RuleWorld · jrfaeder · May 4, 2026 · Mar 31, 2026 · Mar 31, 2026 · Apr 13, 2026
diff --git 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
+        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
diff --git a/Contributed/README.md b/Contributed/README.md
diff --git a/...d_Examples/biology/aktsignaling/README.md → Examples/biology/aktsignaling/README.md b/...d_Examples/biology/aktsignaling/README.md → Examples/biology/aktsignaling/README.md
diff --git a/...s/biology/aktsignaling/akt-signaling.bngl → ...s/biology/aktsignaling/akt-signaling.bngl b/...s/biology/aktsignaling/akt-signaling.bngl → ...s/biology/aktsignaling/akt-signaling.bngl
diff --git a/...amples/biology/aktsignaling/metadata.yaml → Examples/biology/aktsignaling/metadata.yaml b/...amples/biology/aktsignaling/metadata.yaml → Examples/biology/aktsignaling/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: false
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   source_path: "example-models/akt-signaling.bngl"
 playground:
   visible: false
-  gallery_category: "signaling"
+  gallery_categories: ["test-models"]
   featured: false
   difficulty: "advanced"
diff --git a/...es/biology/allostericactivation/README.md → ...es/biology/allostericactivation/README.md b/...es/biology/allostericactivation/README.md → ...es/biology/allostericactivation/README.md
diff --git a/...ericactivation/allosteric-activation.bngl → ...ericactivation/allosteric-activation.bngl b/...ericactivation/allosteric-activation.bngl → ...ericactivation/allosteric-activation.bngl
diff --git a/...iology/allostericactivation/metadata.yaml → ...iology/allostericactivation/metadata.yaml b/...iology/allostericactivation/metadata.yaml → ...iology/allostericactivation/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: false
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/..._Examples/biology/ampksignaling/README.md → Examples/biology/ampksignaling/README.md b/..._Examples/biology/ampksignaling/README.md → Examples/biology/ampksignaling/README.md
diff --git a/...biology/ampksignaling/ampk-signaling.bngl → ...biology/ampksignaling/ampk-signaling.bngl b/...biology/ampksignaling/ampk-signaling.bngl → ...biology/ampksignaling/ampk-signaling.bngl
diff --git a/...mples/biology/ampksignaling/metadata.yaml → Examples/biology/ampksignaling/metadata.yaml b/...mples/biology/ampksignaling/metadata.yaml → 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/...amples/biology/apoptosiscascade/README.md → Examples/biology/apoptosiscascade/README.md b/...amples/biology/apoptosiscascade/README.md → Examples/biology/apoptosiscascade/README.md
diff --git a/...y/apoptosiscascade/apoptosis-cascade.bngl → ...y/apoptosiscascade/apoptosis-cascade.bngl b/...y/apoptosiscascade/apoptosis-cascade.bngl → ...y/apoptosiscascade/apoptosis-cascade.bngl
diff --git a/...es/biology/apoptosiscascade/metadata.yaml → ...es/biology/apoptosiscascade/metadata.yaml b/...es/biology/apoptosiscascade/metadata.yaml → ...es/biology/apoptosiscascade/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: true
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/...ples/biology/autoactivationloop/README.md → ...ples/biology/autoactivationloop/README.md b/...ples/biology/autoactivationloop/README.md → ...ples/biology/autoactivationloop/README.md
diff --git a/...oactivationloop/auto-activation-loop.bngl → ...oactivationloop/auto-activation-loop.bngl b/...oactivationloop/auto-activation-loop.bngl → ...oactivationloop/auto-activation-loop.bngl
diff --git a/.../biology/autoactivationloop/metadata.yaml → .../biology/autoactivationloop/metadata.yaml b/.../biology/autoactivationloop/metadata.yaml → .../biology/autoactivationloop/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: true
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/...les/biology/autophagyregulation/README.md → ...les/biology/autophagyregulation/README.md b/...les/biology/autophagyregulation/README.md → ...les/biology/autophagyregulation/README.md
