M1 Network Model

Description

A multiscale model of mouse primary motor cortex (M1). Note: updated versions of this model exist, see http://netpyne.org.

The code requires the netpyne package, a NEURON/Python-based modularized framework for network simulations with MPI. Using this modularized structure, user can define different models (including cell types, populations, connectivities, etc.) just by modifying a single parameters file.

Additional details of the modelling framework and M1 model can be found here:

• SFN'15 poster
• slides

The parameter file M1.py describes a mouse M1 model with 14 populations; size 300um x 300um x 1350um, has 10,734 Izhikevich cells, 5,029,610 synapses, and cortical depth-dependent connectivity based on multiple published experimental studies.

Setup and execution

Requires NEURON with Python and MPI support.

1. Type or ./compile or the equivalent nrnivmodl mod`. This should create a directory called either i686 or x86_64, depending on your computer's architecture.
2. To run type: ./runsim [num_proc] or the equivalent mpiexec -np [num_proc] nrniv -python -mpi init.py

The simulation should produce a raster plot with 224,173 spikes (avg rate of 20.88 Hz) over 1 second, showing oscillations in different layers (see below).

Overview of file structure:

• M1_run.py: Main executable; calls functions from other modules. Sets what parameter file to use.

• M1.py: Parameters file for M1 Network model. Includes simulation (simConfig) and network (netParams) parameters.

• M1_export.py: Export M1 network to NeuroML

• izhi2007.py: Python class (wrapper) for Izhikevich 2007 neuron model

• izhi2007b.mod: NMODL definition of Izhikevich 2007 neuron model

For further information please contact: [email protected] or [email protected]