CA3 Network Model of Epileptic Activity (Sanjay et. al, 2015)

 Download zip file   Auto-launch 
Help downloading and running models
This computational study investigates how a CA3 neuronal network consisting of pyramidal cells, basket cells and OLM interneurons becomes epileptic when dendritic inhibition to pyramidal cells is impaired due to the dysfunction of OLM interneurons. After standardizing the baseline activity (theta-modulated gamma oscillations), systematic changes are made in the connectivities between the neurons, as a result of step-wise impairment of dendritic inhibition.
1 . Sanjay M, Neymotin SA, Krothapalli SB (2015) Impaired dendritic inhibition leads to epileptic activity in a computer model of CA3. Hippocampus 25:1336-50 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Extracellular;
Brain Region(s)/Organism:
Cell Type(s): Hippocampus CA3 pyramidal cell; Hippocampus CA3 basket cell; Hippocampus CA3 stratum oriens lacunosum-moleculare interneuron;
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s): HCN1; HCN2;
Simulation Environment: NEURON; Python;
Model Concept(s): Activity Patterns; Oscillations; Pathophysiology; Epilepsy; Brain Rhythms;
Implementer(s): Neymotin, Sam [samn at]; Sanjay, M [msanjaycmc at];
Search NeuronDB for information about:  Hippocampus CA3 pyramidal cell; Hippocampus CA3 basket cell; GabaA; AMPA; NMDA;
CA1ih.mod *
CA1ika.mod *
CA1ikdr.mod *
CA1ina.mod *
caolmw.mod *
capr.mod *
icaolmw.mod *
icapr.mod *
iholmkop.mod *
iholmw.mod *
ihpyrkop.mod *
kahppr.mod *
kaolmkop.mod *
kapyrkop.mod *
kcaolmw.mod *
kcpr.mod *
kdrbwb.mod *
kdrolmkop.mod *
kdrpr.mod *
kdrpyrkop.mod *
misc.mod *
MyExp2Syn.mod *
MyExp2SynAlpha.mod *
MyExp2SynBB.mod *
MyExp2SynNMDA.mod *
MyExp2SynNMDABB.mod *
nafbwb.mod *
nafolmkop.mod *
nafpr.mod *
nafpyrkop.mod *
vecst.mod *
wrap.mod * *
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
Epileptic Activity.png
geom.hoc * *
grvec.hoc *
init.hoc *
labels.hoc *
local.hoc *
misc.h * *
nqs.hoc *
nqs_utils.hoc *
nrnoc.hoc * *
simctrl.hoc *
stats.hoc *
syncode.hoc *
xgetargs.hoc *
// $Id: declist.hoc,v 1.157 2010/12/07 14:19:28 billl Exp $

//* 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)
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]=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
  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,$oi)
    s="" // used as temp storage only
  } else if (argtype(1)==1 && argtype(2)==0 && argtype(3)==-1) {
    // printf("Union WARNING: taking single element out of a Vector or List\n")
    if (argtype(1)==1) {
      if (isobj($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() {
    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",$si) }
    } else if (ii==1) { 
      if (ox<sz) { o[ox]=$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)

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

proc list () { local flag
  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]) }
  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]) }
  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])
  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
  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) 
  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
  if (ii==ERR) {printf("Union:og (num get) failed -- \"%s\" not found\n",$s1) return ERR}
  return x[ii] 
// xg() associative get of an obj
obfunc og () { local ii
  if (ii==ERR) {printf("Union:og (obj get) failed -- \"%s\" not found\n",$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=$1 // an index
  } else {
    i=2 ii=fi(xl,$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}
  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 // $1 is an index
  } else {
    i=2 ii=fi(ol,$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}
  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=$si i+=1 
    if ((ty=argtype(i))==0) xo=xl else if (ty==1 || ty==2) xo=ol // use String() for strings
    if (ii==ERR) {
      if (fif==-1) {printf("UNION:set() ERRB: %s full for type %d\n",this,ty)  return ERR}
    if (ty==0) x[ii]=$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}
  } 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 = $o1.object(i)
  } else {
    if (max==1e9) max=$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)
      if (ifl) { $&3+=1 } else { i1+=1 }
    $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) {
    for (i=$o1.count()-1;i>=0;i-=1) {
      XO = $o1.object(i)
    tmpobj=$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)
      if (numarg()==3) { $&3-=1 } else { i1-=1 }
    $o1 = nil

