suny-downstate-medical-center / s1_netpyne

NetPyNE implementation of the somatosensory thalamocortical circuits model

Description

This code reproduces the simulations for the following paper:

Fernando da Silva Borges, Joao V.S. Moreira, Lavinia M. Takarabe, William W. Lytton, Salvador Dura-Bernal. Large-scale biophysically detailed model of somatosensory thalamocortical circuits in NetPyNE. Frontiers in Neuroinformatics. https://doi.org/10.3389/fninf.2022.884245

We have implemented this highly-detailed and complex model S1 model in NetPyNE, using the data available in the Neocortical Microcircuit Collaboration Portal. We also extended the model by adding thalamic circuits, including 6 distinct thalamic populations with intrathalamic, thalamocortical and corticothalamic connectivity derived from experimental data. Our work provides a widely accessible, data-driven and biophysically-detailed model of the somatosensory thalamocortical circuits that can be utilized as a community tool for researchers to study neural dynamics, function and disease.

Branches

1. master: all data, figures, and codes (6,8 GB)
2. coreneuron: only the files needed to run the code (564,7 MB)

Setup and execution

Requires NEURON with Python and MPI support.

NEURON libraries

1. From /sim run nrnivmodl mod. This should create a directory called x86_64.
2. TIn cfg.py make sure cfg.coreneuron = False
3. To run type: python batch.py or mpiexec -n [num_proc] nrniv -python -mpi init.py

CoreNEURON libraries

1. From /sim run nrnivmodl -coreneuron mod. This should create a directory called x86_64.
2. In cfg.py make sure cfg.coreneuron = True
3. To run type: python batch.py or mpirun -n [num_proc] ./x86_64/special -mpi -python init.py

The resumed code to reproduce the Fig. 7: https://github.com/suny-downstate-medical-center/S1_Thal_NetPyNE_Frontiers_2022.

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

• /sim/batch.py: Run multiple simulations

• /sim/cells: source files for the different cell types used in the model; these will be imported into netpyne

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

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

• /info: information about the network and all the cells needed to build the microcircuit

For further information please contact: [email protected]