README

This code generates figures related to the model defined in

Chadderdon GL, Suter BA, Neymotin SA, Kerr CC, Shepherd GMG, 
Lytton WW (2012) Interlaminar activity propagation in a spiking 
model of primary motor cortex.  Frontiers in Neural Circuits.

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.

Instructions:

1. Unzip all files.
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

Run the simulation by typing "nrngui main.hoc" in the directory.  This
saves data for the simulation.  To look at a cell spiking raster, type
"ipython -i --pylab auto load.py" in the directory.  After this loads
the data, it will bring up a figure which corresponds to Figure 2C
from the paper.  Ctrl-D or "exit()" can be used to exit ipython from
the prompt.

To change the synchronous stimulation type and amplitude, the 
following lines (14-15 of main.hoc) should be modified before 
"nrngui main.hoc" is executed:

  grpshocktyp=1   // group shock type (0=none,1=L2/3,2=L5A,3=L5B,4=L6)
  grpshockpct=13  // group shock % cells

"ipython -i --pylab auto load.py" after this will bring up the raster
for those changes.

Examples:
* To get Fig. 2B, set up
  grpshocktyp=1  
  grpshockpct=12
* To get Fig. 3C, set up
  grpshocktyp=2  
  grpshockpct=54
* To get Fig. 5C, set up
  grpshocktyp=4  
  grpshockpct=17

CHANGELOG

20160921 Updates from the Lytton lab to allow the model to run on mac
OS X.

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.

20230228 Fix error due to inconsistent array dimensions. Required by
https://github.com/neuronsimulator/nrn/pull/2024 in NEURON 9+.

20230420 Updated MOD files for compatibility with the new data
structures in the upcoming version 9.0 of NEURON.