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 [PubMed]
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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 V1 L6 pyramidal corticothalamic GLU cell; Neocortex V1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex V1 interneuron basket PV GABA 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 [bill.lytton at downstate.edu]; Neymotin, Sam [Samuel.Neymotin at nki.rfmh.org];
Search NeuronDB for information about:  Neocortex V1 L6 pyramidal corticothalamic GLU cell; Neocortex V1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex V1 interneuron basket PV GABA cell; GabaA; AMPA; NMDA; Gaba; Gaba; Glutamate;
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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 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
//
// for help with simulation/analysis routines: contact email: samn at neurosim dot downstate dot edu
//
// note that paper used matlab's pmtm and fft functions which are only commercially available, so not
// used in this demonstration. some differences in spectral output visible depending on which spectral
// methods employed. see readme.txt and getpsd function below for more information
//
//
//
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////

// load files for running NEURON + analysis, etc.
load_file("nrngui.hoc")
xopen("./setup.hoc")
xopen("./nrnoc.hoc")
load_file("init.hoc")

usens = 1 // if set to 1 uses NetStims (faster to load, less memory). usens set to 0 for paper
mytstop = 20e3 // sets duration of simulation in milliseconds

// load sim-related files
load_file("nqsnet.hoc")
load_file("network.hoc")
print "setting up external inputs...please wait..."
load_file("params.hoc")
load_file("run.hoc")
load_file("nload.hoc")

objref myg[4] // Graph objects

load_file("finish_run.hoc")

xpanel("Neymotin et al. 2011")
  xbutton("long run","{mytstop=20e3 finish_run()}")
  xbutton("short run(auto-launch demo)","{mytstop=0.1e3 tstop=mytstop finish_run()}")
xpanel()