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: boxes.hoc,v 1.58 2010/08/12 14:20:15 billl Exp $

print "Loading boxes.hoc..."

{load_file("grvec.hoc")}
// load_file("boxes.hoc")
proc boxes () {}
objref boxer, boxerl
boxerl = new List()

// factor(num) finds the factors that are closest together
// NB: must be at top since declared external in template BX
func factor () { local num, srt, ii
  num = $1
  srt = int(sqrt(num))
  for (ii=srt;ii<num && num/ii!=int(num/ii);ii+=1) {}
  if (ii>num/ii) ii=num/ii // return smaller factor
  return ii
}

// template for putting up trays and decks
begintemplate BX
public mktray,mkdeck,name,boxes,map,unmap,closebox
public min,max,attrnum,rows,cols,size,trnum,gl,stub,label,getg
external factor,boxerl

objref boxes[3], ob, gitem,gl,XO, nil, this
double min[1],max[1],trnum[1]
strdef temp_string_,name

proc init () {
  min = -1 max = -1
  trnum=$1
  gl = new List()
}

//mktray(panattr) graph out from llist of a panattr
proc mktray () { local ci, ri, gi, m1, m2, bi
  ob = $o1
  cols=$3 rows=$2 size=rows*cols
  if (numarg()==5) {xs=$4 ys=$5} else {xs=100 ys=50}
  ri = 0 // count the rows
  gi = 0 // count the graphs
  boxes[0] = new VBox()
  boxes[0].dismiss_action("closebox()")
  boxes[0].intercept(1)
  xpanel("",1)
  xvarlabel(name)
  xpanel()
  for ri=0,rows-1 {
    boxes[2] = new HBox()
    boxes[2].intercept(1)
    for ci=0,cols-1 {
      gitem = new Graph(0)
      gitem.view(0,-100,1000,50,0,0,xs,ys)
      gl.append(gitem)
      if (ob!=nil) ob.glist.append(gitem)
      gi = gi+1
    }
    boxes[2].intercept(0)
    boxes[2].map("")
  }
  boxes[0].intercept(0)
  if (strcmp(name,"")==0 && ob!=nil) name=ob.filename
  sprint(name,"%d:%s",trnum,name)
  boxes[0].map(name)
}

proc map() { boxes[0].map() }
proc unmap() { boxes[0].unmap() }

proc closebox () { local ii,ix
  ix=boxerl.index(this)
  for (ii=gl.count-1;ii>=0;ii-=1) {
    XO=gl.object(ii)
    XO.unmap
  }
  if (ob!=nil) ob.glist.remove_all
  gl.remove_all
  boxes[0].unmap
  boxes[0]=nil
  boxes[2]=nil
  boxerl.remove(ix)
}

obfunc getg () {
  return gl.o($1*cols+$2)
}

proc mkdeck () { local rows, cols, ci, ri, gi, m1, m2
  ob = $o1
  if (min==-1 || max==-1) {
    m1 = 0 m2 = ob.llist.count()-1
  } else { m1=min    m2=max }
  cnt = m2-m1+1
  cols=factor(cnt) rows=cnt/factor(cnt)
  ri = 0 // count the rows
  gi = 0 // count the graphs
  boxes[0] = new VBox()
  boxes[0].intercept(1)
  xpanel("",1)
  xbutton("Next","boxes[1].flip_to(decknum=decknum+1)")
  xbutton("Previous","boxes[1].flip_to(decknum=decknum-1)")
  xpanel()
  boxes[1] = new Deck()
  boxes[1].intercept(1)
  for ri=0,rows-1 {
    boxes[2] = new HBox()
    boxes[2].intercept(1)
    for ci=0,cols-1 {
      ob.rv(gi+m1)
      gi = gi+1
    }
    boxes[2].intercept(0)
    boxes[2].map("")
  }
  boxes[1].intercept(0)
  boxes[1].map("")
  boxes[0].intercept(0)
  boxes[0].map("Deck")
  decknum = 0
  boxes[1].flip_to(decknum)
  if (! ob.attr0) {
    for ii = 0,gi-1 { 
      ob.glist.object(ii).label(0.3,0.5,ob.llist.object(ii).name)
    }
  }
}