diff --git a/...phagyregulation/autophagy-regulation.bngl → ...phagyregulation/autophagy-regulation.bngl b/...phagyregulation/autophagy-regulation.bngl → ...phagyregulation/autophagy-regulation.bngl
diff --git a/...biology/autophagyregulation/metadata.yaml → ...biology/autophagyregulation/metadata.yaml b/...biology/autophagyregulation/metadata.yaml → ...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/...d_Examples/biology/bcrsignaling/README.md → Examples/biology/bcrsignaling/README.md b/...d_Examples/biology/bcrsignaling/README.md → Examples/biology/bcrsignaling/README.md
diff --git a/...s/biology/bcrsignaling/bcr-signaling.bngl → ...s/biology/bcrsignaling/bcr-signaling.bngl b/...s/biology/bcrsignaling/bcr-signaling.bngl → ...s/biology/bcrsignaling/bcr-signaling.bngl
diff --git a/...amples/biology/bcrsignaling/metadata.yaml → Examples/biology/bcrsignaling/metadata.yaml b/...amples/biology/bcrsignaling/metadata.yaml → 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/.../biology/betaadrenergicresponse/README.md → .../biology/betaadrenergicresponse/README.md b/.../biology/betaadrenergicresponse/README.md → .../biology/betaadrenergicresponse/README.md
diff --git a/...gicresponse/beta-adrenergic-response.bngl → ...gicresponse/beta-adrenergic-response.bngl b/...gicresponse/beta-adrenergic-response.bngl → ...gicresponse/beta-adrenergic-response.bngl
diff --git a/...logy/betaadrenergicresponse/metadata.yaml → ...logy/betaadrenergicresponse/metadata.yaml b/...logy/betaadrenergicresponse/metadata.yaml → ...logy/betaadrenergicresponse/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: true
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/...es/biology/bistabletoggleswitch/README.md → ...es/biology/bistabletoggleswitch/README.md b/...es/biology/bistabletoggleswitch/README.md → ...es/biology/bistabletoggleswitch/README.md
diff --git a/...etoggleswitch/bistable-toggle-switch.bngl → ...etoggleswitch/bistable-toggle-switch.bngl b/...etoggleswitch/bistable-toggle-switch.bngl → ...etoggleswitch/bistable-toggle-switch.bngl
diff --git a/...iology/bistabletoggleswitch/metadata.yaml → ...iology/bistabletoggleswitch/metadata.yaml b/...iology/bistabletoggleswitch/metadata.yaml → ...iology/bistabletoggleswitch/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: true
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/...iology/bloodcoagulationthrombin/README.md → ...iology/bloodcoagulationthrombin/README.md b/...iology/bloodcoagulationthrombin/README.md → ...iology/bloodcoagulationthrombin/README.md
diff --git a/...nthrombin/blood-coagulation-thrombin.bngl → ...nthrombin/blood-coagulation-thrombin.bngl b/...nthrombin/blood-coagulation-thrombin.bngl → ...nthrombin/blood-coagulation-thrombin.bngl
diff --git a/...gy/bloodcoagulationthrombin/metadata.yaml → ...gy/bloodcoagulationthrombin/metadata.yaml b/...gy/bloodcoagulationthrombin/metadata.yaml → ...gy/bloodcoagulationthrombin/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: false
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/...d_Examples/biology/bmpsignaling/README.md → Examples/biology/bmpsignaling/README.md b/...d_Examples/biology/bmpsignaling/README.md → Examples/biology/bmpsignaling/README.md
diff --git a/...s/biology/bmpsignaling/bmp-signaling.bngl → ...s/biology/bmpsignaling/bmp-signaling.bngl b/...s/biology/bmpsignaling/bmp-signaling.bngl → ...s/biology/bmpsignaling/bmp-signaling.bngl
diff --git a/...amples/biology/bmpsignaling/metadata.yaml → Examples/biology/bmpsignaling/metadata.yaml b/...amples/biology/bmpsignaling/metadata.yaml → 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/...s/biology/brusselatoroscillator/README.md → ...s/biology/brusselatoroscillator/README.md b/...s/biology/brusselatoroscillator/README.md → ...s/biology/brusselatoroscillator/README.md
diff --git a/...toroscillator/brusselator-oscillator.bngl → ...toroscillator/brusselator-oscillator.bngl b/...toroscillator/brusselator-oscillator.bngl → ...toroscillator/brusselator-oscillator.bngl
