README

This code generates the key results figures shown in

Kerr CC, Neymotin SA, Chadderdon GL, Fietkiewicz CT, Francis JT, Lytton
WW (2012). Electrostimulation as a prosthesis for repair of information
flow in a computer model of neocortex. IEEE Transactions on Neural
Systems & Rehabilitation Engineering 20(2):153–60.


This document provides brief installation and usage instructions.

INSTALLATION

Note: the code has been designed to work on Linux machines. It may work
on Macs and will definitely not work on Windows. If this is a problem,
please contact Cliff Kerr (cliffk@neurosim.downstate.edu) for assistance.

Dependencies:
1. NEURON
2. Python
3. Pylab, SciPy, NumPy, and Matplotlib.

Instructions:

1. Unzip all files (which it looks like you've already done).
2. Type "nrnivmodl *.mod" in the directory. This should create a
directory called either i686 or x86_64, depending on your computer's
architecture, and put a file called "special" in that directory.


USAGE

1. Type "runsim". Two graphs should appear, corresponding to the two
types of results figures in the paper.


OPTIONS

* To adjust cortical vs. thalamic damage, simulation time, and model
size, please adjust the hopefully-clearly-labeled parameters in runsim.

CHANGELOG

20121210 Unused packages were removed from Python scripts.
20220517 Updated MOD files to contain valid C++ and be compatible with
         the upcoming versions 8.2 and 9.0 of NEURON. Updated to use
         post ~2011 signature of mcell_ran4_init function and fix
         hashseed2 argument.
20230420 Updated MOD files for compatibility with data structures in
         the upcoming version 9.0 of NEURON.