endtemplate BX

obfunc mktray () { local i,na,rows,cols,xsz,ysz localobj o
  if (numarg()==0) { print "mktray(attrnum,rows,cols[,xsize,ysize,label])"
    print "Create a tray for attr panel ATTRNUM to superimpose upon."
    return }
  boxer = new BX(boxerl.count)
  boxerl.append(boxer)
  trnum=boxer.trnum
  if (argtype(numarg())==2) { na=numarg()-1 i=numarg() boxer.name=$si 
  } else                    { na=numarg() }
  if (na==2) o=panobj else if (argtype(1)==0) o=GRV[$1] else if (argtype(1)==1) o=$o1
  if (o!=nil) o.super = 1
  if (argtype(1)==2) {
    boxer.name=$s1
    xsz=100 ysz=50
    if (na/2==int(na/2)) {rows=factor($2) cols=$2/rows i=3} else {rows=$2 cols=$3 i=4}
    if (argtype(i)==0) {xsz=$i i+=1 ysz=$i} // size of graphs
    boxer.mktray(nil,rows,cols,xsz,ysz)
  } else if        (na==5) { boxer.mktray(o,$2,$3,$4,$5)
  } else if (na==3) { boxer.mktray(o,$2,$3) 
  } else if (na==2) { boxer.mktray(o,$1,$2)
    printf("Mapping trays to %s\n",o)
  }
  return boxer
}

proc rmtray () { local ix
  ix=$1
  if (boxerl.count<=1) boxerl.remove_all else {
    for (ii=boxerl.count-1;ii>=0;ii-=1) {
      if (boxerl.object(ii).attrnum==attrnum) boxerl.remove(ii) 
    }}
  remgrs(attrnum)
  GRV[ix].super=0
}

proc trsz () {
  if (boxerl.count>0) for ltr (XO,boxerl) printf("%d:%d x %d\n",XO.attrnum,XO.rows,XO.cols)
}

proc mktrpanl () {
  xgetargs("Make Tray","mktray","Which","rows","cols","xsize","ysize","0,2,3,100,50")
}

//* disptray() redisp() redispv()
proc disptray () { local ix,ii,jj,kk
  if (numarg()==0) {print "disptray(ix[,cols])" return}
  ix=$1
  ii=GRV[ix].llist.count 
  if (numarg()==2) jj=$2 else jj=factor(ii)
  kk=GRV[ix].glist.count
  mktray(GRV[ix],round(ii/jj),jj,100,50) 
  GRV[ix].grall(0,ii-1)
  for ltr(XO,GRV[ix].glist) if(i1>=kk) { 
    XO.size(&x[0]) 
    XO.size(x[0],x[1],x[2],x[3]) }
}

proc redisp () { local supsav
  panobj=$o1
  if (numarg()>=2) trnum=$2
  supsav=panobj.super  panobj.super=1
  for ltr(graphItem,boxerl.object(trnum).gl) {
    graphItem.erase_all()
    panobj.rv(i1)
  }
  panobj.super=supsav
}

