Primary motor cortex (M1) circuits model

Description

Multiscale model of mouse primary motor cortex (M1) developed using NetPyNE (www.netpyne.org).

The model was used to benchmark CoreNEURON in the following paper:

• Awile O, Kumbhar P, Cornu N, Dura-Bernal S, Gonzalo JK, Lupton O, Magkanaris I, McDougal R, Newton AJH, Pereira A, Savulescu A, Carnevale NT, Hines M, Lytton WW, Schurmann F. Modernizing the NEURON Simulator for Sustainability, Portability, and Performance. Frontiers in Neuroinformatics (Under Revision). Research Topic: "Neuroscience, Computing, Performance, and Benchmarks: Why It Matters to Neuroscience How Fast We Can Compute."

Previous versions of the model were described in the following papers:

• Dura-Bernal S, Neymotin SA, Suter BA, Dacre J, Schiemann J, Duguid I, Shepherd GMG, Lytton WW. Multiscale model of primary motor cortex circuits reproduces in vivo cell type-specific dynamics associated with behavior. BioRxiv 2022.02.03.479040; doi: https://doi.org/10.1101/2022.02.03.479040.

• Sivagnanam S, Gorman W, Doherty D, Neymotin SA, Fang S, Hovhannisyan H, Lytton WW, Dura-Bernal S. Simulating large-scale models of brain neuronal circuits using Google Cloud Platform. Practice and Experience in Advanced Research Computing, PEARC2020. 10.1145/3311790.3399621

This specific version of the model was extended to include two new types of interneurons -- NGF and VIP -- and has not been previously published.

Setup and execution

Requires NEURON with Python and MPI support.

1. From /sim run nrnivmodl ../mod. This should create a directory called x86_64.
2. To run type: ./runsim [num_proc]' or the equivalent mpiexec -np [num_proc] nrniv -python -mpi init.py`

Overview of file structure:

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

• /sim/netParams.py: Network parameters

• /sim/cfg.py: Simulation configuration

• /cells: source .py, .hoc, .json or .pkl files for the different cell types used in the model; these will be imported into netpyne

• /conns: source .py, .json or .pkl files for the network connectivity; these will be imported into netpyne

• /mod: NMODL files containing the ionic channel and synaptic mechanisms used in the model

• /data: where the model and simulation data is stored

For further information please contact: salvadordura@gmail.com