//** list iterator ltr2
// usage 'for ltr2(XO, YO, list1, list2) { print XO,YO }'
iterator ltr2() { local i,cnt
  if (numarg()==5) $&5=0 else i1=0
  if ($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)
    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)
    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)
    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()
  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) {
  } else st.t=$s1
  sprint(st.s,"head -1 %s",st.t)
  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)
  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()
    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 }
    return ret
  if (numarg()>1) vers=$2 else vers=0
  if (! vers) vers=rcshead(st.s,1) // vers=0 means get latest version
  // do checkout
  if (sfunc.len(fn.t)>0) {
    print st.s,"::",st.t,"::",fn.s,"::",fn.t
  } else if (fexists(st.t)) {
    if (rcshead(st.s)!=vers) {
      sprint(st.t,"cp -f %s %s.OLD",st.s,st.s)   system(st.t)
      sprint(st.t,"co -f -r1.%d %s",vers,st.s)   system(st.t)
  } else { // look for file in remote location
    if (! fexists(st.t)) {printf("Can't find %s\n",st.t) return 0}
    printf("Found %s at %s -> %s\n",$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 ($3) { 
        return 1
      } else return 1 // 3rd arg 0 does co but no open
    } else { // 3rd arg string means locate a single proc, iter etc.
      sprint(st.s,"hocproc %s %s %s",st.s,$s3,".tmp")
      if (strm(st.t,"ERROR")) return 0 else {
        printf("Loading '%s()' from %s%d (via .tmp)\n",$s3,$s1,vers)
        return 1
  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
  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))

//** lrm(LIST,STR) will remove item with string from LIST
proc lrm () { local cnt
  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 {

//** lcnt(LIST,STR) will count item with string in LIST
func lcnt () { local cnt localobj xo
  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}

//** 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)
  $o1.browser("Double click to remove",temp_string_,"ledt1()")

//** 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,$o1)
  } else if (numarg()==2) {
    sprint(temp_string_,"XO = %s.object(hoc_ac_) print %s.object(hoc_ac_).%s",$o1,$o1,$s2)
  } else if (numarg()==3) {
    sprint(temp_string_,"XO = %s.object(hoc_ac_) print %s.object(hoc_ac_).%s,%s.object(hoc_ac_).%s",$o1,$o1,$s2,$o1,$s3)

//** 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
  for ii=$3,$4 {

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

//* 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 {
  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) {
    } else {

//* prlp() loop through a list printing object name and result of command
proc prlp () {
  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)
    } 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 }

//** 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 }
  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 }
  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) {

//** 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) { 

//** 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) {
    tmpobj=new String(temp_string_)

//* 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
  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 () {

//** strnum(str,"PRE") -- pull number out of a string
func strnum () { local x localobj st
  st=new String2($s1)
  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
  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
  if (cnt==-1) { print "ERR: unable to pop" return } 
  return o

//* time()
strdef tmstr
func time () { local tti,uintmax,cps
  uintmax=4294967295 // UINT_MAX/CLOCKS_PER_SEC
  cps=1e6 // CLOCKS_PER_SEC
  if (numarg()==1) execute1($s1) else execute1(tmstr)
  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"
  return tti/1e3

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

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

proc sortlist () { local a,err,ii,x,rev,na localobj v1,v2,xo,nl,il
  for ii=2,3 if (na>=ii) if (argtype(ii)==0) rev=1
  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))
  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 {
    for ltr(xo,nl) il.append(xo)

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
  // 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==$1) break
  if (o.count!=ii) {
    if (sfunc.len(xo.t)==0) return 0 // empty string
    if (numarg()>2) { 
      for i=3,numarg() {
        if (argtype(i)==2) { sprint(st.s,"%s%s,",st.s,$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) }
    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
  l=new List()
  for ii=0,size-1 l.append(l) // place holder

func set () { local ix
  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
  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)

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

Sanjay M, Neymotin SA, Krothapalli SB (2015) Impaired dendritic inhibition leads to epileptic activity in a computer model of CA3. Hippocampus 25:1336-50[PubMed]

References and models cited by this paper

References and models that cite this paper

Barbarosie M, Avoli M (1997) CA3-driven hippocampal-entorhinal loop controls rather than sustains in vitro limbic seizures. J Neurosci 17:9308-14 [PubMed]

Bihi RI, Jefferys JG, Vreugdenhil M (2005) The role of extracellular potassium in the epileptogenic transformation of recurrent GABAergic inhibition. Epilepsia 46 Suppl 5:64-71 [Journal] [PubMed]

Bikson M, Hahn PJ, Fox JE, Jefferys JG (2003) Depolarization block of neurons during maintenance of electrographic seizures. J Neurophysiol 90:2402-8 [PubMed]

Borhegyi Z, Varga V, Szilágyi N, Fabo D, Freund TF (2004) Phase segregation of medial septal GABAergic neurons during hippocampal theta activity. J Neurosci 24:8470-9 [PubMed]

Buhl EH, Halasy K, Somogyi P (1994) Diverse sources of hippocampal unitary inhibitory postsynaptic potentials and the number of synaptic release sites. Nature 368:823-8 [PubMed]

