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Oct 11, 2024
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Add appendices to README index #42

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# Modelling patch-clamp experiments

When analysing data from whole-cell patch-clamp experiments, it can be useful to have a model of both the biological system of interest _and_ the experimental set up.
Expand All @@ -23,4 +22,26 @@ In the second notebook we update the model to include the compensation circuitry

In notebook number four we derive simplified models of the compensated voltage clamp setup, which can be used in fitting.


## Appendices

- Electronics
- A1. Ideal op amps [![github](../img/github.svg)](appendix-A1-op-amp.ipynb)
- A2. Laplace transforms and filters [![github](../img/github.svg)](appendix-A2-laplace-and-filters.ipynb)
- A3. Non-ideal op amps [![github](../img/github.svg)](appendix-A3-non-ideal-op-amp.ipynb)
- Extended models
- B1. Models without compensation [![github](../img/github.svg)](appendix-B1-uncompensated-models.ipynb)
- B2. Models with compensation [![github](../img/github.svg)](appendix-B2-compensated-models.ipynb)
- B3. Sigworth 1983/1995 Rs compensation [![github](../img/github.svg)](appendix-B3-sigworth-rs.ipynb)
- Parameter names and values
- C1. Names & symbols [![github](../img/github.svg)](appendix-C1-symbols.ipynb)
- C2. Default parameter values used in examples [![github](../img/github.svg)](appendix-C2-parameter-defaults.ipynb)
- C3. Parameter values, estimates for different amplifiers etc. [![github](../img/github.svg)](appendix-C3-parameter-values.ipynb)
- Remaining noise and errors
- D1. Strategies for dealing with experimental error [![github](../img/github.svg)](appendix-D1-strategies.ipynb)
- D2. Stochastic and periodic noise [![github](../img/github.svg)](appendix-D2-inspecting-noise.ipynb)
- D3. Liquid junction potential [![github](../img/github.svg)](appendix-D3-liquid-junction-potential.ipynb)
- D4. Leak (unfinished) [![github](../img/github.svg)](appendix-D4-leak.ipynb)
- D5. Handling remaining capacitance artefacts (unfinished) [![github](../img/github.svg)](appendix-D5-remaining-Cp-artefacts.ipynb)
- Estimating Rs and Cm
- E1. Estimating Rs and Cm; a one-shot approach [![github](../img/github.svg)](appendix-E1-rs-cm-one-shot.ipynb)
- E2. Estimating Rs and Cm; an iterative approach [![github](../img/github.svg)](appendix-E2-rs-cm-iterative.ipynb)