/iPSC-leak-artifact

Simulations and figures for manuscript showing descriptive ability of iPSC-CM+artifact models

Primary LanguageJupyter NotebookBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

Leak current, even with gigaohm seals, can cause misinterpretation of stem-cell derived cardiomyocyte action potential recordings

This repository contains all code, data, and figures for our manuscript: "Leak current, even with gigaohm seals, can cause misinterpretation of stem-cell derived cardiomyocyte action potential recordings"

By: Alexander P. Clark, Michael Clerx, Siyu Wei, Chon Lok Lei, Teun P. de Boer, Gary R. Mirams, David J. Christini, Trine Krogh-Madsen

The code requires Python 3.7+ and two dependencies: Myokit and DEAP. These can be installed using pip install myokit and pip install deap. Alternatively, you can pip install -r requirements.txt to install all dependencies at once.

Files and folders

  • fX-*.py – Each of the numbered files contain the code to reproduce their corresponding figure. For example, f9-fit-base-to-leak.py will first run a GA that fits the Kernik model to Kernik+leak, and then plots Figure 9.
  • data/ – Folder with all experimental data and GA results.
  • mmt/ – Contains all Myokit model files
  • figure-pdfs – PDF files for all manuscript figures.

As mentioned, f9-fit-base-to-leak.py contains the GA code used to produce the results in Figure 9. To run the GA on your own computer you must uncomment fit_model() in main(). The GA results are saved to ./data/ga_results/inds_bCa_bNa_fixed.pkl.

Supporting materials