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NetPyNE implementation of the somatosensory thalamocortical circuits model


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.

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.


  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 make sure cfg.coreneuron = False
  3. To run type: python or mpiexec -n [num_proc] nrniv -python -mpi

CoreNEURON libraries

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

The resumed code to reproduce the Fig. 7:

Overview of file structure:

  • /sim/ Main executable; calls functions from other modules. Sets what parameter file to use.

  • /sim/ Network parameters

  • /sim/ Simulation configuration

  • /sim/ 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: