This simulation was tested/developed on LINUX systems, but may run on
Microsoft Windows or Mac OS.

To run, you will need the NEURON simulator (available at
http://www.neuron.yale.edu)

Unzip the contents of fdemo.zip to a new directory.

compile the mod files from the command line with (linux):
 nrnivmodl *.mod

That will produce an architecture-dependent folder with a script
called special.  On 64 bit systems the folder is x86_64. To run the
simulation from the command line:
 ./x86_64/special
then NEURON will start and load the mechanisms (cell types, etc.)
then from the NEURON prompt:
 load_file("mosinit.hoc")

That will load the simulation and all required files. Network and
inputs will be setup.  Then the simulation will be run for 20 seconds
of simulation time. The simulation duration is modifiable via the
mytstop parameter in mosinit.hoc. Note that setup of the network may
take 10-30 seconds, depending on your processor speed, amount of RAM,
and whether using NetStim (usens flag in mosinit.hoc). Once the
simulation has run, two graphs will be displayed, showing the spike
raster and LFP from a single column. The spike raster is arranged with
y-axis as cell identifier and x-axis as time in milliseconds. The
y-axis is further arranged in order of layer/type displayed with
labels in the graph (top is layer 2, bottom is layer 6).

Once the spikes and LFP are displayed, the multiunit activity vectors
for excitatory and inhibitory cells are formed and their power spectra
are calculated and displayed in separate plots for raw (if the drawraw
variable declared in mosinit.hoc is set to 1 before getpsd is called)
and smoothed power spectra. The red (blue) traces indicate power from
excitatory (inhibitory) MUAs. The PSD smoothing level is set by the
boxszdef variable, and is normalized to the length of the simulation
duration within the getpsd function.

Note that the paper used Matlab's pmtm and fft functions which are
only commercially available.  To allow use/test of this demo to the
widest available audience, the NEURON spctrm Vector function was used
instead. Some differences in spectral output are visible depending on
which spectral methods are employed. See the getpsd function in
mosinit.hoc for other options for spectral methods that are freely
available or contact samn at neurosim dot downstate dot edu for
further information and/or help using these other methods, including
Matlab.

References:
 This simulation was used in an article at Frontiers in Computational
 Neuroscience, special issue on Structure, dynamics and function of
 brains:
  Citation: Neymotin SA, Lee H, Park E, Fenton AA and Lytton WW
  (2011). Emergence of physiological oscillation frequencies in a
  computer model of neocortex. Front. Comput. Neurosci. 5:19. doi:
  10.3389/fncom.2011.00019
  Received: 19 Oct 2010; Accepted: 01 Apr 2011. 
  Edited by:   Ad Aertsen, Albert Ludwigs University, Germany
  Reviewed by: Imre Vida, University of Glasgow, UK 
               Michael Schmuker, Freie Universtiät Berlin, Germany 
               Maxim Bazhenov, University of California, USA 
 
 article available at:

http://www.frontiersin.org/Computational_Neuroscience/10.3389/fncom.2011.00019/abstract

20110418 Updated to run on mswin.  -ModelDB Administrator
20110419 Additional button window for autolaunch. -ModelDB Administrator
20111219 readme reformatted. -ModelDB Administrator
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 the new data
         structures in the upcoming version 9.0 of NEURON.