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;
/
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: declist.hoc,v 1.157 2010/12/07 14:19:28 billl Exp $

print "Loading declist.hoc..."

//* Declarations
strdef mchnms
objref tmplist,tmplist2,tmpobj,aa,XO,YO
if (! name_declared("datestr")) {load_file("setup.hoc")}
tmplist = new List()
proc declist() {}

//* Templates
//** template String2
begintemplate String2
public s,t,x,append,prepend,exec,tinit
strdef s,t
proc init() {
  if (numarg() == 1) { s=$s1 }
  if (numarg() == 2) { s=$s1 t=$s2 }
  if (numarg() == 3) { s=$s1 t=$s2 x=$3 }
}
proc append () { local i
  if (argtype(1)==2) sprint(t,"%s%s",s,$s1)
  for i=2,numarg() sprint(t,"%s%s",t,$si)
}
proc prepend () { local i
  if (argtype(1)==2) sprint(t,"%s%s",$s1,s)
  for i=2,numarg() sprint(t,"%s%s",$si,t)
}
proc exec () {
  if (numarg()==1) sprint(t,"%s%s",$s1,s)
  execute(t)
}
proc tinit() { t=$s1 }

endtemplate String2

//** template DBL
begintemplate DBL
  public x
  proc init () { if (numarg()==1) x=$1 else x=0 }
endtemplate DBL

//** template Union
// USAGE: XO=new Union(val) where val can be a number string or object
//        XO=new Union(list,index) will pick up a string or object from list
//        XO=new Union(vec,index)  will pick up a number from vector
//        XO=new Union(&dbl,index) will pick up a number from double array
// Union allows storage of a double, string or object
// 2 ways of storing strings: directly in XO.s (t,u,v) OR 
//   using XO.set("NAME","STR") which is returned by XO.get("NAME").s
// It is useful as a localobj in an obfunc since it will permit returning anything
// It also makes it easy to pick up any kind of value out of a list, vector or array
// declared() not yet declared
if (!name_declared("isobj")) execute1("func isobj(){return 0}") // place holder
if (!name_declared("isassigned")) execute1("func isassigned(){return 0}") // place holder
if (!name_declared("llist")) execute1("proc llist(){}") // place holder
begintemplate Union
public ty,x,s,t,u,v,o,xptr,xg,xs,optr,og,os,get,set,xl,ol,fi,inc,list,err,pr,sz
strdef s,t,u,v,tstr
objref o[10],xl,ol,this,xo
double x[10],sz[1],err[1]
external sfunc,isobj,isassigned,nil,DBL,llist
// 1arg -- store a num, string or obj
// 2arg -- pick up type out of list
proc init () { local ii,i,ox,xx,sx,flag
  ox=xx=sx=0 ty=argtype(1) // 'type' of Union defined by 1st arg on creation
  sz=10 // 10 is default size of arrays; for ii=0,sz-1 
  for ii=0,sz-1 x[ii]=-1 // Was ERR
  // special case of number in a vector or something in a list -- 2 args: list or vec,index
  err=1 flag=0
  if (numarg()/2==int(numarg()/2)) for (i=1;i<numarg();i+=2) {
    if (argtype(i)!=2 || argtype(i+1)==2) break
    flag=1
  }
  if (flag) { // "name",val,etc
    for (i=1;i<numarg();i+=1) {
      tstr=$si i+=1 
      if (argtype(i)==0) set(tstr,$i) else set(tstr,$oi)
    }
    s="" // used as temp storage only
  } else if (argtype(1)==1 && argtype(2)==0 && argtype(3)==-1) {
    ii=$2
    // printf("Union WARNING: taking single element out of a Vector or List\n")
    if (argtype(1)==1) {
      if (isobj($o1,"Vector")) { 
        if (ii<0 || ii>=$o1.size) {
          printf("Union ERR: vec index (%d) out of bounds for %s\n",ii,$o1)
          return }
        ty=0 x=$o1.x[ii] o=$o1
      } else if (isobj($o1,"List")) {
        if (ii<0 || ii>=$o1.count) {
          printf("Union ERR: list index (%d) out of bounds for %s\n",ii,$o1)
          return }
        if (isobj($o1.object(ii),"String")) { // will handle String2
          ty=2 s=$o1.object(ii).s o=$o1.object(ii) x=ii
        } else { ty=1 o=$o1.object(ii) x=ii }
      }
    } else if (argtype(1)==3) {
      ty=0 x=$&1[ii] // could check - but no + bound checking possible
    }
  } else for i=1,numarg() {
    ii=argtype(i)
    if (ii==0) { 
      if (xx<sz) { 
        x[xx]=$i xx+=1 
      } else printf("Only have %d doubles available so can't store %g\n",sz,$i)
    } else if (ii==2) { 
      if (sx==0) s=$si else if (sx==1) t=$si else if (sx==2) u=$si else if (sx==3) v=$si else {
        printf("Only have 4 strings available so can't store %s\n",$si) }
      sx+=1
    } else if (ii==1) { 
      if (ox<sz) { o[ox]=$oi ox+=1
      } else printf("Only have %d objects available so can't store %s\n",sz,$oi)
    } else printf("Union ERR: argtype not recognized numarg %d %d\n",i,ii)
  }
  err=0
}

