~tfardet/Energy-models-metabolism-2020

Code to reproduce the figures of the 2020 PLOS CB article
Files and instructions to reproduce the figures

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#Energy models and metabolism

#Simple models including energy and spike constraints reproduce complex activity patterns and metabolic disruptions

This repository contains the code to generate the figures from the PLOS CB 2020 paper (also on BioRxiv) by Tanguy Fardet and Anna Levina.

#Installig the requirements

The codes are written in Python and require a working Python installation. Once you have this, you can install the Python libraries required to run the code via:

pip install -r requirements.txt

To run most of the codes, you will also need to install the NEST simulator (version 3 or greater).

#Compiling the models

The eLIF and mAdExp models developed in the paper as well as the instructions to run them are present on this repository. These codes use the NESTML version of the models.

#Running the code

With the previous instructions, you should be able to run most of the files via python name_of_the_file.py. There are two exceptions, Figures 7A and 7B, that are detailed below.

#Reproducing behaviors from the Allen dataset

Figures 7A and 7B require the download of data from the Allen dataset through the allensdk. At the time of writing, this library requires an outdated version of numpy to install but is actually compatible with more recent versions. I advise installing in a virtual environment, then reinstalling the up-to-date version of the other libraries using pip install --ignore-requires-python to ignore the version requirements.