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Installation Instructions

Simulations were run using Python 3.10.12. The instructions below were tested on Ubuntu Linux 22.04.

  1. Install NEURON:

    pip3 install neuron

  2. Install NetPyNE:

    pip3 install netpyne

  3. Install OpenPyXL:

    pip3 install openpyxl

  4. Extract the SCN1A files from the downloaded zip (2019444.zip) and change to the Knox_SCN1A_model directory.

  5. Compile NEURON mechanisms:

    nrnivmodl ./mechanisms

  6. Carry out one run using test_SCN1A_variants.py (optional seed number):

    python3 test_SCN1A_variants.py
    • The figure is saved as vary_epsp_ei3.0_[seed].png, where [seed] is the seed number.

  7. Carry out a batch of simulation runs using run_lots_of_sims.sh:

    ./run_lots_of_sims.sh

  8. Move the results to a subdirectory:

    mkdir results
mv output_data_ei* results

  9. Make the final figure (optional seed number):

    python3 make_fig_3.py
    • The figure is saved as figure_3.png.