Restructuring appendices

tutorial/1-modelling-patch-clamp.ipynb

@@ -142,7 +142,7 @@
    "id": "5597d996",
    "metadata": {},
    "source": [
-    "> For more about op amps and difference amplifiers, see [Appendix A1](./appendix-a/1-op-amp.ipynb)."
+    "> For more about op amps and difference amplifiers, see [Appendix B1](./appendix/b-op-amps/1-op-amp.ipynb)."
    ]
   },
   {
@@ -251,7 +251,7 @@
    "metadata": {},
    "source": [
     "> A detailed analysis of the bandwidth is given in Sigworth 1995a.\n",
-    "> It involves transfer function representations, which are discussed in [Appendix A2](./appendix-a/2-laplace-and-filters.ipynb)."
+    "> It involves transfer function representations, which are discussed in [Appendix A1](./appendix/a-laplace/1-laplace-transforms.ipynb)."
    ]
   },
   {
@@ -283,11 +283,11 @@
    "id": "86015f66-6523-4cd4-aa65-65614fc4d305",
    "metadata": {},
    "source": [
-    "> Further details about these two models are given in [Appendix A3](./appendix-a/3-non-ideal-op-amp.ipynb).\n",
+    "> Further details about these two models are given in [Appendix B2](./appendix/b-op-amps/2-non-ideal-op-amp.ipynb).\n",
     "> In short, the equations used by Weerakoon and Lei et al. are a simplification based on Sigworth's analysis.\n",
-    "> They give rise to slightly different behaviour, as can be seen in [Appendix B1](./appendix-b/1-uncompensated-models.ipynb), but for the analysis of many patch-clamp experiments their influence is overshadowed by the effects of the _series resistance_ and _membrane capacitance_, which are discussed below.\n",
+    "> They give rise to slightly different behaviour, as can be seen in [Appendix B3](./appendix/b-op-amps/3-resulting-vc-models.ipynb), but for the analysis of many patch-clamp experiments their influence is overshadowed by the effects of the _series resistance_ and _membrane capacitance_, which are discussed below.\n",
     "> \n",
-    "> Typical values for $\\tau_a$ are in the order of 10 to 100 ns, as given in [Appendix C3](./appendix-c/3-parameter-values.ipynb)."
+    "> Typical values for $\\tau_a$ are in the order of 10 to 100 ns."
    ]
   },
   {
@@ -499,10 +499,9 @@
    "metadata": {},
    "source": [
     "> The model above differs subtly from the uncompensated model used in [Lei et al., 2020](https://doi.org/10.1098/rsta.2019.0348).\n",
-    "> A comparison is provided in [Appendix B1](./appendix-b/1-uncompensated-models.ipynb).\n",
+    "> A comparison is provided in [Tutorial 4](./4-simplifications.ipynb).\n",
     ">\n",
-    "> A list of alternative names and symbols for the components above is given in [Appendix C1](./appendix-c/1-symbols.ipynb).\n",
-    "> Notably $R_\\text{leak}$ is often called _seal resistance_, while $R_s$ is also referred to as _access resistance_."
+    "> $R_\\text{leak}$ is often called _seal resistance_, while $R_s$ is also referred to as _access resistance_."
    ]
   },
   {
@@ -522,14 +521,6 @@
     "3. We leave out $E_\\text{off}$ and $I_\\text{leak}$, and set $I = 0$ (for now), leaving only the capacitative currents. As a result, at steady state we have $V_p = V_o = V_m$."
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "95a7b298-a320-4658-8ef0-de16277ffee1",
-   "metadata": {},
-   "source": [
-    "> The parameters used here are representitative of a small-cell experiment, and are given in [appendix C2](./appendix-c/2-parameter-defaults.ipynb)."
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 1,
@@ -878,7 +869,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.11"
+   "version": "3.13.12"
   }
  },
  "nbformat": 4,

