Code base for the manuscript "Multi-modal characterization and simulation of human epileptic circuitry"

This repository contains the code that is necessary to reproduce the work of Buchin et al. 2022 (https://www.cell.com/cell-reports/fulltext/S2211-1247(22)01769-7?uuid=uuid%3A4b7f2742-5a1f-4893-9934-bb5c7b271870). The repository contains the code for Python, Matlab and R used in this study. To make is easier to comprehend, the code is organized into subdirectories that correspond to figures.

Getting Started

Prerequisites

Anaconda Python 4.3.13 (Python 2.7)

Brain Modeling Toolkit (https://alleninstitute.github.io/bmtk/)

Allen SDK (https://allensdk.readthedocs.io/)

Neuron 7.4 (https://neuron.yale.edu/neuron/)

Rstudio (https://rstudio.com/)

Matlab R2018a (https://www.mathworks.com/)

Requirements

Enviroment requirements could be found in requirements folder: requirements.txt and epilepsy_human_dg_network.yml file

To install the enviroment run: conda env create -f epilepsy_human_dg.yml

Data analysis code is organized using the corresponding folders. All necessary functions and vizualisations are included into the notebooks. The original data files including nwb, swc and RData files are available upon request.

Installing

The models will run automatickally once you have the required libraries installed on your machine, such as:

Python Anaconda 2.7 including R https://www.anaconda.com/

Brain Modeling Toolkit https://alleninstitute.github.io/bmtk/

Allen SDK https://allensdk.readthedocs.io/

Neuron https://www.neuron.yale.edu/neuron/

Matlab https://www.mathworks.com/

Data availability

The necessary data is available in csv files in corresponding folders. All raw data is available upon request:

anatolyb@alleninstitute.org anat.buchin@gmail.com costasa@alleninstitute.org costas.anastassiou@gmail.com

Contributors

• Anatoly Buchin - abuchin
• Anirban Nandi - anirban6908
• Jeremy Miller - jeremymiller
• Costas Anastassiou - Costas13

License

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Level of support

We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests.