Thalamic quiescence of spike and wave seizures (Lytton et al 1997)

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A phase plane analysis of a two cell interaction between a thalamocortical neuron (TC) and a thalamic reticularis neuron (RE).
1 . Lytton WW, Contreras D, Destexhe A, Steriade M (1997) Dynamic interactions determine partial thalamic quiescence in a computer network model of spike-and-wave seizures. J Neurophysiol 77:1679-96 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Thalamus;
Cell Type(s): Thalamus geniculate nucleus (lateral) principal neuron; Thalamus reticular nucleus cell;
Channel(s): I T low threshold;
Gap Junctions:
Receptor(s): GabaA; Glutamate;
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Temporal Pattern Generation; Oscillations; Calcium dynamics;
Implementer(s): Lytton, William [billl at]; Destexhe, Alain [Destexhe at];
Search NeuronDB for information about:  Thalamus geniculate nucleus (lateral) principal neuron; Thalamus reticular nucleus cell; GabaA; Glutamate; I T low threshold; Gaba; Glutamate;
calciumpump_destexhe.mod *
HH_traub.mod *
Ih_old.mod *
presyn.mod *
pulse.mod *
boxes.hoc *
declist.hoc *
decvec.hoc *
default.hoc *
local.hoc *
nrnoc.hoc *
params.hoc * *
simctrl.hoc * * *
// $Id: decvec.hoc,v 1.63 2001/06/14 21:13:40 billl Exp $

proc decvec() {}

//* Declarations
objref ind, vec, vec0, vec1, tmpvec, vrtmp, veclist
objref tmpobj, XO, YO, rdm
load_file("declist.hoc")  // declare list iterators
print "Loading decvec"

{ MSONUM=100 MSOSIZ=100 msomax=0 msoptr=0 objref mso[MSONUM] }
double x[4],y[4]
xx=0 // declare a scalar 
ind = new Vector(100)
vec = new Vector(100)
vec0 = new Vector()
vec1 = new Vector()
vrtmp = new Vector()
veclist = new List()
rdm = new Random()

if (! xwindows) {
  objref graphItem
  strdef temp_string_, temp_string2_
strdef xtmp
if (wopen("xtmp")) xtmp = "xtmp" else xtmp="/tmp/xtmp"  // scratch file to save system output to

//* stuff that doesn't belong here
objref dir
dir = new List()
//** dired(list,file) - put together list of files matching 'file', calls 'ls -1 file'
//   dired(list,file,1) file name to read for list of files
proc dired () {
  if (numarg()==0) { print "dired(list,filename) adds the filename to list (use wildcards)"
    return }
  if (numarg()==3) { 
  } else {
    sprint(temp_string_,"ls -1R %s > %s",$s2,xtmp) // list in order of creation time
  while (tmpfile.scanstr(temp_string_) != -1) {
    tmpobj=new String()
    tmpfile.gets(temp_string_)  // get rid of the rest of the line

//** lbrw(list,name,action) is used to put up a browser
// note action given without '()'
proc lbrw () {

//* vector iterator vtr
// usage 'for vtr(&x, vec) { print x }'
iterator vtr() { local i
  if (numarg()==3) {$&3=0} else {i1 = 0}
  for i = 0, $o2.size() - 1 {
    $&1 = $o2.x[i]
    if (numarg()==3) { $&3+=1 } else { i1+=1 }

//* vector iterator vtr2, treat two vectors as pairs
// usage 'for vtr2(&x, &y, vec1, vec2) { print x,y }'
iterator vtr2() { local i
  if ($o3.size != $o4.size) { print "vtr2 ERROR: sizes differ." return }
  if (numarg()==5) {$&5=0} else {i1 = 0}
  for i = 0, $o3.size() - 1 {
    $&1 = $o3.x[i]
    $&2 = $o4.x[i]
    if (numarg()==5) { $&5+=1 } else { i1+=1 }