tutorial/2-compensation.ipynb

@@ -14,15 +14,6 @@
     "We will deal mostly with _transient_ distortions of the recorded output signal, which we call _artefacts_, and with transient differences between the true and intended membrane potential, which are an example of _imperfect control_."
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "59df3dd5-7aa9-458e-82c0-9c41fc9191eb",
-   "metadata": {},
-   "source": [
-    "> Artefacts, imperfect control, and general strategies for dealing with their effects, are discussed in [Appendix D1](./appendix-d/1-strategies.ipynb).\n",
-    "Stochastic and periodic noise are not discussed here, but a brief discussion is given in [Appendix D2](./appendix-d/2-inspecting-noise.ipynb)."
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "f2b59884",
@@ -78,7 +69,7 @@
    "id": "f92327ba-b81c-4eed-9e51-05de94f548b3",
    "metadata": {},
    "source": [
-    "> A detailed description of LJP correction and sign conventions is provided in [Appendix D3](./appendix-d/3-liquid-junction-potential.ipynb)."
+    "> A detailed description of LJP correction and sign conventions is provided in [Appendix E1](./appendix/e-offsets/1-liquid-junction-potential.ipynb) and [Appendix E2](./appendix/e-offsets/2-offset-correction.ipynb)."
    ]
   },
   {
@@ -114,7 +105,7 @@
    "id": "e2cbaa02-cd68-4e70-9844-86f1be2fdbcc",
    "metadata": {},
    "source": [
-    "> Values of $R_f$ and $C_f$ for different amplifiers are given in [Appendix C3](./appendix-c/3-parameter-values.ipynb)."
+    "> Values of $R_f$ and $C_f$ for different amplifiers are given in [Appendix Z1](./appendix/z-parameters/1-parameter-values.ipynb)."
    ]
   },
   {
@@ -349,8 +340,8 @@
    "id": "9e1174f8-3454-448d-85f6-96d2ac6241aa",
    "metadata": {},
    "source": [
-    "> See [Appendix A4](./appendix-a/4-bessel-filters.ipynb) for more about filters.\n",
-    "> [Appendix C3](./appendix-c/3-parameter-values.ipynb) provides more amplifier values of $\\tau_\\text{rc}$."
+    "> See [Appendix C](./appendix/) for more about filters.\n",
+    "> [Appendix Z1](./appendix/z-parameters/1-parameter-values.ipynb) provides more amplifier values of $\\tau_\\text{rc}$."
    ]
   },
   {
@@ -418,7 +409,7 @@
    "id": "959a141d-5714-4d3f-8663-e068f528a9c3",
    "metadata": {},
    "source": [
-    "> A derivation of the prediction equations from the schematics by Sigworth is given in [appendix B3](./appendix-b/3-sigworth-rs.ipynb)."
+    "> A derivation of the prediction equations from the schematics by Sigworth is given in [appendix C1](./appendix/c-rs/1-compensation-prediction.ipynb)."
    ]
   },
   {
@@ -573,7 +564,7 @@
    "id": "da60337b-c966-4751-90e6-f68009ea6ff2",
    "metadata": {},
    "source": [
-    "> Background on Bessel filters is provided in [Appendix A4](./appendix-a/4-bessel-filters.ipynb)."
+    "> Background on Bessel filters is provided in [Appendix C](./appendix/)."
    ]
   },
   {
@@ -648,7 +639,7 @@
    "id": "6b334389-337d-425a-a39b-b085707ef62d",
    "metadata": {},
    "source": [
-    "> These equations are derived and discussed in [Appendix A5](./appendix-a/5-bessel-filter-odes.ipynb)."
+    "> These equations are derived and discussed in [Appendix D2](./appendix/d-filters/2-bessel-filters-ode.ipynb) and summarised in [Appendix D3](./appendix/d-filters/3-bessel-filters-ode-summary.ipynb)."
    ]
   },
   {
@@ -874,7 +865,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.11"
+   "version": "3.13.12"
   }
  },
  "nbformat": 4,

tutorial/README.md

@@ -6,44 +6,46 @@ The initial exposition draws on a book chapter by [Sigworth (1995a)](https://doi
 To view the notebooks, use the GitHub or nbviewer links below, or clone the repository and run Jupyter notebook locally.
 Running locally will require the dependencies from `requirements.txt`.
 
-A list of references and further reading is provided [here](./references.ipynb).
+[↩ Back to the main repository](https://github.com/CardiacModelling/VoltageClampModel)
 
-[↩ Back to the main repository](https://github.com/CardiacModelling/VoltageClampModel-new)
 
-
-## Modelling patch-clamp experiments 
+## 1. Modelling patch-clamp experiments 
 [![github](./img/github.svg)](./1-modelling-patch-clamp.ipynb)
-[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/1-modelling-patch-clamp.ipynb)
+[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/1-modelling-patch-clamp.ipynb)
 
 The first notebook describes the uncompensated patch-clamp set up, and derives an ODE model from the electrical schematics.
 
-## Modelling electronic compensation
+## 2. Modelling electronic compensation
 [![github](./img/github.svg)](./2-compensation.ipynb)
-[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/2-compensation.ipynb)
+[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/2-compensation.ipynb)
 
 The model is updated to include the compensation circuitry commonly used in patch-clamp amplifiers.
 
-## Simulating a manual patch clamp experiment 
+## 3. Simulating a manual patch clamp experiment 
 [![github](./img/github.svg)](./3-simulations.ipynb) 
-[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/3-simulations.ipynb)
+[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/3-simulations.ipynb)
 
 We walk through and simulate the early steps of a manual patch-clamp experiment.
 
-## Simplified models 
+## 4. Simplified models 
 [![github](./img/github.svg)](./4-simplifications.ipynb) 
-[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/4-simplifications.ipynb)
+[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/4-simplifications.ipynb)
 
 In the final notebook, we derive simplified models and compare with previous work.
 
----
+## Resources
+
+- [![github](./img/github.svg)](./symbols.ipynb) 
+  [![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/symbols.ipynb)
+  **Names and symbols** A table of all symbols, their meanings, and names used in other publications.
 
-## Appendices
+- [![github](./img/github.svg)](./tour.ipynb) 
+  [![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/tour.ipynb)
+  **Default parameter values** and comments on how to reparameterise the model, are given in the Model Tour.
 
-Finally, there are several appendices:
+- [![github](./img/github.svg)](./references.ipynb) 
+  [![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/references.ipynb)
+  **References** and further reading.
 
-- [Appendix A](./appendix-a/README.md) adds details on electronics and filters.
-- [Appendix B](./appendix-b/README.md) looks at details of the model derivation.
-- [Appendix C](./appendix-c/README.md) provides default parameter values, and amplifier-specific ones.
-- [Appendix D](./appendix-d/README.md) discusses remaining sources of error.
-- [Appendix E](./appendix-e/README.md) looks at Rs and Cm estimates.
+Finally, there are [several appendices](./appendix), which provide background on electronics and details of the model derivation.