An electrodiffusive, ion conserving Pinsky-Rinzel model with homeostatic mechanisms

This code was used to produce the results presented in Sætra et al., PLoS Computational Biology, 16(4), e1007661 (2020): An electrodiffusive, ion conserving Pinsky-Rinzel model with homeostatic mechanisms.

Installation

To install the code, clone or download the repo, navigate to the top directory of the repo and enter the following command in the terminal:

python setup.py install

Requirements are given in requirements.txt and can be installed by the following command:

pip install -r requirements.txt

You must also have EDPRmodel and PRmodel installed. They can be downloaded from https://github.com/CINPLA/EDPRmodel and https://github.com/CINPLA/PRmodel, respectively.

The code was run with Ubuntu 18.04.3 and Python 3.6.9.

Reproducing the results of the paper

To reproduce the results of the paper, run bash run_all.sh. Note that this might run for a couple of days on a normal computer. To plot and save the figures, run bash plot_all.sh from the folder named figures.

If you have problems reading the initial_values.npz-file, install git lfs and try git-lfs pull.

Errata

In a previous version of this code, U_Cadec was not set to zero in functions/solve_EDPRmodel_WoD.py, which is needed to reproduce Figure 8 of the paper (see figure caption). This is now corrected. Many thanks to Johanna Marstrander for making us aware of this error.