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nav-artefact-model

Code for reproducing "Resolving artefacts in voltage-clamp experiments with computational modelling: an application to fast sodium current recordings"

https://github.com/cardiacmodelling/nav-artefact-model

Science Score: 52.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 4 DOI reference(s) in README
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    Academic publication links
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    Academic email domains
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    Institutional organization owner
    Organization cardiacmodelling has institutional domain (www.maths.nottingham.ac.uk)
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    Scientific vocabulary similarity
    Low similarity (9.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Code for reproducing "Resolving artefacts in voltage-clamp experiments with computational modelling: an application to fast sodium current recordings"

Basic Info
  • Host: GitHub
  • Owner: CardiacModelling
  • License: bsd-3-clause
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 19.4 MB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created over 4 years ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

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 and SUNDIALS are required (tested on Python 3.9 and 3.11, and SUNDIALS 7.2.1).

Reproducing result figures

  • Figure 3C: Change directory to src and run python simulate-mc4auto-minimum.py nav.
  • Figure 4C: Change directory to src and run python compensation-level-sweeps.py.
  • Figure 5C: Run python figure-plot.py -m iyer -p NaIV_35C_80CP -d cell6 -l 90.
  • Figure 6A: Change directory to src and run python averaging-issue.py.
  • Figure 6B: Change directory to src and run Jupyter notebook mutant-issue.ipynb.
  • Figure 7: Change directory to src/ap and run Jupyter notebook ap-effects.ipynb.
  • Figure 8: 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.

Owner

  • Name: Cardiac Modelling
  • Login: CardiacModelling
  • Kind: organization
  • Location: United Kingdom

Codes and Resources from the University of Nottingham's cardiac modelling team

Citation (CITATION) 

To cite this repository or the article in publications, please use:

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.

https://doi.org/10.1101/2024.07.23.604780

A BibTeX entry for LaTeX users is
@article {Lei2024bioRxiv,
	author = {Lei, Chon Lok and Clark, Alexander P. and Clerx, Michael and Wei, Siyu and Bloothooft, Meye and de Boer, Teun P. and Christini, David J. and Krogh-Madsen, Trine and Mirams, Gary R.},
	title = {Resolving artefacts in voltage-clamp experiments with computational modelling: an application to fast sodium current recordings},
	year = {2024},
	doi = {10.1101/2024.07.23.604780},
	URL = {https://www.biorxiv.org/content/early/2024/07/24/2024.07.23.604780},
	eprint = {https://www.biorxiv.org/content/early/2024/07/24/2024.07.23.604780.full.pdf},
	journal = {bioRxiv}
}

GitHub Events

Total
  • Release event: 2
  • Delete event: 1
  • Push event: 17
  • Pull request event: 2
  • Create event: 2
Last Year
  • Release event: 2
  • Delete event: 1
  • Push event: 17
  • Pull request event: 2
  • Create event: 2

Dependencies

requirements.txt pypi
  • myokit ==1.33.1
  • pandas ==1.4.0
  • pints ==0.4.0
  • seaborn ==0.13.2