m1networkmodel
A multiscale model of the M1 region of motor cortex
Science Score: 44.0%
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Repository
A multiscale model of the M1 region of motor cortex
Basic Info
- Host: GitHub
- Owner: OpenSourceBrain
- License: other
- Language: Python
- Default Branch: master
- Size: 16.1 MB
Statistics
- Stars: 2
- Watchers: 5
- Forks: 1
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
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:
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.
- Type or
./compile or the equivalentnrnivmodl mod`. This should create a directory called either i686 or x86_64, depending on your computer's architecture. - To run type:
./runsim [num_proc]or the equivalentmpiexec -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: salvadordura@gmail.com or p.gleeson@ucl.ac.uk
Owner
- Name: OpenSourceBrain
- Login: OpenSourceBrain
- Kind: organization
- Website: www.opensourcebrain.org
- Repositories: 141
- Profile: https://github.com/OpenSourceBrain
Citation (CITATION.md)
## Citing this model The software in this repository is provided under the terms of the [software licence](LICENCE) included with it. If you use this model in your research, we respectfully ask you to cite: **The main NetPyNE paper** - **NetPyNE: a tool for data-driven multiscale modeling of brain circuits**, Salvador Dura-Bernal, Benjamin Suter, Padraig Gleeson, Matteo Cantarelli, Adrian Quintana, Facundo Rodriguez, David J Kedziora, George L Chadderdon, Cliff C Kerr, Samuel A Neymotin, Robert McDougal, Michael Hines, Gordon MG Shepherd, William W Lytton bioRxiv 461137; doi: https://doi.org/10.1101/461137 **The latest release of this Open Source Brain repository** - This link should provide a DOI/citation for the latest version released: https://www.zenodo.org/badge/latestdoi/47782551. If you would like us to make a new release, please [open an issue](../../issues).
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Dependencies
- actions/checkout v3 composite
- actions/setup-python v3 composite