//* iterator lvtr, step through a list and a vector together
// usage 'for lvtr(XO, &x, list, vec) { print XO,x }'
iterator lvtr() { local i
  if ($o3.count <  $o4.size) { print "lvtr ERROR: vecsize>listsize." return }
  if ($o3.count != $o4.size) { print "lvtr WARNING: sizes differ." }
  if (numarg()==5) {$&5=0} else {i1 = 0}
  for i = 0, $o4.size()-1 {
    $o1 = $o3.object(i)
    $&2 = $o4.x[i]
    if (numarg()==5) { $&5+=1 } else { i1+=1 }

//* other iterators: case, scase, ocase
iterator case() { local i
  i1 = 0
  for i = 2, numarg() {
    $&1 = $i

iterator scase() { local i
  i1 = 0
  for i = 1, numarg() {
    temp_string_ = $si

// eg for scase2("a","b","c","d","e","f") print temp_string_,temp_string2_
iterator scase2() { local i
  i1 = 0
  if (numarg()%2==1) {print "ERROR: scase2 needs even number of args" return }
  for i = 1, numarg() {
    tmpobj=new String2()
    tmpobj.s=$si i+=1  tmpobj.t=$si

iterator ocase() { local i
  i1 = 0
  for i = 1, numarg() {
    XO = $oi

//* nind(targ,data,ind) fill the target vector with data NOT index by ind (opposite of v.index)
proc nind () { 
  if (! eqobj($o1,$o2)) $o1.copy($o2)

//* vlk(vec)
// vlk(vec,max)
// vlk(vec,min,max)
// prints out a segment of a vector
proc vlk () { local i,j,min,max,dual,wdh,nonl
  j=dual=0 nl=1 wdh=vlk_width
  if (numarg()==1) { min=0 max=$o1.size-1 }
  if (numarg()==2) if ($2==0) { nl=min=0 max=$o1.size-1 // vlk(vec,0) flag to suppress new lines
      } else if ($2>0) { min=0 max=$2-1 } else { min=$o1.size+$2 max=$o1.size-1 }
  if (numarg()==3) if ($3>-1) { min=$2 max=$3 } else { min=0 max=$o1.size-1 dual=1 }
  if (numarg()==4) { min=$3 max=$4 dual=1 }
  if (min<0) min=0
  if (max>$o1.size-1) max=$o1.size-1
  if (dual) if (max>$o2.size-1) max=$o2.size-1
  for i=min,max { 
    if (dual) printf("%g:%g ",$o1.x[i],$o2.x[i]) else printf("%g ",$o1.x[i]) 
    if ((j=j+1)%vlk_width==0 && nl) { print "" }
  if (nl) print ""

//* vprf() prints 1,2 or 3 vectors in parallel to output file
proc vprf () { local x2
  if (! tmpfile.isopen()) {
    print "Writing to temp file 'temp'"
  if (numarg()==1) { 
    for vtr(&x,$o1) { tmpfile.printf("%g\n",x) }
  } else if (numarg()==2) { 
    for vtr2(&x,&y,$o1,$o2) { tmpfile.printf("%g %g\n",x,y) }
  } else if (numarg()==3) { 
    for vtr2(&x,&y,$o1,$o2,&ii) { x2=$o3.x[ii] tmpfile.printf("%g %g %g\n",x,y,x2) }

//* vpr() prints 1,2 or 3 vectors in parallel to STDOUT
proc vpr () { local x2
  if (numarg()==1) { 
    for vtr(&x,$o1) { printf("%g ",x) }
  } else if (numarg()==2) { 
    for vtr2(&x,&y,$o1,$o2) { printf("%g:%g ",x,y) }
  } else if (numarg()==3) { 
    for vtr2(&x,&y,$o1,$o2,&ii) { x2=$o3.x[ii] printf("%g:%g:%g ",x,y,x2) }
  print ""

