LSNM (Large-Scale Neural Modeling) 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

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
cd demo
../lsnm -m model.txt -w weightslist.txt -s script_DMS_198_seconds

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