proc pr () { print "Use Union[].list" }

proc list () { local flag
  flag=0
  if (ol!=nil) {
    for ii=0,sz-1 if ((! isojt(ol,ol.o(ii)))||o[ii]!=nil) {
      if (isojt(ol,ol.o(ii))) printf("%10s\t%s\n","NO NAME", o[ii]) else {
                              printf("%10s\t%s\n",ol.o(ii).s,o[ii]) }
    }
    printf("%s\n","================================") 
    flag=1
  }
  if (xl!=nil) {
    for ii=0,sz-1 if ((! isojt(xl,xl.o(ii)))||x[ii]!=ERR) {
      if (isojt(xl,xl.o(ii))) printf("%10s\t%g\n","NO NAME", x[ii]) else {
                              printf("%10s\t%g\n",xl.o(ii).s,x[ii]) }
    }
    printf("%s\n","================================") 
    flag=1
  }
  if (!flag) {
    printf("%s\nSCALARS: ","================================") 
    for ii=0,sz-1 if (x[ii]!=ERR) printf("%d:%g ",ii,x[ii])
    printf("\n%s\nOBJECTS: ","================================") 
    for ii=0,sz-1 if (o[ii]!=nil) printf("%d:%s ",ii,o[ii])
    printf("\n%s\n","================================") 
  }
  if (sfunc.len(s)>0) printf("%10s\t%s\n","s",s)
  if (sfunc.len(t)>0) printf("%10s\t%s\n","t",t)
  if (sfunc.len(u)>0) printf("%10s\t%s\n","u",u)
  if (sfunc.len(v)>0) printf("%10s\t%s\n","v",v)
}

// full List
obfunc newl () { localobj o
  o=new List() 
  for ii=0,sz-1 o.append(o)
  return o
} 
proc repl () { 
  if (isobj($o1.o($2),"String")) { $o1.o($2).s=$s3
  } else { $o1.remove($2) $o1.insrt($2,new String($s3)) }
}

func fi () { local ii
  fif=-1
  for ii=0,sz-1 {
    if ($o1.o(ii)==$o1) {
      if (fif==-1) fif=ii // first empty slot if any
    } else if (strcmp($o1.o(ii).s,$s2)==0) return ii
  }
  return ERR
}
// put in pointers for the x values
func xptr () { local i,ii
  if (numarg()>sz) {printf("More names (%d) than x items (%d) in %s:xptr\n",numarg(),sz,this) 
    error()}
  if (!isassigned(xl)) xl=newl()
  for i=1,numarg() repl(xl,i-1,$si)
  return xl.count
}
func optr () { local i,ii
  if (numarg()>sz) {printf("More names %d than o items (%d) in %s:optr\n",numarg(),sz,this) error()}
  if (!isassigned(ol)) ol=newl()
  for i=1,numarg()  repl(ol,i-1,$si)
  return ol.count
}
// xg() associative get of a num
func xg () { local ii
  ii=fi(xl,$s1)
  if (ii==ERR) {printf("Union:og (num get) failed -- \"%s\" not found\n",$s1) return ERR}
  return x[ii] 
}
// xg() associative get of an obj
obfunc og () { local ii
  ii=fi(ol,$s1)
  if (ii==ERR) {printf("Union:og (obj get) failed -- \"%s\" not found\n",$s1) return nil}
  return o[ii] 
}
// xs(index,"label",num) set a specific location using a string -- see set()
// xs("label",num) set an existing one only
func xs () { local ii,i
  if (!isassigned(xl)) xl=newl()
  if (argtype(1)==0) {
    i=3 ii=$1 // an index
    repl(xl,ii,$s2)
  } else {
    i=2 ii=fi(xl,$s1)
    if (ii==ERR) {printf("Union:xs (num set) failed -- no %s found\n",$s1) return ERR}
  }
  if (argtype(i)!=0) {printf("Union:xs err -- arg %d must be object\n",i) return ERR}
  x[ii]=$i
  return $i
}
// os(index,"label",obj) set a specific location using a string -- see set()
// os("label",obj) set an existing one only
obfunc os () { local ii,i
  if (!isassigned(ol)) ol=newl()
  if (argtype(1)==0) {
    i=3 ii=$1 // $1 is an index
    repl(ol,ii,$s2)
  } else {
    i=2 ii=fi(ol,$s1)
    if (ii==ERR) {printf("Union:os (obj set) failed -- \"%s\" not found\n",$s1) return nil}
  }
  if (argtype(i)!=1) {printf("Union:os err -- arg %d must be object\n",i) return nil}
  o[ii]=$oi
  return $oi
}

// get() get any type
obfunc get () { local ii
  if        ((ii=fi(ol,$s1))!=ERR) { 
    return o[ii] 
  } else if ((ii=fi(xl,$s1))!=ERR) { 
    if (argtype(2)==3) { $&2=x[ii] return this } else { return new DBL(x[ii]) }
  } else {
    // printf("Union:get() \"%s\" not found\n",$s1) 
    return nil // make returning nil the unique error
  }
}

