Prosthetic electrostimulation for information flow repair in a neocortical simulation (Kerr 2012)

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Accession:141505
This model is an extension of a model (<a href="http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=138379">138379</a>) recently published in Frontiers in Computational Neuroscience. This model consists of 4700 event-driven, rule-based neurons, wired according to anatomical data, and driven by both white-noise synaptic inputs and a sensory signal recorded from a rat thalamus. Its purpose is to explore the effects of cortical damage, along with the repair of this damage via a neuroprosthesis.
Reference:
1 . Kerr CC, Neymotin SA, Chadderdon GL, Fietkiewicz CT, Francis JT, Lytton WW (2012) Electrostimulation as a prosthesis for repair of information flow in a computer model of neocortex IEEE Transactions on Neural Systems & Rehabilitation Engineering 20(2):153-60 [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 V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-5 cell; Neocortex V1 interneuron basket PV cell; Neocortex fast spiking (FS) interneuron; Neocortex spiny stellate cell;
Channel(s): I Chloride; I Sodium; I Potassium;
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA; Gaba;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Deep brain stimulation; Information transfer; Brain Rhythms;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu]; Neymotin, Sam [samn at neurosim.downstate.edu]; Kerr, Cliff [cliffk at neurosim.downstate.edu];
Search NeuronDB for information about:  Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-5 cell; Neocortex V1 interneuron basket PV cell; GabaA; AMPA; NMDA; Gaba; I Chloride; I Sodium; I Potassium; Gaba; Glutamate;
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neuroprosthesis
README
infot.mod *
intf6_.mod *
intfsw.mod *
misc.mod *
nstim.mod *
staley.mod *
stats.mod *
vecst.mod *
batch.hoc
boxes.hoc
bsmart.py
col.hoc
comparecausality.py
comparerasters.py
declist.hoc
decmat.hoc *
decnqs.hoc *
decvec.hoc
default.hoc *
drline.hoc *
filtutils.hoc
flexinput.hoc
grvec.hoc
infot.hoc *
init.hoc
intfsw.hoc
labels.hoc
local.hoc *
misc.h *
mosinit.hoc
network.hoc
nload.hoc
nqs.hoc
nqsnet.hoc
nrnoc.hoc
params.hoc
pyhoc.py
ratlfp.dat *
run.hoc
runsim
setup.hoc *
simctrl.hoc *
spkts.hoc *
staley.hoc *
stats.hoc *
stdgui.hoc *
syncode.hoc *
updown.hoc *
xgetargs.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_)
}


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