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: simctrl.hoc,v 1.14 2000/11/27 21:59:33 billl Exp $
// Graphic routines for neuremacs simulation control

proc sim_panel () {
  xpanel(simname)
        xvarlabel(output_file)
	xbutton("Init", "stdinit()")
	xbutton("Init & Run", "run()")
	xbutton("Stop", "stoprun=1")
	xbutton("Continue till Tstop", "continueRun(tstop)")
	xvalue("Continue till", "runStopAt", 1, "{continueRun(runStopAt) stoprun=1}", 1, 1)
	xvalue("Continue for", "runStopIn", 1, "{continueRun(t + runStopIn) stoprun=1}", 1,1)
	xbutton("Single Step", "steprun()")
	xvalue("Tstop", "tstop", 1, "tstop_changed()", 0, 1)
	graphmenu()
	sim_menu_bar()
	misc_menu_bar()
  xpanel()
}

proc misc_menu_bar() {
  xmenu("Miscellaneous")
    xbutton("Label Graphs", "labelgrs()")
    xbutton("Label With String", "labelwith()")
    xbutton("Label Panel", "labelpanel()")
	xbutton("Parameterized Function", "load_template(\"FunctionFitter\") makefitter()")
  xmenu()
}

proc sim_menu_bar() {
  xmenu("Simulation Control")
    xbutton("File Vers", "elisp(\"sim-current-files\")")
    xbutton("File Status...", "elisp(\"sim-rcs-status\")")
    xbutton("Sim Status", "elisp(\"sim-portrait\")")
    xbutton("Load Current Files", "elisp(\"sim-load-sim\")")
    xbutton("Load Templates", "elisp(\"sim-load-templates\")") 
    xbutton("Load File...", "elisp(\"sim-load-file\")") 
    xbutton("Save Sim...", "elisp(\"sim-save-sim\")")
    xbutton("Set File Vers...", "elisp(\"sim-set-file-ver\")")
    xbutton("Read Current Vers From Index", "elisp(\"sim-read-index-file\")")
    xbutton("Read Last Saved Vers", "elisp(\"sim-read-recent-versions\")")
    xbutton("Output to sim buffer", "elisp(\"sim-direct-output\")")
  xmenu()
}

proc labelpanel() {
  xpanel(simname,1)
	xvarlabel(output_file)
  xpanel()
}

proc labels () {
  labelwith($s1)
  labelgrs()
}

proc labelgrs () { local i, j, cnt
  for j=0,n_graph_lists-1 {
    cnt = graphList[j].count() - 1
    for i=0,cnt labelgr(graphList[j].object(i))
  }
}

proc labelwith () { local i, j, cnt
  temp_string_ = user_string_  // save the old one
  if (numarg() == 1) { /* interactive mode */  
    user_string_ = $s1
  } else {
    string_dialog("write what?", user_string_)
  }
  for j=0,n_graph_lists-1 {
    cnt = graphList[j].count() - 1
    for i=0,cnt {
      graphList[j].object(i).color(0)
      graphList[j].object(i).label(0.5,0.9,temp_string_)
      graphList[j].object(i).color(1)
      graphList[j].object(i).label(0.5,0.9,user_string_)
    }
  }
}

proc labelgr () { local i
  $o1.color(0)  // white overwrite
  for (i=0;i<10;i=i+1) { // erase every possible runnum for this date
    sprint(temp_string_,"%s %d%d",datestr,i,i)
    $o1.label(0.1,0.7,temp_string_) }
  $o1.color(1) // back to basic black
  sprint(temp_string_,"%s %02d",datestr,runnum)
  $o1.label(0.1,0.7,temp_string_)
}


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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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]

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

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

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

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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)