Basic commands

Generally speaking, there are two scripts used in LSNM, both written in Python 2.7: netgen.py, which is used to generate connecting weights among nodes in the neural network, and sim.py, which is used to create nodes in the neural network (i.e., brain regions) and to simulate an experimental script.

Netgen

SYNOPSIS: python netgen.py *.ws

DESCRIPTION: For the given *.ws file, describing the connecting weights from brain region A to brain region B, it generates a weights file *.w, specifying each individual connecting weight from A to B. Batch processing can be used to execute netgen on several files at once (i.e., batch processing).

Sim

SYNOPSIS: python sim.py

DESCRIPTION: Given a description of neural network nodes (i.e., brain regions), connecting weights among nodes, and an experimental trial script, it executes a simulation and generates output files. It can be used to simulate network under different experimental conditions to simulate multi-trial, multi-subject experiments. It can also be used to embed a given model into a given connectome, by linking the LSNM simulator to The Virtual Brain (TVB) simulator.