Emergence of physiological oscillation frequencies in neocortex simulations (Neymotin et al. 2011)

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Accession:138379
"Coordination of neocortical oscillations has been hypothesized to underlie the “binding” essential to cognitive function. However, the mechanisms that generate neocortical oscillations in physiological frequency bands remain unknown. We hypothesized that interlaminar relations in neocortex would provide multiple intermediate loops that would play particular roles in generating oscillations, adding different dynamics to the network. We simulated networks from sensory neocortex using 9 columns of event-driven rule-based neurons wired according to anatomical data and driven with random white-noise synaptic inputs. ..."
Reference:
1 . Neymotin SA, Lee H, Park E, Fenton AA, Lytton WW (2011) Emergence of physiological oscillation frequencies in a computer model of neocortex. Front Comput Neurosci 5:19-75 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex layer 5-6 pyramidal cell; Neocortex layer 2-3 pyramidal cell; Neocortex interneuron basket cell; Neocortex fast spiking (FS) interneuron; Neocortex spiny stellate cell;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA; Gaba;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Oscillations; Synchronization; Laminar Connectivity;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu]; Neymotin, Sam [samn at neurosim.downstate.edu];
Search NeuronDB for information about:  Neocortex layer 5-6 pyramidal cell; Neocortex layer 2-3 pyramidal cell; Neocortex interneuron basket cell; GabaA; AMPA; NMDA; Gaba; Gaba; Glutamate;
/
fdemo
readme.txt
intf6_.mod
misc.mod *
nstim.mod *
stats.mod *
vecst.mod
col.hoc
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
filtutils.hoc
finish_run.hoc
grvec.hoc *
init.hoc *
labels.hoc *
local.hoc *
misc.h
mosinit.hoc
network.hoc
nload.hoc
nqs.hoc *
nqsnet.hoc *
nrnoc.hoc *
params.hoc
python.hoc *
pywrap.hoc *
run.hoc
setup.hoc
simctrl.hoc *
spkts.hoc *
stats.hoc *
syncode.hoc *
xgetargs.hoc *
                            
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

Neymotin SA, Lee H, Park E, Fenton AA, Lytton WW (2011) Emergence of physiological oscillation frequencies in a computer model of neocortex. Front Comput Neurosci 5:19-75[PubMed]

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