This is the readme for the models associated with the paper:

Aussel A, Buhry L, Tyvaert L, Ranta R (2018) A detailed anatomical and mathematical model of the hippocampal formation for the generation of sharp-wave ripples and theta-nested gamma oscillations. J Comput Neurosci 45:207-221

These models were contributed by A. Aussel. The python scripts require the freely available brian2 package:

The model also requires at least python version 3.6. In addition EEG data files must be supplied (unfortunately the ones used for the paper are not allowed to be released). See the around line 505 for filenames. The sampling rate was 1024 Hz.

To run on a linux cluster you may need to execute commands like (if when you try running the python script it reports missing requirements, add those names to the pip3 command like the examples below:

module load Python/3.6
pip3 install --user --upgrade pip
pip3 install --user brian2
pip3 install --user matplotlib
python3 -i

Then type into the python prompt:

main_process([0], 60*psiemens,600*psiemens,0.1,0.06)

Although the simulation will stop when it needs the real data for stimulation it will generate these graphs:

screenshot 1

screenshot 2