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.
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 installRequirements are given in requirements.txt and can be installed by the following command:
pip install -r requirements.txtYou 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.
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.
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.