M1 Network Model

M1 Network Model

Description

A multiscale model of mouse primary motor cortex (M1).

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:

The parameter file M1_ynorm_izhi.py describes a mouse M1 model with 14 populations; size 300um x 300um x 1350um, has 10,734 Izhikevich cells, 5,050,532 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 equivalentnrnivmodl 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 54,562 spikes (avg rate of 5.08 Hz) over 1 second, showing ~15 Hz oscillations (see below).

Raster plot

Overview of file structure:

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

  • /sim/M1_ynorm_izhi.py: Parameters file for M1 Network model. Includes simulation (simConfig) and network (netParams) parameters.

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

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

  • /data: where the model and simulation data is stored (eg. .pkl, .mat, .json files)

For further information please contact: salvadordura@gmail.com

Working on conversion of model to NeuroML 2 via export from NetPyNE

Developer: Adrian Quintana, Padraig Gleeson

Scientific Coordinator: Salvador Dura-Bernal

This model was originally developed in: NetPyNE

The code for this model is hosted on GitHub: https://github.com/OpenSourceBrain/M1NetworkModel.git