// increment or with neg decrement something
func inc () { local n
  if (numarg()==2) n=$2 else n=1
  if ((ii=fi(xl,$s1))==ERR) {printf("Union:inc ERR: %s %s\n",this,$s1) return ERR}
  return x[ii]+=n
}

// set() set any type
func set () { local ii,i,ty,fo,fx
  if (xl==nil) xl=newl() if (ol==nil) ol=newl()
  for (i=1;i<numarg();i+=1) {
    tstr=$si i+=1 
    if ((ty=argtype(i))==0) xo=xl else if (ty==1 || ty==2) xo=ol // use String() for strings
    ii=fi(xo,tstr)
    if (ii==ERR) {
      if (fif==-1) {printf("UNION:set() ERRB: %s full for type %d\n",this,ty)  return ERR}
      repl(xo,(ii=fif),tstr)
    }
    if (ty==0) x[ii]=$i else if (ty==1) o[ii]=$oi else if (ty==2) { // don't use s,t,u,v
      o[ii]=new String($si)
    }
  }
  return ii
}
endtemplate Union

//* Iterators
//** list iterator ltr
// usage 'for ltr(tmplist) { print XO }' :: 1 arg, assumes XO as dummy
// usage 'for ltr(YO, tmplist) { print YO }' 2 arg, specify dummy
// usage 'for ltr(XO, tmplist, &x) { print XO,x }' :: x is counter (else use global i1)
// usage 'for ltr(XO, tmplist, 5) { print XO,x }' :: max; only print out 0-5
// usage 'for ltr(XO, tmplist, 5, 7) { print XO,x }' :: print 5-7
// usage 'for ltr(XO, tmplist, &x, 5) { print XO,x }' :: counter with max
// usage 'for ltr(XO, tmplist, &x, 5, 7) { print XO,x }' :: counter,min,max
iterator ltr () { local i,min,max,ifl
  min=0 max=1e9 ifl=0 // iterator flag
  if (numarg()==3) {
    if (argtype(3)==3) {ifl=1 $&3=0}
    if (argtype(3)==0) max=$3
  } else if (numarg()==4) { 
    if (argtype(3)==0) i1=min=$3 else {ifl=1 $&3=0}
    max=$4 
  } else if (numarg()==5) { 
    $&3=min=$4 max=$5 ifl=1 
  }
  if (! ifl) i1=0
  if (numarg()==1) {
    for i = 0, $o1.count-1 {
      XO = $o1.object(i)
      iterator_statement
      i1+=1
    }
    tmpobj=$o1
    XO=nil
  } else {
    if (max==1e9) max=$o2.count()-1 else if (max<0) { min=$o2.count+max max=$o2.count-1 
    } else if (max>$o2.count-1) max=$o2.count-1
    for i = min, max {
      $o1 = $o2.object(i)
      iterator_statement
      if (ifl) { $&3+=1 } else { i1+=1 }
    }
    tmpobj=$o2
    $o1 = nil
  }
}

//** list iterator ltrb -- backwards list iterator
// usage 'for ltrb(tmplist) { print XO }' :: 1 arg, assumes XO as dummy
// usage 'for ltrb(YO, tmplist) { print YO }' 2 arg, specify dummy
// usage 'for ltrb(XO, tmplist, &x) { print XO,x }' :: 3 args, define counter (else i1 default)
//                                                 :: note that x, i1 must be defined
iterator ltrb () { local i
  if (numarg()==1) {
    i1=$o1.count-1
    for (i=$o1.count()-1;i>=0;i-=1) {
      XO = $o1.object(i)
      iterator_statement
      i1-=1
    }
    tmpobj=$o1 XO=nil
  } else {
    if (numarg()==3) $&3=$o2.count-1 else i1=$o2.count-1
    for (i=$o2.count()-1;i>=0;i-=1) {
      $o1 = $o2.object(i)
      iterator_statement
      if (numarg()==3) { $&3-=1 } else { i1-=1 }
    }
    tmpobj=$o2
    $o1 = nil
  }
}

//** list iterator ltr2
// usage 'for ltr2(XO, YO, list1, list2) { print XO,YO }'
iterator ltr2() { local i,cnt
  if (numarg()==5) $&5=0 else i1=0
  cnt=$o4.count
  if ($o3.count != $o4.count) { print "ltr2 WARNING: lists have different lengths" 
    if ($o3.count<$o4.count) cnt=$o3.count }
  for i = 0, cnt-1 {
    $o1 = $o3.object(i)
    $o2 = $o4.object(i)
    iterator_statement
    if (numarg()==5) { $&5+=1 } else { i1+=1 }
  }
  $o1=nil $o2=nil
}

//** list pairwise iterator ltrp
// usage 'for ltrp(XO, YO, list) { print XO,YO }' takes them pairwise
iterator ltrp() { local i
  if (numarg()==4) {$&4=0} else {i1 = 0}
  for (i=0;i<$o3.count()-1;i+=2) {
    $o1 = $o3.object(i) $o2 = $o3.object(i+1)
    iterator_statement
    if (numarg()==4) { $&4+=1 } else { i1+=1 }
  }
  $o1=nil $o2=nil
}

//** list iterator sltr
// usage 'for sltr(XO, string) { print XO }'
iterator sltr() { local i
  tmplist = new List($s2)
  if (numarg()==3) {$&3=0} else {i1=0}
  for i = 0, tmplist.count() - 1 {
    $o1 = tmplist.object(i)
    iterator_statement
    if (numarg()==3) { $&3+=1 } else { i1+=1 }
  }
  $o1 = nil
}

//* Procedures
//** append(LIST,o1,o2,...) -- like revec() makes a list of objects
proc append () { local i,max
  if (!isassigned($o1)) $o1=new List()
  max=numarg()
  if (argtype(max)==0) {max-=1 $o1.remove_all}
  for i=2,max $o1.append($oi)
}

//** rcshead([flag])
// with flag does head from archive
func rcshead () { local x,flag localobj st
  x=-1 flag=0
  st=new String2()
  if (numarg()==2) {
    st=dirname($s1)
    sprint(st.t,"%sRCS/%s,v",st.s,st.t)
    flag=1
  } else st.t=$s1
  sprint(st.s,"head -1 %s",st.t)
  system(st.s,st.s)
  if (flag) sscanf(st.s,"head\t1.%d",&x) else sscanf(st.s,"%*[^,],v 1.%d",&x)
  return x
}

//** getenv()
obfunc getenv () { localobj st
  st=new String()
  sprint(st.s,"echo $%s",$s1)
  system(st.s,st.s)
  sfunc.left(st.s,sfunc.len(st.s)-1)
  if (numarg()==2) $s2=st.s
  return st
}

//** rcsopen(file,vers[,flag])  -- version open, flag to do load_file
// rcsopen(file,vers,proc_name)  -- just load the single proc or func from that vers
//  rcsopen("nqsnet.hoc,43,network.hoc,17,params.hoc,842,run.hoc,241") will open several files
func rcsopen () { local a,vers,ii,x,ret localobj st,fn,v1,o,xo
  st=new String2()   ret=1
  if (argtype(1)==2) st.s=$s1 else st.s=$o1.s
  // open network.hoc,params.hoc,run.hoc files for "#.#.#" 
  if (strm(st.s,"^[^,]+,[^,]+,[^,]+,[^,]+")) {
    a=allocvecs(v1)  o=new List()
    split(st.s,o)
    for (ii=1;ii<o.count;ii+=2) v1.append(str2num(o.o(ii).s))
    if (o.count!=v1.size*2) { printf("rcsopen() discrepency: ") vlk(v1) llist(o) dealloc(a) 
      return 0 }
    for ltr(xo,o,&x) if (x%2==0) { // every other
      printf("Opening %s%d\n",xo.s,v1.x[x/2])
      if (!rcsopen(xo.s,v1.x[x/2])) { dealloc(a) ret=0 }
    }
    dealloc(a)
    return ret
  }
  if (numarg()>1) vers=$2 else vers=0
  if (! vers) vers=rcshead(st.s,1) // vers=0 means get latest version
  // do checkout
  fn=filname(st.s)
  sprint(st.t,"RCS/%s,v",st.s)
  if (sfunc.len(fn.t)>0) {
    sprint(st.t,"%sRCS/%s,v",fn.t,fn.s)
    print st.s,"::",st.t,"::",fn.s,"::",fn.t
  } else if (fexists(st.t)) {
    if (rcshead(st.s)!=vers) {
      sprint(st.t,"cp -f %s %s.OLD",st.s,st.s)   system(st.t)
      sprint(st.t,"co -f -r1.%d %s",vers,st.s)   system(st.t)
    }
  } else { // look for file in remote location
    getenv("SITE",st.t)
    sprint(st.t,"%s/nrniv/local/hoc/%s",st.t,st.s)
    if (! fexists(st.t)) {printf("Can't find %s\n",st.t) return 0}
    sprint(st.s,"%s%d",st.s,vers)
    printf("Found %s at %s -> %s\n",$s1,st.t,st.s)
    sprint(st.t,"co -f -p1.%d %s > %s",vers,st.t,st.s) system(st.t)
  }
  if (numarg()>2) {
    if (argtype(3)==0) {  // 3rd arg 1 means do load_file statt xopen
      if ($3) { 
        load_file(st.s)
        return 1
      } else return 1 // 3rd arg 0 does co but no open
    } else { // 3rd arg string means locate a single proc, iter etc.
      sprint(st.s,"hocproc %s %s %s",st.s,$s3,".tmp")
      system(st.s,st.t)
      if (strm(st.t,"ERROR")) return 0 else {
        printf("Loading '%s()' from %s%d (via .tmp)\n",$s3,$s1,vers)
        xopen(".tmp")
        return 1
      } 
    }
  }
  xopen(st.s)
  return 1
}

//** simopen()
proc simopen () { local x localobj o,xo
  o=new List()
  if (numarg()==1) split(allfiles,o) else split(simfiles,o)
  for ltr(xo,o,&x) xopen(xo.s)
}

