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

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This model is an extension of a model (<a href="">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.
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;
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]; Neymotin, Sam [samn at]; Kerr, Cliff [cliffk at];
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;
infot.mod *
intf6_.mod *
intfsw.mod *
misc.mod *
nstim.mod *
staley.mod *
stats.mod *
vecst.mod *
decmat.hoc *
decnqs.hoc *
default.hoc *
drline.hoc *
infot.hoc *
local.hoc *
misc.h *
ratlfp.dat *
setup.hoc *
simctrl.hoc *
spkts.hoc *
staley.hoc *
stats.hoc *
stdgui.hoc *
syncode.hoc *
updown.hoc *
xgetargs.hoc *
// $Id: xgetargs.hoc,v 1.20 2008/05/11 17:19:11 billl Exp $

print "Loading xgetargs.hoc..."

strdef mesg
objref xgabxl,xgabxo

//* xgetargs()
// xgetargs(panel_name,command,arg1[,arg2,...],defaults) // existing or new params -- flag 2
//   may have no named params in this case since just set with call to command
//   eg xgetargs("New","redo","do this","do that","1,2")
// xgetargs(panel_name,command,"a1,a2,..") // existing params -- flag 1
// xgetargs(panel_name,command,strlist)
// xgetargs(1,...) // dismiss after setting
// xgetargs(list,...) // list of helper functions returned by xgetclrfunc()
// eg xgetargs("Random session","newrand","# of patts","patt size  ","overlap   ","5,33,7")
// optional 1st arg flag=1 means to remove panel after command is called
// Union contains: o[0]=VBox, o[1]=argv, [o[2]=param name list] o[3]=orig update
//                 o[4]=helper functions
//                 x[0]=#args, x[1]=flag, x[2]=dismiss x[3-5] reserved for future use
//                 s=panel/button name,t=quit call,u=varlable,v=scratch
obfunc xgetargs () { local i,j,args,flag,dismiss,na localobj o,argv,vb,l,st,xo
  if (!isassigned(xgabxl)) xgabxl=new List()
  st=new String2()
  dismiss=0 i=1 
  xgabxl.append(o=new Union())
  if (argtype(i)==0) { dismiss=$1 i+=1 }
  if (argtype(i)==1) {xo=$oi i+=1} else xo=xgetclrfunc()
  o.os(4,"funcs",xo) // list of helper functions
  o.xs(2,"dismiss",dismiss) // dismiss=1 means dismiss at end
  o.os(1,"argv",argv=new Vector(na))
  o.os(0,"vb",vb=new VBox())
  o.s=$si i+=1 o.t=$si i+=1
  if (i==na) { // this should be a list of existing params
    o.xs(1,"flag",flag=1) // flag -- variables have names
    o.os(2,"plist",l=new List()) // list of param names
    if (argtype(i)==2) {
      split($si,l) // list of strings
      split($si,argv) // list of values
    } else if (argtype(i)==1) {
      for ltr(xo,$oi) {
    } else { printf("xgetargs ERRA\n") xpanel() return o=nil}
    if (args==0) { // create them
      for ltr(xo,l) {
        sprint(st.s,"%s=1",xo.s) execute(st.s)
        args=l.count argv.resize(args) argv.fill(1)
    } else if (args!=l.count) {printf("xgetargs ERRB %d %d\n",args,l.count) xpanel() return o=nil}
    o.os(3,"orig",argv.c)   // save original values
    for j=0,args-1 {
      xvalue(l.o(j).t, o.v, 1, st.s, 1)
  } else {
    j=i i=na
    if (strm($si,"^[a-z]")) { // a named variable; should all be name vars
      o.xs(1,"flag",flag=3) // flag -- variables have names and routine is called with args
      o.os(2,"plist",l=new List()) // list of param names
      split($si,l) // list of strings
    } else {
      o.xs(1,"flag",flag=2) // flag -- variables may have no names; are just args to a function
    i=j // restore i
    if (args!=na-i) { printf("xgetargs ERRC: mismatch %d %d\n",args,na-i) xpanel() return o=nil }
    o.os(3,"orig",argv.c)   // save original values
    for j=0,args-1 {
      if (flag==3) l.o(j).t=$si
  o.u=o.s // start with this label
  // xbutton("Help (2 clicks)","xgah()")
  xgabxo=o // global for current xgab object
  return o

//* xgah() should provide help -- doesn't
proc xgah () { 
  if (xgahfl==1) {
    continue_dialog("Press help button first, then elsewhere for button-specific help")
  } else xgahfl=1

//* xgetclrfunc() -- set up the callbacks as empty functions
obfunc xgetclrfunc () { local flag localobj st,xo,o
  if (numarg()==1) if (isobj($o1,"List")) flag=1
  if (flag) { // just clear the functions
    for ltr(xo,$o1) xo.t="" // clear
    return $o1
  } else { // create
    st=new String() o=new List()
    for scase(st,"xgetchg2","xgetexec2","xgaqt2","xgetlabl","xgetbuttn") {
      o.append(new String2(st.s)) }
    if (numarg()==1) $o1=o
    return o

//* xgetchg() done after a value is changed
proc xgetchg () { local i localobj o
  o=$o1 i=$2
print "A",o,i,o.o[4]
  if (excu("xgetchg2",o.o[4],o,i)) return
  sprint(o.u,"Press '%s' button for effect",o.s)

//* xgetexec() done when the 'make changes' button is pressed
proc xgetexec () { local i,args,dismiss,flag localobj o,l,av,vb,xo
  if (excu("xgetexec2",o.o[4],o)) return
  args=o.x flag=o.x[1] dismiss=o.x[2] av=o.o[1] vb=o.o
  if (flag==1 || flag==3) {
    if (args!=l.count || args!=av.size) {
      printf("xgetexec() ERRA %d,%d,%d\n",args,l.count,av.size) return
    for ltr(xo,l,&i) {
    if (flag==1) { // call the routine -- else will call below
      if (strm(o.t,"[(]")) o.v=o.t else sprint(o.v,"%s(%s)",o.t,o) // no args passed to function
  if (flag==2 || flag==3) {
    for i=0,args-2 sprint(o.v,"%s%g,",o.v,av.x[i])
  o.u="Changes submitted"
  if (dismiss) { xgaqt(o) // get rid of the box
  } else { o.o[3].copy(o.o[1]) } // new set of origs
//* xgaqt() called when the panel is dismissed
proc xgaqt () { local x localobj av,vb,o
  if (excu("xgaqt2",o.o[4],o)) return
  av=o.o[1] vb=o.o
  if ((x=xgabxl.index(o))!=-1) xgabxl.remove(x)
  if (xgabxo==o) xgabxo=nil

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]

References and models cited by this paper

References and models that cite this paper

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