Motor cortex microcircuit simulation based on brain activity mapping (Chadderdon et al. 2014)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:146949
"... We developed a computational model based primarily on a unified set of brain activity mapping studies of mouse M1. The simulation consisted of 775 spiking neurons of 10 cell types with detailed population-to-population connectivity. Static analysis of connectivity with graph-theoretic tools revealed that the corticostriatal population showed strong centrality, suggesting that would provide a network hub. ... By demonstrating the effectiveness of combined static and dynamic analysis, our results show how static brain maps can be related to the results of brain activity mapping."
Reference:
1 . Chadderdon GL, Mohan A, Suter BA, Neymotin SA, Kerr CC, Francis JT, Shepherd GM, Lytton WW (2014) Motor cortex microcircuit simulation based on brain activity mapping. Neural Comput 26:1239-62 [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 M1 pyramidal intratelencephalic L2-6 cell; Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Oscillations; Laminar Connectivity;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu]; Neymotin, Sam [samn at neurosim.downstate.edu]; Shepherd, Gordon MG [g-shepherd at northwestern.edu]; Chadderdon, George [gchadder3 at gmail.com]; Kerr, Cliff [cliffk at neurosim.downstate.edu];
Search NeuronDB for information about:  Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex M1 pyramidal intratelencephalic L2-6 cell; GabaA; AMPA; NMDA; Gaba; Glutamate;
/
src
README
infot.mod *
intf6.mod *
intfsw.mod *
matrix.mod
misc.mod *
nstim.mod *
staley.mod *
stats.mod *
vecst.mod *
boxes.hoc *
col.hoc
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
filtutils.hoc *
gcelldata.hoc
gmgs102.nqs
grvec.hoc *
infot.hoc *
init.hoc
intfsw.hoc *
labels.hoc *
load.py
local.hoc *
main.hoc
misc.h *
miscfuncs.py
network.hoc
neuroplot.py *
nload.hoc
nqs.hoc *
nqsnet.hoc
nrnoc.hoc *
params.hoc
run.hoc
samutils.hoc *
saveoutput.hoc
saveweights.hoc
setup.hoc *
simctrl.hoc *
spkts.hoc *
staley.hoc *
stats.hoc *
stdgui.hoc *
syncode.hoc *
updown.hoc *
wdmaps2.nqs
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 nil }
  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)
}

Loading data, please wait...