Multiscale model of the macaque auditory thalamocortical circuits developed using NetPyNE (www.netpyne.org).
The model is described in the following publication:
Dura-Bernal S, Griffith EY, Barczak A, O’Connell MN, McGinnis T, Moreira JV, Schroeder C, Lytton WW, Lakatos P, Neymotin SA. (2023) Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics. Cell Reports (In Press)
This repository contains all the source code and data required to generate the paper results. Each subfolder has a separate README.md with instructions:
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/model: Python source code of the auditory thalamocortical circuit model. Implemented in NetPyNE/NEURON.
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/analysis: Python source code to perform the analyses used to generate the paper results.
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/data: Experimental data and data generated by model used to generate the paper results.
The computational model has the following software dependencies:
- NetPyNE v1.0.2
- NEURON v8.0
- UR_EAR 2.0
The experimental and model data analysis has the following software dependencies:
- MATLAB v9.3 (64bit) 2017b
- OEvent v51cc9b
The computational model and analysis code has been tested on Mac OS 12.1 and Linux Ubuntu 16.04
Detailed installation instructions for the software dependencies are available in the links below:
- NetPyNE: http://netpyne.org/install.html
- NEURON v8.0: https://neuron.yale.edu/neuron/
- UR_EAR 2.0: https://www.urmc.rochester.edu/MediaLibraries/URMCMedia/labs/carney-lab/codes/UR_EAR_2020b.zip
Typical install time on a "normal" desktop computer is 1 hour.
Instructions, expected output and expected run time to simulate a demo version of the thalamocortical circuit model can be found in model/README.md.
Instructions on how to run the full thalamocortical model and analyses can be found in the model/README.md, analysis/README.md and data/README.md files.
For further information please contact: salvador.dura-bernal@downstate.edu, erica.griffith@downstate.edu and/or samuel.neymotin@nki.rfmh.org