CardiacModelling / L-type-Ca-rundown-experiments

An investigation of rundown in automated patch clamp L-type calcium current

Investigation of the contribution of intracellular calcium to the rundown of the L-type calcium current

This repository contains all data, protocols, codes, and figure generating files used in this study.

Table of Contents

• extract_data.py analyses the raw data, post-processes it, and outputs the ICaL extracted from the selected cells and the rundown rate
• helpers.py provides supporting functions used by extract_data.py
• extensions.py provides supporting functions used to analyse the results and generate figures
• regression.r runs a multi-linear regression on the rundown rate with three independent variables
• The raw_data directory has the raw data of the current measured by patch-clamp experiments
• The resources directory has files that are generated by extract_data.py and outputs of the ExtendedData.ipynb that are used as input for analysis of other results
• The output directory has the output from extract_data.py
• The figures directory has the files that generate all figures in the paper and their output
  • Figure 1 is generated by figure1.py
  • Figure 2 is generated by figure2.py
  • Figure 4 is generated by figure4.py
  • Figure 5 is generated by figure5.py
  • Figures 6, 7, and 8 are genrated by figure6_7_8.py
• Figure 9 is generated by figure9.py
• Supporting material for the paper is provided at ExtendedData.ipynb
• run.py runs extract_data.py and all figure generating files in the figures directory

Software

• Python The code requires Python (version 3.3+) and the Python dependencies pandas, scipy, and statsmodels
  • The Python packages used in this project can be installed by running pip install -r requirements.txt in an environment with Python 3.9.5
• R The linear regression requires R (version 4+)