LSNM (Large-Scale Neural Modeling) Brain Simulator

Command line version of LSNM

The following syntax should be used:

lsnm -m model.txt -w weightslist.txt -s script -l lsnm_tvb_link.txt

• lsnm is the python script that runs the simulation.
• weightlist.txt contains a list of individual *.w weight files (all should be included in working directory).
• script is a python script that describes all events in the simulated experiment.
• lsnm_tvb_link.txt is an optional parameter that describes how the LSNM model is embedded into a Virtual Brain (TVB) connectome.

The output is a number of *.out files in text format that contain time-series of simulated neural and synaptic activity.

Requirements

Core Dependencies

• Python 3.6 or higher
• NumPy >= 1.19.0
• Standard Python libraries (re, random, math, json, time, sys, argparse, importlib)

Optional Dependencies (for TVB Integration)

• The Virtual Brain (TVB) packages
  • tvb-simulator
  • tvb-datatypes
  • tvb-plot
  • tvb-library

Note: For TVB integration, it's recommended to use a conda environment with TVB packages installed from the TVB repository.

Docker Setup

Building and Running with Docker

1. Build the Docker image:

docker build -t lsnm .

2. Run the Docker container:

docker run -it --rm lsnm

This will start a container with:

• All required dependencies installed
• A conda environment named 'lsnm' with all necessary packages
• The LSNM simulator ready to use

Using the Conda Environment in Docker

The Docker container comes with a pre-configured conda environment. To use it:

1. Start the container:

docker run -it --rm lsnm

2. The conda environment is automatically activated. You can verify this by running:

conda env list

3. To run the demo:

demo/run_demo.sh

Mounting Local Directories

To work with local files, you can mount directories when running the container:

docker run -it --rm -v $(pwd):/app lsnm

This will mount your current directory to /app in the container, allowing you to:

• Access local files
• Save output files to your local system
• Modify and test code changes

How to download / install LSNM:

git clone https://github.com/NIDCD/lsnm.git

How to run the LSNM demo:

cd lsnm
chmod u+x lsnm
cdmod u+x demo/run_demo
demo/run_demo

After the last command above you should see the following output:

Start Time:  Mon Feb  6 12:27:51 2023
Building network...
Saving neural network to file...
Running simulation...
Simulation Finished.
Output data files saved.
End Time:  Mon Feb  6 12:34:27 2023

How to run the LSNM demo embedded in The Virtual Brain (TVB)

To run LSNM and TVB together you will need to build a conda environment that contains the TVB packages along with its dependencies. The TVB packages can be downloaded from the TVB github repository at: https://github.com/the-virtual-brain/tvb-root. After you have built the TVB enviroment, simply run LSNM as follows:

../lsnm -m model.txt -w weightslist.txt -s script_DMS_198_seconds -l lsnm_tvb_link.txt