diff --git a/...ology/brusselatoroscillator/metadata.yaml → ...ology/brusselatoroscillator/metadata.yaml b/...ology/brusselatoroscillator/metadata.yaml → ...ology/brusselatoroscillator/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: true
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/.../biology/calcineurinnfatpathway/README.md → .../biology/calcineurinnfatpathway/README.md b/.../biology/calcineurinnfatpathway/README.md → .../biology/calcineurinnfatpathway/README.md
diff --git a/...nfatpathway/calcineurin-nfat-pathway.bngl → ...nfatpathway/calcineurin-nfat-pathway.bngl b/...nfatpathway/calcineurin-nfat-pathway.bngl → ...nfatpathway/calcineurin-nfat-pathway.bngl
diff --git a/...logy/calcineurinnfatpathway/metadata.yaml → ...logy/calcineurinnfatpathway/metadata.yaml b/...logy/calcineurinnfatpathway/metadata.yaml → ...logy/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/...s/biology/calciumspikesignaling/README.md → ...s/biology/calciumspikesignaling/README.md b/...s/biology/calciumspikesignaling/README.md → ...s/biology/calciumspikesignaling/README.md
diff --git a/...ikesignaling/calcium-spike-signaling.bngl → ...ikesignaling/calcium-spike-signaling.bngl b/...ikesignaling/calcium-spike-signaling.bngl → ...ikesignaling/calcium-spike-signaling.bngl
diff --git a/...ology/calciumspikesignaling/metadata.yaml → ...ology/calciumspikesignaling/metadata.yaml b/...ology/calciumspikesignaling/metadata.yaml → ...ology/calciumspikesignaling/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: true
   uses_energy: false
   uses_functions: true
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/...s/biology/caspaseactivationloop/README.md → ...s/biology/caspaseactivationloop/README.md b/...s/biology/caspaseactivationloop/README.md → ...s/biology/caspaseactivationloop/README.md
diff --git a/...tivationloop/caspase-activation-loop.bngl → ...tivationloop/caspase-activation-loop.bngl b/...tivationloop/caspase-activation-loop.bngl → ...tivationloop/caspase-activation-loop.bngl
diff --git a/...ology/caspaseactivationloop/metadata.yaml → ...ology/caspaseactivationloop/metadata.yaml b/...ology/caspaseactivationloop/metadata.yaml → ...ology/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/..._Examples/biology/cd40signaling/README.md → Examples/biology/cd40signaling/README.md b/..._Examples/biology/cd40signaling/README.md → Examples/biology/cd40signaling/README.md
diff --git a/...biology/cd40signaling/cd40-signaling.bngl → ...biology/cd40signaling/cd40-signaling.bngl b/...biology/cd40signaling/cd40-signaling.bngl → ...biology/cd40signaling/cd40-signaling.bngl
diff --git a/...mples/biology/cd40signaling/metadata.yaml → Examples/biology/cd40signaling/metadata.yaml b/...mples/biology/cd40signaling/metadata.yaml → 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/...les/biology/cellcyclecheckpoint/README.md → ...les/biology/cellcyclecheckpoint/README.md b/...les/biology/cellcyclecheckpoint/README.md → ...les/biology/cellcyclecheckpoint/README.md
diff --git a/...yclecheckpoint/cell-cycle-checkpoint.bngl → ...yclecheckpoint/cell-cycle-checkpoint.bngl b/...yclecheckpoint/cell-cycle-checkpoint.bngl → ...yclecheckpoint/cell-cycle-checkpoint.bngl
diff --git a/...biology/cellcyclecheckpoint/metadata.yaml → ...biology/cellcyclecheckpoint/metadata.yaml b/...biology/cellcyclecheckpoint/metadata.yaml → ...biology/cellcyclecheckpoint/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: true
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/...ology/checkpointkinasesignaling/README.md → ...ology/checkpointkinasesignaling/README.md b/...ology/checkpointkinasesignaling/README.md → ...ology/checkpointkinasesignaling/README.md
diff --git a/...ignaling/checkpoint-kinase-signaling.bngl → ...ignaling/checkpoint-kinase-signaling.bngl b/...ignaling/checkpoint-kinase-signaling.bngl → ...ignaling/checkpoint-kinase-signaling.bngl