//** pxopen(FILE) prints out the version before opening a file
proc pxopen () { local flag localobj o
  flag=1
  o=new List("ParallelContext")
  if (o.count>0) if (o.o(0).id!=0) flag=0
  if (flag) printf("%s version %d\n",$s1,rcshead($s1))
  xopen($s1)
}

//** lrm(LIST,STR) will remove item with string from LIST
proc lrm () { local cnt
  cnt=0
  if (argtype(2)==2) {
    for ltrb(XO,$o1) if (strm(XO.s,$s2)) { $o1.remove(i1) cnt+=1 }
    printf("%s found %d time\n",$s2,cnt)
  } else {
    $o1.remove($o1.index($o2))
  }
}

//** lcnt(LIST,STR) will count item with string in LIST
func lcnt () { local cnt localobj xo
  cnt=0
  for ltr(xo,$o1) if (strm(xo.s,$s2)) cnt+=1
  return cnt
}

//** lrepl(LIST,#,OBJ) will replace item at location # with OBJ
proc lrepl () { $o1.remove($2) $o1.insrt($2,$o3) }

//** lswap(list,#1,#2) swap items on a list
proc lswap () { local a,b
  if ($2<$3) {a=$2 b=$3} else {a=$3 b=$2}
  $o1.insrt(a,$o1.object(b))
  $o1.remove(b+1)
  $o1.insrt(b+1,$o1.object(a+1))
  $o1.remove(a+1)
}

//** proc shl() show a list
proc shl () { 
  if (numarg()==1) tmpobj=$o1 else tmpobj=tmplist 
  if (tmpobj.count==0) return
  if (isstring(tmpobj.object(0),tstr)) {
    for ltr(XO,tmpobj) print XO.s
  } else for ltr(XO,tmpobj) print XO
}

//** lfu() = ltr follow-up, pick out a single item from the last ltr request
// lfu(list,num[,obj])
proc lfu () { 
  if (numarg()==1) { 
    if (argtype(1)==0) XO=tmpobj.object($1)
    if (argtype(1)==1) tmpobj=$o1
  }
  if (numarg()==2) {
    if (argtype(1)==1 && argtype(2)==0) {tmpobj=$o1 XO=$o1.object($2)}
    if (argtype(1)==0 && argtype(2)==1) {$o2=tmpobj.object($1)}
  }
  if (numarg()==3) {
    if (argtype(1)==1 && argtype(2)==0 && argtype(3)==1) { tmpobj=$o1 $o3=$o1.object($2) }
  }
  if (numarg()==4) {
    $o2=tmpobj.object($1)  $o4=tmpobj.object($3) 
  }
}

//** listedit() allows you to remove things by clicking
proc listedit () {
  if (numarg()==0) { print "listedit(list,str) gives browser(list,str) for removing items" return}
  if (numarg()==1) {
  if (! isstring($o1.object(0),temp_string_)) {print "Give name for string of object?" return }
    sprint(temp_string_,"proc ledt1 () {sprint(temp_string_,%s,hoc_ac_,%s.object(hoc_ac_).%s)}","\"%d:%s\"",$o1,"s")
  } else {
    sprint(temp_string_,"proc ledt1 () {sprint(temp_string_,%s,hoc_ac_,%s.object(hoc_ac_).%s)}","\"%d:%s\"",$o1,$s2)
  }
  execute1(temp_string_)
  $o1.browser("Double click to remove",temp_string_,"ledt1()")
  sprint(temp_string_,"%s.remove(hoc_ac_)",$o1)
  $o1.accept_action(temp_string_)
}

//** crac() create and access
proc crac () {
  execute("create acell_home_")
  execute("access acell_home_")
}

//** listXO() connects stuff to XO from a list
proc listXO () {
  if (numarg()==1) {
    $o1.browser("Double click")
    sprint(temp_string_,"print hoc_ac_,\":XO -> \",%s.object(hoc_ac_) XO = %s.object(hoc_ac_)",$o1,$o1)
    $o1.accept_action(temp_string_)
  } else if (numarg()==2) {
    $o1.browser($s2)
    sprint(temp_string_,"XO = %s.object(hoc_ac_) print %s.object(hoc_ac_).%s",$o1,$o1,$s2)
    $o1.accept_action(temp_string_)
  } else if (numarg()==3) {
    $o1.browser($s2)
    sprint(temp_string_,"XO = %s.object(hoc_ac_) print %s.object(hoc_ac_).%s,%s.object(hoc_ac_).%s",$o1,$o1,$s2,$o1,$s3)
    $o1.accept_action(temp_string_)
  }
}

//** lcatstr(list,s1,s2,...) make new List("s1") new List("s2") ... in one list
proc lcatstr() { local i
  if (numarg()<3) { print "lcatstr(l1,s1,s2,...) puts new Lists into l1" return }
  $o1 = new List($s2)
  for i=3,numarg() {
    tmplist2 = new List($si)
    for ltr(XO,tmplist2) { $o1.append(XO) }  
  }
}

//** sublist() places a sublist in LIST0 from LIST1 index BEGIN to END inclusive
proc sublist () { local ii
  $o1.remove_all
  for ii=$3,$4 {
    $o1.append($o2.object(ii))
  }
}

