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 *
                            
// $Id: default.hoc,v 1.5 2003/07/08 16:16:52 billl Exp $
/* This file contains various global defaults for hoc

** Users should not edit nrnoc.hoc or default.hoc.  Any local 
changes to these files should be made in local.hoc.
----------------------------------------------------------------*/

/*------------------------------------------------------------
Object defaults
------------------------------------------------------------*/

/*** Define a "nil" object ***/
objectvar nil

/*------------------------------------------------------------
String defaults
------------------------------------------------------------*/

/*** "Section" is used if errors are found in the initializiations ***/
strdef section

/*** Misc defines used by graphic routines ***/
temp_string_ = "t"
tempvar = 0

/*------------------------------------------------------------
Simulation defaults
------------------------------------------------------------*/

                        /* To be consistent w/the nmodl values */
FARADAY = 96520.        /* Hoc default = 96484.56 */
PI      = 3.14159       /* Hoc default = 3.1415927 */

                        /* 0=off, 1=on */
print_flag  = 0         /* Write to output file */
graph_flag  = 1         /* Plot output */
iv_flag     = 1         /* Using Interviews plotting */
batch_flag  = 0         /* Using batch_run() */
compress_flag = 0       /* Compress output file when saved */
stoprun     = 0         /* 0=running, 1=stopped */
iv_loaded   = 0         /* Load initial iv stuff on once */

init_seed   = 830529
run_seed    = 680612

t           = 0         /* msec */
dt          = .01       /* msec */
tstop       = 100       /* msec */
printStep   = 0.1       /* msec */
plotStep    = 0.1       /* msec */
flushStep   = 0.1       /* msec */
eventStep   = 50        /* Number of nstep's before a doEvent */

secondorder = 0

celsius     = 6.3       /* degC */

v_init      = -70       /* (mV) */
global_ra   = 200       /* (ohm-cm) specific axial resisitivity */

/*** Ion parameters ***/
ca_init     = 50e-6     /* mM */
na_init     = 10        /* mM */
k_init      = 54.4      /* mM */


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]

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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]

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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]

Monaco JD, Knierim JJ, Zhang K (2011) Sensory feedback, error correction, and remapping in a multiple oscillator model of place cell activity Frontiers in Computational Neuroscience 5(0):39 [Journal]

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

Okamoto H, Isomura Y, Takada M, Fukai T (2007) Temporal integration by stochastic recurrent network dynamics with bimodal neurons. J Neurophysiol 97:3859-67 [PubMed]

   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]

Welday AC, Shlifer IG, Bloom ML, Zhang K, Blair HT (2011) Cosine Directional Tuning of Theta Cell Burst Frequencies: Evidence for Spatial Coding by Oscillatory Interference J. Neurosci. 31:16157-16176 [Journal] [PubMed]

   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)