diff --git a/...y/checkpointkinasesignaling/metadata.yaml → ...y/checkpointkinasesignaling/metadata.yaml b/...y/checkpointkinasesignaling/metadata.yaml → ...y/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/...gy/chemotaxissignaltransduction/README.md → ...gy/chemotaxissignaltransduction/README.md b/...gy/chemotaxissignaltransduction/README.md → ...gy/chemotaxissignaltransduction/README.md
diff --git a/...ction/chemotaxis-signal-transduction.bngl → ...ction/chemotaxis-signal-transduction.bngl b/...ction/chemotaxis-signal-transduction.bngl → ...ction/chemotaxis-signal-transduction.bngl
diff --git a/...hemotaxissignaltransduction/metadata.yaml → ...hemotaxissignaltransduction/metadata.yaml b/...hemotaxissignaltransduction/metadata.yaml → ...hemotaxissignaltransduction/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: true
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/...les/biology/circadianoscillator/README.md → ...les/biology/circadianoscillator/README.md b/...les/biology/circadianoscillator/README.md → ...les/biology/circadianoscillator/README.md
diff --git a/...adianoscillator/circadian-oscillator.bngl → ...adianoscillator/circadian-oscillator.bngl b/...adianoscillator/circadian-oscillator.bngl → ...adianoscillator/circadian-oscillator.bngl
diff --git a/...biology/circadianoscillator/metadata.yaml → ...biology/circadianoscillator/metadata.yaml b/...biology/circadianoscillator/metadata.yaml → ...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/...s/biology/clockbmal1genecircuit/README.md → ...s/biology/clockbmal1genecircuit/README.md b/...s/biology/clockbmal1genecircuit/README.md → ...s/biology/clockbmal1genecircuit/README.md
diff --git a/...genecircuit/clock-bmal1-gene-circuit.bngl → ...genecircuit/clock-bmal1-gene-circuit.bngl b/...genecircuit/clock-bmal1-gene-circuit.bngl → ...genecircuit/clock-bmal1-gene-circuit.bngl
diff --git a/...ology/clockbmal1genecircuit/metadata.yaml → ...ology/clockbmal1genecircuit/metadata.yaml b/...ology/clockbmal1genecircuit/metadata.yaml → ...ology/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/...ogy/competitiveenzymeinhibition/README.md → ...ogy/competitiveenzymeinhibition/README.md b/...ogy/competitiveenzymeinhibition/README.md → ...ogy/competitiveenzymeinhibition/README.md
diff --git a/...bition/competitive-enzyme-inhibition.bngl → ...bition/competitive-enzyme-inhibition.bngl b/...bition/competitive-enzyme-inhibition.bngl → ...bition/competitive-enzyme-inhibition.bngl
diff --git a/...competitiveenzymeinhibition/metadata.yaml → ...competitiveenzymeinhibition/metadata.yaml b/...competitiveenzymeinhibition/metadata.yaml → ...competitiveenzymeinhibition/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: false
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/...ogy/complementactivationcascade/README.md → ...ogy/complementactivationcascade/README.md b/...ogy/complementactivationcascade/README.md → ...ogy/complementactivationcascade/README.md
diff --git a/...ascade/complement-activation-cascade.bngl → ...ascade/complement-activation-cascade.bngl b/...ascade/complement-activation-cascade.bngl → ...ascade/complement-activation-cascade.bngl
diff --git a/...complementactivationcascade/metadata.yaml → ...complementactivationcascade/metadata.yaml b/...complementactivationcascade/metadata.yaml → ...complementactivationcascade/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: true
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/...ology/contactinhibitionhippoyap/README.md → ...ology/contactinhibitionhippoyap/README.md b/...ology/contactinhibitionhippoyap/README.md → ...ology/contactinhibitionhippoyap/README.md
diff --git a/...ippoyap/contact-inhibition-hippo-yap.bngl → ...ippoyap/contact-inhibition-hippo-yap.bngl b/...ippoyap/contact-inhibition-hippo-yap.bngl → ...ippoyap/contact-inhibition-hippo-yap.bngl
diff --git a/...y/contactinhibitionhippoyap/metadata.yaml → ...y/contactinhibitionhippoyap/metadata.yaml b/...y/contactinhibitionhippoyap/metadata.yaml → ...y/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/...ples/biology/cooperativebinding/README.md → ...ples/biology/cooperativebinding/README.md b/...ples/biology/cooperativebinding/README.md → ...ples/biology/cooperativebinding/README.md
