Extracellular stimulation in NetPyNE
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"
main: files needed to run the code (4.5 GB)
Requires NEURON with Python and MPI support.
- From /sim run
nrnivmodl mod. This should create a directory called x86_64. - In cfg.py make sure cfg.coreneuron = False
- To run type:
python batch.pyormpiexec -n [num_proc] nrniv -python -mpi init.py
- From /sim run
nrnivmodl -coreneuron mod. This should create a directory called x86_64. - In cfg.py make sure cfg.coreneuron = True
- To run type:
python batch.pyormpirun -n [num_proc] ./x86_64/special -mpi -python init.py
-
/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
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: fernandodasilvaborges@gmail.com