// for bxit () {}  go through all the graphs in tray trnum
// for bxit (g1,g2,g3,g4) {}  go through selected graphs
// for bxit (-1,g1,g2) {}  go through g1-g2
bxn=-1
proc bxop () { g=boxerl.object(trnum).gl.object($1) graphItem=g}
proc bxinc () { 
  if (bxn>=boxerl.object(trnum).gl.count) bxn=0 else bxn+=1
  g=boxerl.object(trnum).gl.object(bxn) 
  graphItem=g
}
iterator bxit () { local i,ii
  i1=0
  if (numarg()>0) {
    if (numarg()==3  && $1==-1) {
      for ii = $2, $3 {
        g=boxerl.object(trnum).gl.object(ii)
        graphItem=g
        iterator_statement
        i1+=1
      }
    } else {
      for i = 1, numarg() {
        if (numarg()==1) XO=$o1.object(ii)
        g=boxerl.object(trnum).gl.object($i)
        graphItem=g
        iterator_statement
        i1+=1
      }
    }
  } else {
    for ii=0,boxerl.object(trnum).gl.count-1 {
      g=boxerl.object(trnum).gl.object(ii)
      graphItem=g
      iterator_statement
      i1+=1
    }
  }
}

// redispv(VEC,ATTRNUM,TRNUM) -- all args optional
proc redispv () { local supsav
  panobj=$o1
  if (numarg()>=2) trnum=$2
  supsav=panobj.super  panobj.super=1
  for bxit() {
    g.erase_all()
    if (numarg()>0) panobj.rv($o1.x[i1]) else panobj.rv(vec.x[i1])
  }
  panobj.super=supsav
}

proc bxcomm () { 
  if (numarg()==1) boxerl.object(boxerl.count-1).name=$s1 else {
    boxerl.object(boxerl.count-1).name=comment }
}

//* gin() search through param strings to graph particular members of llist
// eg regexp="SPCX SPTC SPSM " then 'gin(1)' to create regexp: 'SPCX.+%sSPTC.+%sSPSM.+%s'
// gin("5","","") will find examples with SPCX=5 and graph SPTC against SPSM
// ginpr() will search through llist and just print out the file names
// meant to be used after running dir2pr() to get a summary file
strdef regexp
proc gin () { local i,a
  a=allocvecs(1)
  revec(mso[a]) tstr=regexp
  for i=1,numarg() repl_str(tstr,"%s",$si,temp_string2_)  // replace sprint
  for ltr(XO,panobj.llist,&y) if (strm(XO.name,tstr)) mso[a].append(y)
  if (mso[a].size!=boxer.rows*boxer.cols) {
    printf("gin() ERR: %d!=%dx%d\n",mso[a].size,boxer.rows,boxer.cols)
    dealloc(a) return
  }
  geall(1)
  for bxit() panobj.rv(mso[a].x[i1]) 
  tstr=regexp 
  repl_mstr(tstr,".\\+%s","=%s,",temp_string2_)
  chop(tstr)
  for i=1,numarg() repl_str(tstr,"%s",$si,temp_string2_)
  sprint(tstr,"%s: %s",panobj.filename,tstr)
  bxcomm(tstr)  print tstr
  dealloc(a)
}

proc ginpr () { local base,i
  if (numarg()==0) { 
    print "Set regexp to begin: eg\n\tregexp=\"SMTC SPSM NSTC \" (space at end)"
    print "Then call ginpr(regexp) to reset regexp"
    print "Then call eg ginpr(\"0.015\",\"\",\"\") to list or gin(...) to graph"
    return }
  if (numarg()==1) { 
    regexp=$s1 repl_mstr(regexp," ",".+%s,",tstr) 
    chop(regexp,",")
    print regexp return }
  base=1 tstr=regexp // where they start numbering
  for i=1,numarg() repl_str(tstr,"%s",$si,temp_string2_)  // replace sprint
  for ltr(XO,panobj.llist,&y) if (strm(XO.name,tstr)) printf("%03d %s\n",base+y,XO.name)
}

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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Dura-Bernal S, Neymotin SA, Kerr CC, Sivagnanam S, Majumdar A, Francis JT, Lytton WW (2017) Evolutionary algorithm optimization of biological learning parameters in a biomimetic neuroprosthesis. IBM Journal of Research and Development (Computational Neuroscience special issue) 61(2/3):6:1-6:14 [Journal]

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(38 refs)