Hopfield and Brody model (Hopfield, Brody 2000) (NEURON+python)

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Accession:144549
Demonstration of Hopfield-Brody snychronization using artificial cells in NEURON+python.
Reference:
1 . Hopfield JJ, Brody CD (2001) What is a moment? Transient synchrony as a collective mechanism for spatiotemporal integration. Proc Natl Acad Sci U S A 98:1282-7 [PubMed]
2 . Hopfield JJ, Brody CD (2000) What is a moment? "Cortical" sensory integration over a brief interval. Proc Natl Acad Sci U S A 97:13919-24 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Pattern Recognition; Coincidence Detection; Temporal Pattern Generation; Synchronization; Attractor Neural Network;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu]; Neymotin, Sam [samn at neurosim.downstate.edu];
/
hoppy
readme.txt
invlfire.mod
misc.mod *
stats.mod
vecst.mod *
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
grvec.hoc *
init.hoc
labels.hoc
local.hoc *
misc.h
mysetup.py
net.py
nqs.hoc *
nqs_utils.hoc *
nrnoc.hoc *
pyinit.py
simctrl.hoc *
syncode.hoc *
                            
//  $Header: /usr/site/nrniv/simctrl/hoc/RCS/local.hoc,v 1.15 2003/02/13 15:32:06 billl Exp $
//
//  This file contains local modifications to nrnoc.hoc and default.hoc
//
//  Users should not edit nrnoc.hoc or default.hoc.  Any local 
//  changes to these files should be made in this file.

// ------------------------------------------------------------
//* MODIFICATIONS TO NRNOC.HOC
// The procedures declared here will overwrite any duplicate
// procedures in nrnoc.hoc.
// ------------------------------------------------------------

//*MODIFICATIONS TO DEFAULT.HOC
//
// Vars added here may not be handled properly within nrnoc.hoc
//------------------------------------------------------------

//** String defaults

//** Simulation defaults

long_dt     = .001      // msec 

objref sfunc,tmpfile
sfunc = hoc_sf_   // needed to use is_name()
tmpfile = new File()  // check for existence before opening a user's local.hoc file

proc write_comment () {
  tmpfile.aopen("index")
  tmpfile.printf("%s\n",$s1)
  tmpfile.close()  
}

func asin () { return atan($1/sqrt(1-$1*$1)) }
func acos () { return atan(sqrt(1-$1*$1)/$1) }

objref mt[2]
mt = new MechanismType(0)
proc uninsert_all () { local ii
  forall for ii=0,mt.count()-1 {
    mt.select(ii)
    mt.selected(temp_string_)
    if (strcmp(temp_string_,"morphology")==0) continue
    if (strcmp(temp_string_,"capacitance")==0) continue
    if (strcmp(temp_string_,"extracellular")==0) continue
    if (sfunc.substr(temp_string_,"_ion")!=-1) continue
    mt.remove()
    // print ii,temp_string_
  }
}

condor_run = 0  // define for compatability

Hopfield JJ, Brody CD (2001) What is a moment? Transient synchrony as a collective mechanism for spatiotemporal integration. Proc Natl Acad Sci U S A 98:1282-7[PubMed]

References and models cited by this paper

References and models that cite this paper

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Hopfield JJ (1996) Transforming neural computations and representing time. Proc Natl Acad Sci U S A 93:15440-4 [PubMed]

Hopfield JJ (1999) Odor space and olfactory processing: collective algorithms and neural implementation. Proc Natl Acad Sci U S A 96:12506-11 [PubMed]

Hopfield JJ, Brody CD (2000) What is a moment? "Cortical" sensory integration over a brief interval. Proc Natl Acad Sci U S A 97:13919-24 [Journal] [PubMed]

   Hopfield and Brody model (Hopfield, Brody 2000) (NEURON+python) [Model]
   Hopfield and Brody model (Hopfield, Brody 2000) [Model]

Hopfield JJ, Brody CD, Roweis S (1998) Adv Neural Inf Processing 10:166-172

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Cebulla C (2007) Asymptotic behavior and synchronizability characteristics of a class of recurrent neural networks. Neural Comput 19:2492-514 [PubMed]

Cymbalyuk G, Shilnikov A (2005) Coexistence of Tonic Spiking Oscillations in a Leech Neuron Model J Comp Neurosci 18:255-263 [Journal]

Gutig R, Sompolinsky H (2009) Time-warp-invariant neuronal processing. PLoS Biol 7:e1000141 [Journal] [PubMed]

   Time-warp-invariant neuronal processing (Gutig & Sompolinsky 2009) [Model]

Legenstein R, Pecevski D, Maass W (2008) A learning theory for reward-modulated spike-timing-dependent plasticity with application to biofeedback. PLoS Comput Biol 4:e1000180 [Journal] [PubMed]

   Reward modulated STDP (Legenstein et al. 2008) [Model]

Migliore M, Hines ML, Shepherd GM (2005) The role of distal dendritic gap junctions in synchronization of mitral cell axonal output. J Comp Neurosci 18:151-161 [Journal] [PubMed]

   Olfactory bulb mitral cell: synchronization by gap junctions (Migliore et al 2005) [Model]

Migliore M, Messineo L, Cardaci M, Ayala GF (2001) Quantitative modeling of perception and production of time intervals. J Neurophysiol 86:2754-60 [Journal] [PubMed]

   Estimation and Production of Time Intervals (Migliore et al 2001) [Model]

Miller JA, Kenyon GT (2007) Extracting number-selective responses from coherent oscillations in a computer model. Neural Comput 19:1766-97 [PubMed]

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   Sensory feedback in an oscillatory interference model of place cell activity (Monaco et al. 2011) [Model]

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   Temporal integration by stochastic recurrent network (Okamoto et al. 2007) [Model]

Salinas E, Sejnowski TJ (2001) Correlated neuronal activity and the flow of neural information. Nat Rev Neurosci 2:539-50 [PubMed]

Talathi SS, Abarbanel HD, Ditto WL (2008) Temporal spike pattern learning. Phys Rev E Stat Nonlin Soft Matter Phys 78:031918 [Journal] [PubMed]

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   Synthesis of spatial tuning functions from theta cell spike trains (Welday et al., 2011) [Model]

Zilli EA (2012) Models of grid cell spatial firing published 2005-2011. Front Neural Circuits 6:16 [Journal] [PubMed]

   Grid cell spatial firing models (Zilli 2012) [Model]

(40 refs)

Hopfield JJ, Brody CD (2000) What is a moment? "Cortical" sensory integration over a brief interval. Proc Natl Acad Sci U S A 97:13919-24[PubMed]

References and models cited by this paper

References and models that cite this paper

Gutig R, Sompolinsky H (2009) Time-warp-invariant neuronal processing. PLoS Biol 7:e1000141 [Journal] [PubMed]

   Time-warp-invariant neuronal processing (Gutig & Sompolinsky 2009) [Model]

Hopfield JJ, Brody CD (2001) What is a moment? Transient synchrony as a collective mechanism for spatiotemporal integration. Proc Natl Acad Sci U S A 98:1282-7 [Journal] [PubMed]

   Hopfield and Brody model (Hopfield, Brody 2000) (NEURON+python) [Model]
   Hopfield and Brody model (Hopfield, Brody 2000) [Model]

Migliore M, Hines ML, Shepherd GM (2005) The role of distal dendritic gap junctions in synchronization of mitral cell axonal output. J Comp Neurosci 18:151-161 [Journal] [PubMed]

   Olfactory bulb mitral cell: synchronization by gap junctions (Migliore et al 2005) [Model]

(3 refs)