Voltage clamp model with NaV current project

This is a repository to reproduce results for the work "Resolving artefacts in voltage-clamp experiments with computational modelling: an application to fast sodium current recordings".

Dependencies

To run the code, run pip install -r requirements.txt to install all the necessary dependencies. Python >3.6 is required (tested on Python 3.9 and 3.11).

Reproducing result figures

• Figure 2C: Change directory to src and run python simulate-mc4auto-minimum.py nav.
• Figure 3C: Change directory to src and run python compensation-level-sweeps.py.
• Figure 4C: Run python figure-plot.py -m iyer -p NaIV_35C_80CP -d cell6 -l 90.
• Figure 5A: Change directory to src and run python averaging-issue.py.
• Figure 5B: Change directory to src and run Jupyter notebook mutant-issue.ipynb.
• Figure 6: Run python figure-plot-diff-models.py -m gray -p NaIV_35C_80CP -d cell9 -l 90.

Content

• data: Experimental data (see below for how to download this).
• methods: Main python codes.
• models: Myokit models.
• protocols: Voltage clamp protocols.
• src: Other source code for studying experimental artefact effects.
• fit.py: Run model fitting to produce results in results.

Data source

Experimental data of this study may be downloaded from the following link: https://doi.org/10.6084/m9.figshare.27193878.

The whole dataset should be placed within this repository as data such that data can be loaded and read properly.

Units

• time in [ms]
• voltage in [mV]
• current in [pA]
• capacitance in [pF]
• resistance in [GOhm]

Acknowledging this work

If you publish any work based on the contents of this repository please cite (CITATION file):

Chon Lok Lei, Alexander P. Clark, Michael Clerx, Siyu Wei, Meye Bloothooft, Teun P. de Boer, David J. Christini, Trine Krogh-Madsen, Gary R. Mirams. (2024). Resolving artefacts in voltage-clamp experiments with computational modelling: an application to fast sodium current recordings. bioRxiv, 2024.07.23.604780.