NetPyNE implementation of Extracellular stimulation

Extracellular stimulation in NetPyNE

Description

This code reproduces the simulations of Fig 4 (poster_TMS_SfN_2024.pdf)

Fernando S Borges, Jacob Tajchman, Tarek Khashan, Eugenio Urdapilleta, Emiliano Santarnecchi, Salvador Dura-Bernal. Towards a detailed mechanistic model of human cortical microcircuits that accurately predicts the cellular- and circuit-level effects of TMS. Society for Neuroscience, 2024.

The "v1_batch5" reproduces "data/v1_batch5_TMS_Human.png"

Branches

1. main: files needed to run the code (4.5 GB)

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. In 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

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

• /test: tests, comparations, and validations

Extra description see:

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/10.1101/2022.02.03.479029

https://github.com/suny-downstate-medical-center/S1_Thal_NetPyNE_Frontiers_2022

For further information please contact: [email protected]