An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain

This code was used to produce the results presented in Sætra et al., PLoS Computational Biology, 17(7), e1008143 (2021): An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain.

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:

python3 setup.py install

You must have edNEGmodel v1.0.0 installed, which can be downloaded from https://github.com/CINPLA/edNEGmodel.

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 several 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.