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‎tutorial/README.md‎

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@@ -6,54 +6,46 @@ The initial exposition draws on a book chapter by [Sigworth (1995a)](https://doi
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To view the notebooks, use the GitHub or nbviewer links below, or clone the repository and run Jupyter notebook locally.
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Running locally will require the dependencies from `requirements.txt`.
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A list of references and further reading is provided [here](./references.ipynb).
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[↩ Back to the main repository](https://github.com/CardiacModelling/VoltageClampModel)
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[↩ Back to the main repository](https://github.com/CardiacModelling/VoltageClampModel-new)
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## Modelling patch-clamp experiments
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## 1. Modelling patch-clamp experiments
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[![github](./img/github.svg)](./1-modelling-patch-clamp.ipynb)
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[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/1-modelling-patch-clamp.ipynb)
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[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/1-modelling-patch-clamp.ipynb)
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The first notebook describes the uncompensated patch-clamp set up, and derives an ODE model from the electrical schematics.
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## Modelling electronic compensation
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## 2. Modelling electronic compensation
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[![github](./img/github.svg)](./2-compensation.ipynb)
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[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/2-compensation.ipynb)
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[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/2-compensation.ipynb)
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The model is updated to include the compensation circuitry commonly used in patch-clamp amplifiers.
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## Simulating a manual patch clamp experiment
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## 3. Simulating a manual patch clamp experiment
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[![github](./img/github.svg)](./3-simulations.ipynb)
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[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/3-simulations.ipynb)
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[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/3-simulations.ipynb)
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We walk through and simulate the early steps of a manual patch-clamp experiment.
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## Simplified models
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## 4. Simplified models
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[![github](./img/github.svg)](./4-simplifications.ipynb)
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[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/4-simplifications.ipynb)
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[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/4-simplifications.ipynb)
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In the final notebook, we derive simplified models and compare with previous work.
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---
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## Names and symbols
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[![github](./img/github.svg)](./symbols.ipynb)
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[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/symbols.ipynb)
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A table of all symbols, their meanings, and names used in other publications.
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## Parameter values
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[![github](./img/github.svg)](./tour.ipynb)
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[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/tour.ipynb)
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## Resources
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Default parameter values, and comments on how to reparameterise the model, are given in the Model Tour.
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- [![github](./img/github.svg)](./symbols.ipynb)
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[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/symbols.ipynb)
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**Names and symbols** A table of all symbols, their meanings, and names used in other publications.
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---
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- [![github](./img/github.svg)](./tour.ipynb)
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[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/tour.ipynb)
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**Default parameter values** and comments on how to reparameterise the model, are given in the Model Tour.
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## Appendices
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- [![github](./img/github.svg)](./references.ipynb)
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[![nbviewer](./img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/references.ipynb)
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**References** and further reading.
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Finally, there are [several appendices](./appendix), which provide background on electronics and details of the model derivation.
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‎tutorial/appendix/README.md‎

