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.
Note: the code has been designed to work on Linux machines. It may
work on Macs and will definitely not work on Windows.
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.
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
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.
* To get Fig. 2B, set up
* To get Fig. 3C, set up
* To get Fig. 5C, set up
20160921 Updates from the Lytton lab to allow the model to run on mac
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.