adam2392 / tng_tvb

Workspace for my code at TNG in Marseille, France.

Theoretical Neurosciences Group

Adam Li

Visiting PhD student under Whitaker and Chateaubriand Fellowship

This repo will house the code I develop in collaboration with The Virtual Brain here at Marseille, France in INS at Aix-Marseille Universite.

Prerequisites

You will need to have installed tvb library, tvb data, and peakdetection.

git clone https://github.com/the-virtual-brain/tvb-library
git clone https://github.com/the-virtual-brain/tvb-data

Download files from here for peakdetection
https://gist.github.com/sixtenbe/1178136

Installing

To install this, just simply clone from github repo along with the prerequisite files.

git clone https://github.com/adam2392/tng_tvb

Setup a virtual env and then run

source activate venv
pip install -r requirements.txt

Running Simulations

1. Locally Running on Notebook

Modify the shell file to include your local paths to tvb lib and data, and then run it.

./launch_tvb.command

To run a jupyter notebook with tvb on path.

2. Locally Running Via Script

(Untested as of 12/19/17): Run

python runmainsim.py

Running Simulations (SLURM Cluster)

In /cluster/ directory, you can modify the script to run simulations on your own cluster. Then you can just run:

./tng_job_submissions.sh

and specify some parameters, and it will run. Or if you want to vary distances with respect to a certain implantation scheme:

./tng_distance_submissions.sh

Local Modules:

1. peakdetect Used for peakdetection on the z time series to robustly automatically get onset/offset times for seizure.
2. tvbsim Utility module for customizing tvb simulations. For example, can move contacts, can get the closest region-contact pairs for a given electrode layout.
3. binmarcc For running slurm jobs on MARCC cluster at JHU.
4. bintng For running slurm jobs on the TNG cluster at INS.