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) compiled with python enabled.
Unzip the contents of the zip file to a new directory.
compile the mod files from the command line with:
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 -python mosinit.py
then NEURON will start with the python interpreter and load the
mechanisms and simulation. Next, the network and inputs will be setup.
Then the simulation will be run for 3 seconds of simulation time. The
simulation consists of 3 periods: 0-1000 ms (baseline), 1000ms-2000ms
(simulated ketamine application), 2000ms-3000ms (return to
baseline). The simulation duration is modifiable via the h.tstop
parameter in params.py. Note that setup of the network may take 10-30
seconds, depending on your processor speed and amount of RAM. Once the
simulation has run, two graphs will be displayed,
showing the spike raster and local field potential. 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 cell-types
(red=pyramidal, green=basket, blue=OLM). The LFP and raster displayed
with the demo are a shortened version of figure 7, which has this
caption, "Ketamine effect on network firing. Raster (top) and LFP
(bottom) for baseline and ketamine application between the dashed
lines." There are no dashed lines displayed in the demo, but the
ketamine is applied between 1e3 - 2e3 milliseconds.
This simulation was used in an article in press at the
Journal of Neuroscience: Neymotin SA, Lazarewicz MT, Sherif M,
Contreras D, Finkel LH, Lytton WW Ketamine disrupts theta modulation
of gamma in a computer model of hippocampus Submitted: January 28th,
2011 Accepted: June 10th, 2011
For questions email: samn at neurosim dot downstate dot edu
20120625 applied updates from Bill that work toward compatibility with
Mac OS X: infot.mod was removed and misc.h, stats.mod replaced.
20120920 an update from Sam where h.v_init is set to -65 in params.py,
which corrects initialization differences (and therefore different
output) when this model is used with nrngui.
20121206 applied updated screenshot.png from Amy Delman which reflects the
latest version of the model.