//* catlist() concats LIST2...LISTN on end of LIST1
proc catlist () { local i
  for i = 2, numarg() {
    for ltr(YO,$oi) {
      $o1.append(YO)
    }
  }
}  

//* mechlist() creates a LIST of all this CELL type's TEMPLATE type
// list, cell, template
// make a list of mechanisms belonging to a certain template
proc mechlist () { local num,ii
//  mchnms = ""  // not a good storage since runs out of room
  if (numarg()==0) { print "mechlist(list, cell, template)" return}
  $o1 = new List($s2)
  num = $o1.count
  for ii=0,num-1 {
    sprint(temp_string_,"%s.append(%s.%s)",$o1,$o1.object(ii),$s3)
    execute(temp_string_)
    sprint(mchnms,"%s/%d/%s.%s",mchnms,ii,$o1.object(ii),$s3)
  }
  for (ii=num-1;ii>=0;ii=ii-1) { $o1.remove(ii) }
}

//* lp() loop through a list running command in object's context
// assumes list in tmplist
// with 1 args run $o1.object().obj_elem
// with 2 args run comm($o1.object().obj_elem)
proc lp () {
  for ii=0,tmplist.count-1 {
    printf("%s ",tmplist.object(ii))
    if (numarg()==2) {
      sprint(temp_string_,"%s(%s.%s)",$s2,tmplist.object(ii),$s1)
    } else {
      sprint(temp_string_,"%s.%s",tmplist.object(ii),$s1)
    }
    execute(temp_string_)
  }
}

//* prlp() loop through a list printing object name and result of command
proc prlp () {
  tmpobj=tmplist
  if (numarg()>0) if (argtype(1)==1) tmpobj=$o1
  for ltr(XO,tmpobj) {
    printf("%d %s ",i1,XO)
    if (numarg()>1) {
      sprint(temp_string_,"print %s.%s",XO,$s2)
      execute(temp_string_)
    } else { print "" }
  }
}

//* String functions
//** repl_str(str,stra,strb): replace stra with strb in string
// will only replace first string match
proc repl_str() { localobj scr
  scr=new String()
  if (sfunc.head($s1,$s2,scr.s) == -1) { print $s2," not in ",$s1  return }
  sfunc.tail($s1,$s2,scr.s)
  sprint(scr.s,"%s%s",$s3,scr.s)
  sfunc.head($s1,$s2,$s1)
  sprint($s1,"%s%s",$s1,scr.s)
}

//** find_str(str,left,right): pull out dest flanked by left and right
obfunc find_str() { localobj st
  st=new String2()
  if (sfunc.tail($s1,$s2,st.t) == -1) { print $s2," not in ",$s1  return }
  sfunc.head(st.t,$s3,st.s)
  return st
}

//** find_num(str,left,right): pull out number flanked by left and right
func find_num() { local x localobj st
  st=new String()
  if (sfunc.tail($s1,$s2,st.s) == -1) { print $s2," not in ",$s1  return }
  sfunc.head(st.s,$s3,st.s)
  sscanf(st.s,"%g",&x)
  return x
}

//** repl_mstr(str,stra,strb): replace stra with strb in string
// multiple replace
proc repl_mstr () { localobj scr
  scr=new String()
  while (sfunc.head($s1,$s2,scr.s) != -1) {
    sfunc.tail($s1,$s2,scr.s)
    sprint(scr.s,"%s%s",$s3,scr.s)
    sfunc.head($s1,$s2,$s1)
    sprint($s1,"%s%s",$s1,scr.s)
  }
}

//** extract(str,stra,strb[,dest]): pull out piece of string surrounded by stra,strb
obfunc str_extract() { local b,e,err localobj scr
  scr=new String2() err=0
  b=sfunc.tail($s1,$s2,scr.s) // scr.s contains after s2
  if (b==-1){printf("%s not found in %s\n",$s2,$s1) err=1}
  e=sfunc.head(scr.s,$s3,scr.t) // beg of s3
  if (e==-1){printf("%s not found in %s\n",$s3,scr.s) err=1}
  if (err) scr.s="" else sfunc.left(scr.s,e)
  if (numarg()==4) $s4=scr.s
  return scr
}

//** clean_str(str,scratch,s1,s2,s3,...)
// remove serial $si from string
proc clean_str () { local i
  for i=3,numarg() {
    while (sfunc.head($s1,$si,$s2) != -1) { 
      sfunc.tail($s1,$si,$s2)
      sfunc.head($s1,$si,$s1)
      sprint($s1,"%s%s",$s1,$s2)      
    }
  }
}

//** aaaa() (or $o2) becomes a list of strings from file $s1
proc aaaa () { local flag
  if (numarg()==2) { tmpfile.ropen($s1) aa=$o2 flag=0
  } else if (numarg()==1) { tmpfile.ropen($s1) flag=1
  } else { tmpfile.ropen("aa") flag=1 }
  if (flag==1) if (isobj(aa,"List")) { aa.remove_all() } else { aa=new List() }
  while (tmpfile.gets(temp_string_)>0) {
    chop(temp_string_)
    tmpobj=new String(temp_string_)
    aa.append(tmpobj)
  }
  tmpobj=nil
}