//* readvec(vec) read from line
proc readvec () { 
  while (read(xx)) $o1.append(xx)
//* popvec(), savenums, readnums, vecsprint, savevec
proc pushvec () { local i // same as .append, retained for compatability
  for i=2, numarg() $o1.append($i)

proc revec () { local i // clear vector then append
  for i=2, numarg() $o1.append($i)

// savenums(x[,y,...]) save numbers to tmpfile via a vector
proc savenums () { local vv,i
  for i=1, numarg() mso[vv].append($i)

// readnums(&x[,&y...]) recover nums from tmpfile via a vector
proc readnums () { local vv,i
  if (numarg()!=mso[vv].size) { print "Error: size in readnums" return }
  for i=1,numarg() $&i = mso[vv].x[i-1]

//* remove last entry
func popvec () { local sz, ret
  sz = $o1.size-1
  ret = $o1.x[sz]
  return ret

//* chkvec (look at last entry)
func chkvec () { if ($o1.size>0) return $o1.x[$o1.size-1] else return -1e10 }

// vecsprint(strdef,vec)
proc vecsprint () { local ii
  if ($o2.size>100) { return }
  for ii=0,$o2.size-1 { sprint($s1,"%s %g ",$s1,$o2.x[ii]) }

// savevec([list,]vec1[,vec2,...]) add vector onto veclist or other list if given as 1st arg
proc savevec () { local i,flag,beg
  if (isobj($o1,"List")) beg=2 else beg=1
  for i=beg, numarg() { 
    tmpvec = new Vector($oi.size)
    if (beg==2) $o1.append(tmpvec) else veclist.append(tmpvec)
    tmpvec = nil

// tvecl() -- transpose veclist
proc tvecl () { local cnt,sz,err,ii,p
  err = 0
  cnt = veclist.count
  sz = veclist.object(0).size
  for ltr(XO,veclist) if (XO.size!=sz) err=i1
  if (err) { print "Wrong size vector is #",i1 return }
  p = allocvecs(1,cnt)  mso[p].resize(cnt)
  for ii=0,sz-1 {
    for jj=0,cnt-1 {
      mso[p].x[jj] = XO.x[ii]
  for (jj=cnt-1;jj>=0;jj-=1) veclist.remove(jj)

//* vinsect(v1,v2,v3) -- v1 gets intersection (common members) of v2,v3
//  replaced by v.insct() in vecst.mod
proc vinsect () {
  for vtr(&x,$o2) for vtr(&y,$o3) if (x==y) $o1.append(x)

//* vecsplit(vec,vec1,vec2[,vec3,...])
// splits vec into other vecs given
proc vecsplit () { local num,ii,i
  num = numarg()-1 // how many
  for i=2,numarg() $oi.resize(0)
  for (ii=0;ii<$o1.size;ii+=num) {
    for i=2,numarg() if (ii+i-2<$o1.size) $oi.append($o1.x[ii+i-2])

//* vecsort(vec,vec1,vec2[,vec3,...])
// sorts n vecs including first vec by first one
proc vecsort () { local i,inv,scr,narg
  if (narg<2 || narg>10) {print "Wrong #args in decvec.hoc:vecsort" return}
  scr=inv=allocvecs(2) scr+=1
  for i=3,narg sprint(temp_string_,"%s,%s",temp_string_,$oi)

//* vdelind()  -- delete a single index
proc vdelind () { local i,iin
  iin = $2
  if (iin<0) iin=$o1.size+iin
  if (iin>$o1.size-1 || iin<0) {
    printf("vdelind Error: index %d doesn't exist.\n",iin) return }
  if (iin<$o1.size-1) $o1.copy($o1,iin,iin+1,$o1.size-1)

//* mkveclist(num[,sz]) recreate veclist to have NUM vecs each of size SZ (or MSOSIZ)
proc mkveclist () { local ii,num,sz,diff
  diff = num-veclist.count
  if (numarg()==2) { sz=$2 } else { sz = MSOSIZ }
  if (diff>0) {
    for ii=0,diff-1 {
    tmpvec = new Vector(sz)
  } else if (diff<0) {
    for (ii=veclist.count-1;ii>=num;ii=ii-1) { veclist.remove(ii) }
  for ltr(XO,veclist) { XO.resize(sz) }

