lauramedlock / sdh-network

SDH model network from Medlock et al. 2022

Simulation of the SDH Network Model

1. Install all necessary packages:

pip install netpyne
pip install neuron
pip install mpi4py

2. Clone SDH-network repo

3. Run the network model (one stimulus intensity/simulation):

Step 1: Compile the mod files

> cd ~/SDH-network
> nrnivmodl

Step 2A: Initialize and simulate the network (without MPI)

> ipython
>> run init_mechanical.py  

Files used are cfg_mechanical.py (configuration parameters), netParams_mechanical.py (network parameters), cells.py (cell types and attributes), genrn.py (generic neuron template), spkt_gen.py, plus .JSON files for primary afferent spike trains and .mod files for spinal neurons.

Step 2B: Initialize and simulate the network (with MPI)

> ipython
>> mpiexec -np X nrniv -python -mpi init_mechanical.py  

Where X is the number of nodes you want to use.