//* Object identification
//** objid() find information about object -- replaces var2obj, canobj, objnum
obfunc objid () { local flag localobj xo
  xo=new Union()
  if (argtype(1)==1) sprint(xo.s,"tmpobj=%s",$o1) else sprint(xo.s,"tmpobj=%s",$s1)
  execute(xo.s) // change variable name to object name
  xo.o=tmpobj
  sprint(xo.s,"%s",xo.o)
  sscanf(xo.s,"%*[^[][%d]",&xo.x)
  return xo
}

//** var2obj() and canobj() -- find true object names
// var2obj("tstr"[,"objvar"]) replaces variable name with actual name of the object
// default into XO; optional second arg allows to place somewhere else
// eg tstr="TC[0].ampa" var2obj(tstr) -> AMPA[0]
proc var2obj () { local flag
  if (numarg()==1) flag=1 else flag=0
  if (flag) sprint($s1,"XO=%s",$s1) else sprint($s1,"%s=%s",$s2,$s1)
  execute($s1) // change variable name to object name
  if (flag) sprint($s1,"%s",XO) else sprint($s1,"%s",$s2)
  printf("var2obj() PLEASE REPLACE WITH objid()\n") 
}

//** objnum(OBJ) -- find object number
func objnum () { local x localobj st
  st=new String()
  if (argtype(1)==1) sprint(st.s,"%s",$o1) else st.s=$s1
  if (sscanf(st.s,"%*[^[][%d]",&x) != 1) x=-1
  return x
}

proc allobjs () {
  hoc_stdout($s1)
  allobjects()
  hoc_stdout()
}

//** strnum(str,"PRE") -- pull number out of a string
func strnum () { local x localobj st
  st=new String2($s1)
  sfunc.tail(st.s,$s2,st.t)
  if (sscanf(st.t,"%d",&x) != 1) x=-99e99
  return x
}

//** canobj(obj[,"OBJVAR"]) -- default will assign to XO
// canonical object -- return canonical identity for an object
// eg canobj(tc,"YO") -- figure out what tc is and assign it to YO
proc canobj () { local flag
  if (numarg()==1) flag=1 else flag=0
  if (flag) sprint(tstr,"XO=%s",$o1) else sprint(tstr,"%s=%s",$s2,$o1)
  execute(tstr) // change variable name to object name
  sprint(tstr,"%s",$o1)
  printf("canobj() PLEASE REPLACE WITH objid()\n") 
}

//* push() and pop() for objects -- returns
proc push () { local i
  for i=2,numarg() $o1.append($oi)
}

//** pop()
obfunc pop () { local i,cnt localobj o
  cnt=$o1.count-1
  if (cnt==-1) { print "ERR: unable to pop" return } 
  o=$o1.object(cnt)
  $o1.remove(cnt)
  return o
}

//* time()
strdef tmstr
tmstr="run()"
func time () { local tti,uintmax,cps
  uintmax=4294967295 // UINT_MAX/CLOCKS_PER_SEC
  cps=1e6 // CLOCKS_PER_SEC
  tti=prtime()
  system("date")
  if (numarg()==1) execute1($s1) else execute1(tmstr)
  tti=prtime()-tti
  if (tti<0) tti+=uintmax
  if (tti<cps) {           print tti/1e3,       "kilocycles" 
  } else if (tti<60*cps) { print tti/cps,   "s" 
  } else                   print tti/cps/60,"m"
  system("date")
  return tti/1e3
}

func ftime () { local tti
  prtime()
  if (numarg()==1) execute($s1) else execute(tmstr)
  tti=prtime()
  return tti
}

proc setdate () {
  system("date +%y%b%d",datestr)
  chop(datestr)
  downcase(datestr)
}

proc sortlist () { local a,err,ii,x,rev,na localobj v1,v2,xo,nl,il
  il=$o1
  err=rev=0
  na=numarg()
  for ii=2,3 if (na>=ii) if (argtype(ii)==0) rev=1
  a=allocvecs(v1,v2,il.count)
  nl=new List()
  if (!name_declared("oform")) err=1
  if (!err) if (oform(v1)==NOP) err=1
  if (err) {printf("sortlist uses oform()\n") error()}
  for ltr(xo,il) v1.append(oform(xo))
  v1.sortindex(v2)
  if (rev) v2.reverse
  for ii=0,v2.size-1 nl.append(il.o(v2.x[ii]))
  if ((na==2 && !rev) || na==3) $o2=nl else {
    il.remove_all
    for ltr(xo,nl) il.append(xo)
  }
  dealloc(a)
}

func assoc () { local i,ty,ii localobj xo
  // object_push(xo) ty=name_declared("s",1) object_pop() // strdef:4, dbl:5
  for ltr(xo,$o2,&ii) {
    if (argtype(1)==2) {
      if (strcmp(xo.s,$s1)==0) break
    } else if (argtype(1)==0) {
      if (xo.x==$1) break
    }
  }
  if ($o2.count==ii) return -1 else return ii
}