//* allocvecs
// create temp set of vectors on mso
// returns starting point on mso 
// eg p = allocvecs(3)
// access these vectors by mso[p+0] ... [p+2]
func allocvecs () { local ii, llen, sz, newv
  if (numarg()==0) { print "p=allocvecs(#), access with mso[p], mso[p+1]..." return 0}
  newv = $1
  if (numarg()==2) { sz=$2 } else { sz=MSOSIZ }
  llen = msoptr
  for ii=msomax,msoptr+newv-1 { // may need new vectors
    if (ii>=MSONUM) { print "alloc ERROR: MSONUM exceeded." return 0 }
    mso[ii] = new Vector(sz)
  for ii=0,newv-1 {
    msoptr = msoptr+1
  if (msomax<msoptr) msomax = msoptr
  return llen

//** dealloc(start)
// remove temp set of vectors from mso
proc dealloc () { local ii,min
  if (numarg()==0) { min = 0 } else { min = $1 }
  msomax = msoptr
  msoptr = min

//* vecconcat(vec1,vec2,...)
// destructive: concatenates all vecs onto vec1
proc vecconcat () { local i
  if (numarg()<2) { print "vecconcat(v1,v2,...) puts all into v1" return }
  for i=2,numarg() {
//** vecelim(v1,v2)  eliminates items in v1 given by index vec v2
proc vecelim () {
  for vtr(&x,$o2) { $o1.x[x]= -1e20 }

//** veceq()  like vec.eq but don't have to be same size and shows discrepency
func veceq () { local sz1,sz2,eq,beg,ii,jj,kk
  sz1=$o1.size sz2=$o2.size
  if (numarg()==3) beg=$3 else beg=0
  if (sz1!=sz2) printf("%s %d; %s %d\n",$o1,sz1,$o2,sz2)
  ii=0 jj=beg
  while (ii<sz1 && jj<sz2) {
    if ($o1.x[ii]!=$o2.x[jj]) { 
      printf("Differ at %d %d\n",ii,jj) 
      for kk=-10,10 if ((ii+kk)>=0 && (ii+kk)<sz1 && (jj+kk)>=0 && (jj+kk)<sz2) {
        printf("(%d)%g:(%d)%g ",(ii+kk),$o1.x[ii+kk],(jj+kk),$o2.x[jj+kk])  }
      print ""
    } else eq=1
    ii+=1 jj=ii+beg
  return eq

//* isstring() determine if object $o1 is of type string, if so return the string in $s2
func isstring () {
  if (sfunc.substr($s2,"String")==0) {
    return 1
  } else {
    return 0

//** isassigned() checks whether an object is Null
func isassigned () {
  if (sfunc.substr(temp_string_,"NULLobject")==0) {
    return 0
  } else {
    return 1

//** eqobj(o1,o2) checks whether 2 objects are the same
func eqobj () {	return object_id($o1) == object_id($o2) }

//** isobj(o1,s2) checks whether object $o1 is of type $s2
func isobj () {
  if (sfunc.substr(temp_string_,$s2)==0) {
    return 1
  } else {
    return 0

// destructive of $s1
func str2num () { local ii
  return x

// like perl chop -- removes the last character
proc chop () { sfunc.left($s1,sfunc.len($s1)-1) }

// newlst() puts a newline in the middle of a string
proc newlst () { local l
  if (numarg()>1) l=$2 else l=int(sfunc.len($s1)/2)

Lytton WW, Contreras D, Destexhe A, Steriade M (1997) Dynamic interactions determine partial thalamic quiescence in a computer network model of spike-and-wave seizures. J Neurophysiol 77:1679-96[PubMed]

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