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.