// assoco() like assoc but returns the object instead of the index
obfunc assoco () { local i,ty,ii localobj xo
  // object_push(xo) ty=name_declared("s",1) object_pop() // strdef:4, dbl:5
  for ltr(xo,$o2,&ii) {
    if (argtype(1)==2) {
      if (strcmp(xo.s,$s1)==0) break
    } else if (argtype(1)==0) {
      if (xo.x==$1) break
    }
  }
  if ($o2.count==ii) return nil else return xo
}

// excu() does the associative search and executes the resultant string 
// eg excu("key",list) excu("key",list,"arg1"[,"arg2","arg3"...]) 
func excu () { local i,ty,ii localobj xo,o,st
  o=$o2
  // object_push(xo) ty=name_declared("s",1) object_pop() // strdef:4, dbl:5
  for ltr(xo,o,&ii) {
    if (argtype(1)==2) {
      if (strcmp(xo.s,$s1)==0) break
    } else if (argtype(1)==0) {
      if (xo.x==$1) break
    }
  }
  if (o.count!=ii) {
    if (sfunc.len(xo.t)==0) return 0 // empty string
    st=strcat(st,"hoc_ac_=",xo.t,"(")
    if (numarg()>2) { 
      for i=3,numarg() {
        if (argtype(i)==2) { sprint(st.s,"%s%s,",st.s,$si)
        } else if (argtype(i)==0) { sprint(st.s,"%s%g,",st.s,$i)
        } else if (argtype(i)==1) { sprint(st.s,"%s%s,",st.s,$oi) }
      }
      chop(st.s)
    }
    strcat(st,")")
    execute(st.s)    // print st.s
    return hoc_ac_
  } else return 0
}

// LAR: list_array is list used as an array
begintemplate LAR
public l,set,x,size,nil,resize,get,lt
objref l,nil
double size[1]

proc init () { local ii
  size=$1
  l=new List()
  for ii=0,size-1 l.append(l) // place holder
}

func set () { local ix
  ix=$1
  if (ix>=size) {printf("LAR set OOR %d>=%d\n",ix,size) return -1}
  l.remove(ix) l.insrt(ix,$o2) 
  return ix
}

obfunc x ()   { if (eqojt(l,l.o($1))) return nil else return l.o($1) }
obfunc get () { if (eqojt(l,l.o($1))) return nil else return l.o($1) }

proc resize () { local newsz,ii
  newsz=$1
  if (newsz<size) {
    for (ii=size-1;ii>=newsz;ii-=1) l.remove(ii)
  } else if (newsz>size) {
    for ii=size,newsz-1 l.append(l)
  }
  size=newsz
}

iterator lt () { local ii
  for ii=0,size-1 if (!eqojt(l,l.o(ii))) { 
    $o1=l.o(ii)
    iterator_statement
  }
}
endtemplate LAR

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]

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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]

   Motor system model with reinforcement learning drives virtual arm (Dura-Bernal et al 2017) [Model]

Dura-Bernal S, Zhou X, Neymotin SA, Przekwas A, Francis JT, Lytton WW (2015) Cortical Spiking Network Interfaced with Virtual Musculoskeletal Arm and Robotic Arm. Front Neurorobot 9:13 [Journal] [PubMed]

   Cortical model with reinforcement learning drives realistic virtual arm (Dura-Bernal et al 2015) [Model]

Kerr CC, Van Albada SJ, Neymotin SA, Chadderdon GL, Robinson PA, Lytton WW (2013) Cortical information flow in Parkinson's disease: a composite network-field model. Front Comput Neurosci 7:39:1-14 [Journal] [PubMed]

   Composite spiking network/neural field model of Parkinsons (Kerr et al 2013) [Model]

Neymotin SA, Chadderdon GL, Kerr CC, Francis JT, Lytton WW (2013) Reinforcement learning of 2-joint virtual arm reaching in a computer model of sensorimotor cortex Neural Computation 25(12):3263-93 [Journal] [PubMed]

   Sensorimotor cortex reinforcement learning of 2-joint virtual arm reaching (Neymotin et al. 2013) [Model]

Neymotin SA, Dura-Bernal S, Lakatos P, Sanger TD, Lytton WW (2016) Multitarget Multiscale Simulation for Pharmacological Treatment of Dystonia in Motor Cortex. Front Pharmacol 7:157 [Journal] [PubMed]

   Multitarget pharmacology for Dystonia in M1 (Neymotin et al 2016) [Model]

Neymotin SA, Lee H, Park E, Fenton AA, Lytton WW (2011) Emergence of physiological oscillation frequencies in a computer model of neocortex. Front Comput Neurosci 5:19-75 [Journal] [PubMed]

   Emergence of physiological oscillation frequencies in neocortex simulations (Neymotin et al. 2011) [Model]

Rowan MS, Neymotin SA, Lytton WW (2014) Electrostimulation to reduce synaptic scaling driven progression of Alzheimer's disease. Front Comput Neurosci 8:39 [Journal] [PubMed]

   Electrostimulation to reduce synaptic scaling driven progression of Alzheimers (Rowan et al. 2014) [Model]

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