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# Voltage Clamp (VC) model Appendices
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# Voltage Clamp (VC) Model Tutorial Appendices
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The tutorials come with appendices, which provide either necessary background or technical details for the main text.
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## A: Laplace transforms and frequency response
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1. The Laplace transform [![github](../img/github.svg)](2-laplace-and-filters.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/appendix-a/2-laplace-and-filters.ipynb), and
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2. its use in analysing a dynamical system's frequency response.
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## B: Op-amps in the VC model
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1. Ideal op amps [![github](../img/github.svg)](1-op-amp.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/appendix-a/1-op-amp.ipynb)
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2. Models of an op amp with a finite speed
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3. VC models based on different op-amp models
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## C: Bessel filters
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3. Non-ideal op amps [![github](../img/github.svg)](3-non-ideal-op-amp.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/appendix-a/3-non-ideal-op-amp.ipynb)
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4. Bessel low-pass filters [![github](../img/github.svg)](4-bessel-filters.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/appendix-a/4-bessel-filters.ipynb)
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5. Bessel filter ODEs [![github](../img/github.svg)](5-bessel-filter-odes.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/appendix-a/5-bessel-filter-odes.ipynb)
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6. Stimulus filter [![github](../img/github.svg)](6-stimulus-filter.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/appendix-a/6-stimulus-filter.ipynb)
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# Appendix D: Remaining noise and errors
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1. Strategies for dealing with experimental error [![github](../img/github.svg)](1-strategies.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/1-strategies.ipynb)
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2. Stochastic and periodic noise [![github](../img/github.svg)](2-inspecting-noise.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/2-inspecting-noise.ipynb)
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3. Liquid junction potential [![github](../img/github.svg)](3-liquid-junction-potential.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/3-liquid-junction-potential.ipynb)
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4. Handling voltage offsets [![github](../img/github.svg)](4-offset-correction.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/4-offset-correction.ipynb)
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5. Leak (unfinished) [![github](../img/github.svg)](5-leak-correction.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/5-leak-correction.ipynb)
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6. Handling remaining capacitance artefacts (unfinished) [![github](../img/github.svg)](6-remaining-Cp-artefacts.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/6-remaining-Cp-artefacts.ipynb)
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These appendices provide background or technical details that did not fit the main text.
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[↩ Back to the tutorial index](../README.md)
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# Z: Parameter names and values
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1. Names & symbols [![github](../img/github.svg)](1-symbols.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/appendix-c/1-symbols.ipynb)
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2. Default parameter values used in examples [![github](../img/github.svg)](2-parameter-defaults.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/appendix-c/2-parameter-defaults.ipynb)
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3. Parameter values, estimates for different amplifiers etc. [![github](../img/github.svg)](3-parameter-values.ipynb) [![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel-new/tree/main/tutorial/appendix-c/3-parameter-values.ipynb)
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[↩ Back to the tutorial index](../README.md)
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## A: Laplace transforms and frequency response
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1. [![github](../img/github.svg)](./a-laplace/1-laplace-transforms.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/a-laplace/1-laplace-transforms.ipynb)
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The Laplace transform
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2. [![github](../img/github.svg)](./a-laplace/2-frequency-response)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/a-laplace/2-frequency-response.ipynb)
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Analysing a dynamical system's frequency response
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## B: Op-amps in the VC model
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1. [![github](../img/github.svg)](./b-op-amps/1-op-amp.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/b-op-amps/1-op-amp.ipynb)
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Ideal op amps
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2. [![github](../img/github.svg)](./b-op-amps/2-non-ideal-op-amp.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/b-op-amps/2-non-ideal-op-amp.ipynb)
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Models of an op amp with a finite speed
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3. [![github](../img/github.svg)](./b-op-amps/3-resulting-vc-models.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/b-op-amps/3-resulting-vc-models.ipynb)
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VC models based on different op-amp models
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## C: Series resistance compensation
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1. [![github](../img/github.svg)](./c-rs/1-compensation-prediction.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/c-rs/1-compensation-prediction.ipynb)
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Correction-prediction ODEs
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2. [![github](../img/github.svg)](./c-rs/2-rs-cm-one-shot.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/c-rs/2-rs-cm-one-shot.ipynb)
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One-shot Rs and Cm estimation
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3. [![github](../img/github.svg)](./c-rs/3-rs-cm-iterative.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/c-rs/3-rs-cm-iterative.ipynb)
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Iterative Rs and Cm estimation
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## D: Bessel filters
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1. [![github](../img/github.svg)](./d-filters/1-bessel-filters-laplace.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/d-filters/1-bessel-filters-laplace.ipynb)
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Bessel low-pass filters in the Laplace domain
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2. [![github](../img/github.svg)](./d-filters/2-bessel-filters-ode.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/d-filters/2-bessel-filters-ode.ipynb)
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Bessel low-pass filters in ODE form
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3. [![github](../img/github.svg)](./d-filters/3-bessel-filter-ode-summary.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/d-filters/3-bessel-filter-ode-summary.ipynb)
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Summary of ODE forms
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4. [![github](../img/github.svg)](./d-filters/4-stimulus-filter.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/d-filters/4-stimulus-filter.ipynb)
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The stimulus filter
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## E: Voltage offsets
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1. [![github](../img/github.svg)](./e-offsets/1-liquid-junction-potential.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/e-offsets/1-liquid-junction-potential.ipynb)
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Liquid junction potential
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2. [![github](../img/github.svg)](./e-offsets/2-offset-correction.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/e-offsets/2-offset-correction.ipynb)
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Offset correction
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## Z: Parameter values
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1. [![github](../img/github.svg)](./z-parameters/1-parameter-values.ipynb)
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[![nbviewer](../img/nbviewer.svg)](https://nbviewer.jupyter.org/github/CardiacModelling/VoltageClampModel/tree/main/tutorial/appendix/z-parameters/1-parameter-values.ipynb)
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Parameter value estimates from the literature and from different manufacturers
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[↩ Back to the tutorial index](../README.md)

tutorial/appendix/b-op-amps/3-uncompensated-models.ipynb renamed to tutorial/appendix/b-op-amps/3-resulting-vc-models.ipynb

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‎tutorial/tour.ipynb‎

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"The given values of $\\tilde{C}_f$ and $\\tau_a$ were estimated by fitting to model cell experiments with a Heka EPC-10."
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