diff --git a/...operativebinding/cooperative-binding.bngl → ...operativebinding/cooperative-binding.bngl b/...operativebinding/cooperative-binding.bngl → ...operativebinding/cooperative-binding.bngl
diff --git a/.../biology/cooperativebinding/metadata.yaml → .../biology/cooperativebinding/metadata.yaml b/.../biology/cooperativebinding/metadata.yaml → .../biology/cooperativebinding/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: false
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   source_path: "example-models/cooperative-binding.bngl"
 playground:
   visible: false
-  gallery_category: "signaling"
+  gallery_categories: ["test-models"]
   featured: false
   difficulty: "advanced"
diff --git a/...xamples/biology/dnadamagerepair/README.md → Examples/biology/dnadamagerepair/README.md b/...xamples/biology/dnadamagerepair/README.md → Examples/biology/dnadamagerepair/README.md
diff --git a/...gy/dnadamagerepair/dna-damage-repair.bngl → ...gy/dnadamagerepair/dna-damage-repair.bngl b/...gy/dnadamagerepair/dna-damage-repair.bngl → ...gy/dnadamagerepair/dna-damage-repair.bngl
diff --git a/...les/biology/dnadamagerepair/metadata.yaml → ...les/biology/dnadamagerepair/metadata.yaml b/...les/biology/dnadamagerepair/metadata.yaml → ...les/biology/dnadamagerepair/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: false
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/.../biology/dnamethylationdynamics/README.md → .../biology/dnamethylationdynamics/README.md b/.../biology/dnamethylationdynamics/README.md → .../biology/dnamethylationdynamics/README.md
diff --git a/...iondynamics/dna-methylation-dynamics.bngl → ...iondynamics/dna-methylation-dynamics.bngl b/...iondynamics/dna-methylation-dynamics.bngl → ...iondynamics/dna-methylation-dynamics.bngl
diff --git a/...logy/dnamethylationdynamics/metadata.yaml → ...logy/dnamethylationdynamics/metadata.yaml b/...logy/dnamethylationdynamics/metadata.yaml → ...logy/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/...s/biology/dr5apoptosissignaling/README.md → ...s/biology/dr5apoptosissignaling/README.md b/...s/biology/dr5apoptosissignaling/README.md → ...s/biology/dr5apoptosissignaling/README.md
diff --git a/...sissignaling/dr5-apoptosis-signaling.bngl → ...sissignaling/dr5-apoptosis-signaling.bngl b/...sissignaling/dr5-apoptosis-signaling.bngl → ...sissignaling/dr5-apoptosis-signaling.bngl
diff --git a/...ology/dr5apoptosissignaling/metadata.yaml → ...ology/dr5apoptosissignaling/metadata.yaml b/...ology/dr5apoptosissignaling/metadata.yaml → ...ology/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/...biology/dualsitephosphorylation/README.md → ...biology/dualsitephosphorylation/README.md b/...biology/dualsitephosphorylation/README.md → ...biology/dualsitephosphorylation/README.md
diff --git a/...horylation/dual-site-phosphorylation.bngl → ...horylation/dual-site-phosphorylation.bngl b/...horylation/dual-site-phosphorylation.bngl → ...horylation/dual-site-phosphorylation.bngl
diff --git a/...ogy/dualsitephosphorylation/metadata.yaml → ...ogy/dualsitephosphorylation/metadata.yaml b/...ogy/dualsitephosphorylation/metadata.yaml → ...ogy/dualsitephosphorylation/metadata.yaml
@@ -11,14 +11,14 @@ compatibility:
   uses_compartments: false
   uses_energy: false
   uses_functions: false
-  nfsim_compatible: false
+  nfsim_compatible: true
 source:
   origin: "ai-generated"
   original_format: "bngl"
   original_repository: "bionetgen-web-simulator"
   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/...es/biology/e2frbcellcycleswitch/README.md → ...es/biology/e2frbcellcycleswitch/README.md b/...es/biology/e2frbcellcycleswitch/README.md → ...es/biology/e2frbcellcycleswitch/README.md
diff --git a/...cycleswitch/e2f-rb-cell-cycle-switch.bngl → ...cycleswitch/e2f-rb-cell-cycle-switch.bngl b/...cycleswitch/e2f-rb-cell-cycle-switch.bngl → ...cycleswitch/e2f-rb-cell-cycle-switch.bngl