This is the model associated with Jones et al 2009 and Lee and
    Jones (2013). (See reference below).  The archive was downloaded
    from the github repository:

    on July 26th, 2017.

    It runs with  Neuron (7.3+ +parallel +python) + Python (3.5.x), parallel (mpi4py, mpich2/openmpi)

Notes and runtime

This is primarily a model of neocortical L2 and L5, featuring
simplified neuronal geometries, excitatory pyramidal cells, and single
compartmental fast spiking inhibitory interneurons. The defining
feature of the model is the current dipole output consisting of the
intracellular current contributions of the pyramidal cells in L2 and

The present version was tested to run on Python 3.5 on both Mac OS X
and Linux-based platforms. Please get installation help from the
software vendors. There is no support available for Windows. Please
report any issues you may have with Python 2.7.x.

To run the model, you must have a working Neuron with MPI and Python

You must run nrnivmodl to compile the mod files in the mod/ directory.

`$ nrnivmodl mod/*`

Alternatively, you may be able to run GNU make on the included

`$ make`

If that completes successfully, then run:

`$ mpiexec -n 4 python param/gamma_L5weak_L2weak.param`

where "4" is the number of cores you wish to use.

This saves data and a plot in the `data` directory.

Approximate expected output is seen in png files in this directory.

.param files
The model uses a flat text file (.param) that holds a "key: value"
string per line. The keys are valid param names, and the values have
to be values that are loosely valid. The model will fail to run
without checks if this file is not well formed. Param values that are
not explicitly given by the .param file will default to a value in Editable params are also in the
file. See debug.param or any of the param files as examples.

Undefined params will be ignored.

Known Issues
On some platforms, there is sometimes output such as:

stty: 'standard input': Bad file descriptor

that is multiplied by the number of cores run. This can be ignored.

License and citation

This code is released under the GNU GPLv3, except for some files that
do not include a license and were taken from other sources (noted in
headers, see mod files). Please cite usage of this model as:

Lee, Shane, and Stephanie R. Jones. "Distinguishing mechanisms of
gamma frequency oscillations in human current source signals using a
computational model of a laminar neocortical network." Frontiers in
human neuroscience 7 (2013).

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or (at
your option) any later version.

This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see .