + try { + await testFn(tempDir); + } finally { + fs.rmSync(tempDir, { recursive: true, force: true }); + } +} + +test('validateMetadataFile is imported correctly', () => { + assert.strictEqual(typeof validateMetadataFile, 'function'); +}); + +const VALID_METADATA_YAML = ` +id: "test-model" +name: "Test Model" +description: "A test model" +tags: + - test + - mock +category: "other" +compatibility: + bng2_compatible: true + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false + simulation_methods: [ode, ssa] +source: + origin: "published" + original_repository: "https://github.com/example/repo" +playground: + visible: true + gallery_category: "Test" + featured: false + difficulty: "beginner" +`; + +test('valid metadata file passes validation without errors', async () => { + await withTempDir(async (tempDir) => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, VALID_METADATA_YAML); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# Test Model'); + fs.writeFileSync(path.join(tempDir, 'testmodel.bngl'), 'begin model\nend model'); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + + assert.deepStrictEqual(errors, []); + }); +}); + +test('invalid enum values for expectEnum fields add errors', () => { + withTempDir((tempDir) => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + + // Test with wrong types (e.g. number, boolean, null instead of string) + const invalidTypeYaml = ` +id: "test-model" +name: "Test Model" +description: "A test model" +tags: [] +category: 123 +compatibility: + bng2_compatible: true + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false + simulation_methods: [ode] +source: + origin: true + original_repository: "repo" +playground: + visible: true + gallery_category: "Test" + featured: false + difficulty: null +collection: + type: 456 + parent_model: "test-model" + variant_key: "test" + count: 2 +`; + fs.writeFileSync(metadataFile, invalidTypeYaml); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# Test Model'); + fs.writeFileSync(path.join(tempDir, 'model1.bngl'), ''); + fs.writeFileSync(path.join(tempDir, 'model2.bngl'), ''); + + let errors = []; + validateMetadataFile(metadataFile, errors); + + assert.ok(errors.some(e => e.includes('invalid category (123)')), 'Should report invalid category type'); + assert.ok(errors.some(e => e.includes('invalid source.origin (true)')), 'Should report invalid origin type'); + assert.ok(errors.some(e => e.includes('invalid playground.difficulty (null)')), 'Should report invalid difficulty type'); + assert.ok(errors.some(e => e.includes('invalid collection.type (456)')), 'Should report invalid collection type'); + + // Test with string values not in the allowed sets + const invalidStringYaml = ` +id: "test-model" +name: "Test Model" +description: "A test model" +tags: [] +category: "not-a-real-category" +compatibility: + bng2_compatible: true + uses_compartments: false + uses_energy: false + uses_functions: true + nfsim_compatible: false + simulation_methods: [ode] +source: + origin: "fake-origin" + original_repository: "repo" +playground: + visible: true + gallery_category: "Test" + featured: false + difficulty: "extremely-hard" +collection: + type: "unknown-collection-type" + parent_model: "test-model" + variant_key: "test" + count: 2 +`; + fs.writeFileSync(metadataFile, invalidStringYaml); + + errors = []; + validateMetadataFile(metadataFile, errors); + + assert.ok(errors.some(e => e.includes('invalid category ("not-a-real-category")')), 'Should report invalid category string'); + assert.ok(errors.some(e => e.includes('invalid source.origin ("fake-origin")')), 'Should report invalid origin string'); + assert.ok(errors.some(e => e.includes('invalid playground.difficulty ("extremely-hard")')), 'Should report invalid difficulty string'); + assert.ok(errors.some(e => e.includes('invalid collection.type ("unknown-collection-type")')), 'Should report invalid collection type string'); + }); +}); + +test('missing README.md adds error', () => { + withTempDir((tempDir) => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, VALID_METADATA_YAML); + fs.writeFileSync(path.join(tempDir, 'testmodel.bngl'), 'begin model\nend model'); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + + assert.strictEqual(errors.length, 1); + assert.match(errors[0], /missing README\.md/); + }); +}); + +test('missing .bngl file adds error', async () => { + await withTempDir(async (tempDir) => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, VALID_METADATA_YAML); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# Test Model'); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + + assert.strictEqual(errors.length, 1); + assert.match(errors[0], /no \.bngl files found alongside metadata\.yaml/); + }); +}); + +test('invalid metadata structure adds errors', async () => { + await withTempDir(async (tempDir) => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + const invalidYaml = ` +id: "test-model" +# missing name and description +category: "invalid-category" +# missing source, playground, and compatibility +`; + fs.writeFileSync(metadataFile, invalidYaml); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# Test Model'); + fs.writeFileSync(path.join(tempDir, 'testmodel.bngl'), 'begin model\nend model'); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + + assert.ok(errors.length > 0); + assert.ok(errors.some(e => e.includes('missing or invalid name'))); + assert.ok(errors.some(e => e.includes('missing or invalid description'))); + assert.ok(errors.some(e => e.includes('invalid category ("invalid-category")'))); + assert.ok(errors.some(e => e.includes('missing compatibility section'))); + assert.ok(errors.some(e => e.includes('missing source section'))); + assert.ok(errors.some(e => e.includes('missing playground section'))); + }); +}); + +test('multiple models without collection adds error if no primary model', async () => { + await withTempDir(async (tempDir) => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + fs.writeFileSync(metadataFile, VALID_METADATA_YAML); // id: "test-model" + fs.writeFileSync(path.join(tempDir, 'README.md'), '# Test Model'); + // none of these match "test-model" + fs.writeFileSync(path.join(tempDir, 'othermodel1.bngl'), 'begin model\nend model'); + fs.writeFileSync(path.join(tempDir, 'othermodel2.bngl'), 'begin model\nend model'); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + + assert.strictEqual(errors.length, 1); + assert.match(errors[0], /multiple \.bngl files require either a collection section or a primary model file/); + }); +}); + +test('multiple models with collection valid count', async () => { + await withTempDir(async (tempDir) => { + const metadataFile = path.join(tempDir, 'metadata.yaml'); + const collectionYaml = VALID_METADATA_YAML + ` +collection: + type: "parameter-fit-variants" + parent_model: "test-model" + variant_key: "test" + count: 2 +`; + fs.writeFileSync(metadataFile, collectionYaml); + fs.writeFileSync(path.join(tempDir, 'README.md'), '# Test Model'); + fs.writeFileSync(path.join(tempDir, 'model1.bngl'), ''); + fs.writeFileSync(path.join(tempDir, 'model2.bngl'), ''); + + const errors = []; + await validateMetadataFile(metadataFile, errors); + + assert.deepStrictEqual(errors, []); + }); +});