Carnevale NT, Hines ML (2006) The NEURON Book

Cobb SR, Halasy K, Vida I, Nyiri G, Tamas G, Buhl EH, Somogyi P (1997) Synaptic effects of identified interneurons innervating both interneurons and pyramidal cells in the rat hippocampus. Neuroscience 79:629-48 [PubMed]

Colgin LL, Moser EI (2010) Gamma oscillations in the hippocampus. Physiology (Bethesda) 25:319-29 [PubMed]

Cooke SF, Bliss TV (2006) Plasticity in the human central nervous system. Brain 129:1659-73 [PubMed]

Cossart R, Dinocourt C, Hirsch JC, Merchan-Perez A, De Felipe J, Ben-Ari Y, Esclapez M, Berna (2001) Dendritic but not somatic GABAergic inhibition is decreased in experimental epilepsy. Nat Neurosci 4:52-62 [PubMed]

Curley AA, Lewis DA (2012) Cortical basket cell dysfunction in schizophrenia. J Physiol 590:715-24 [Journal] [PubMed]

Cymerblit-Sabba A, Schiller Y (2012) Development of hypersynchrony in the cortical network during chemoconvulsant-induced epileptic seizures in vivo. J Neurophysiol 107:1718-30 [Journal] [PubMed]

Dinocourt C, Petanjek Z, Freund TF, Ben-Ari Y, Esclapez M (2003) Loss of interneurons innervating pyramidal cell dendrites and axon initial segments in the CA1 region of the hippocampus following pilocarpine-induced seizures. J Comp Neurol 459:407-25 [Journal] [PubMed]

Dragoi G, Carpi D, Recce M, Csicsvari J, Buzsáki G (1999) Interactions between hippocampus and medial septum during sharp waves and theta oscillation in the behaving rat. J Neurosci 19:6191-9 [PubMed]

Dudek FE,Stanley KJ (2007) How does the balance of excitation and inhibition shift during epileptogenesis? Epilepsy Curr 7:86-88

Dzhala VI, Staley KJ (2003) Transition from interictal to ictal activity in limbic networks in vitro. J Neurosci 23:7873-80 [PubMed]

El-Hassar L, Milh M, Wendling F, Ferrand N, Esclapez M, Bernard C (2007) Cell domain-dependent changes in the glutamatergic and GABAergic drives during epileptogenesis in the rat CA1 region. J Physiol 578:193-211 [PubMed]

Furman M (2013) Seizure initiation and propagation in the pilocarpine rat model of temporal lobe epilepsy. J Neurosci 33:16409-11 [Journal] [PubMed]

Gloveli T, Dugladze T, Rotstein HG, Traub RD, Monyer H, Heinemann U, Whittington MA, Kopell N (2005) Orthogonal arrangement of rhythm-generating microcircuits in the hippocampus. Proc Natl Acad Sci U S A 102:13295-300 [Journal] [PubMed]

   Gamma and theta rythms in biophysical models of hippocampus circuits (Kopell et al. 2011) [Model]

Hines ML, Davison AP, Muller E (2009) NEURON and Python Frontiers in Neuroinformatics 3:1 [Journal] [PubMed]

   NEURON + Python (Hines et al. 2009) [Model]

Jahr CE, Stevens CF (1990) Voltage dependence of NMDA-activated macroscopic conductances predicted by single-channel kinetics. J Neurosci 10:3178-82 [PubMed]

Jung S, Warner LN, Pitsch J, Becker AJ, Poolos NP (2011) Rapid loss of dendritic HCN channel expression in hippocampal pyramidal neurons following status epilepticus. J Neurosci 31:14291-5 [Journal] [PubMed]

Karlócai MR, Kohus Z, Káli S, Ulbert I, Szabó G, Máté Z, Freund TF, Gulyás AI (2014) Physiological sharp wave-ripples and interictal events in vitro: what's the difference? Brain 137:463-85 [Journal] [PubMed]

Kurz JE, Moore BJ, Henderson SC, Campbell JN, Churn SB (2008) A cellular mechanism for dendritic spine loss in the pilocarpine model of status epilepticus. Epilepsia 49:1696-710 [Journal] [PubMed]

Lazarewicz MT, Migliore M, Ascoli GA (2002) A new bursting model of CA3 pyramidal cell physiology suggests multiple locations for spike initiation. Biosystems 67:129-37 [Journal] [PubMed]

   CA3 pyramidal neuron (Lazarewicz et al 2002) [Model]

Leite JP, Neder L, Arisi GM, Carlotti CG, Assirati JA, Moreira JE (2005) Plasticity, synaptic strength, and epilepsy: what can we learn from ultrastructural data? Epilepsia 46 Suppl 5:134-41 [Journal] [PubMed]

Lytton WW (2008) Computer modelling of epilepsy. Nat Rev Neurosci 9:626-37 [Journal] [PubMed]

Lytton WW, Orman R, Stewart M (2005) Computer simulation of epilepsy: implications for seizure spread and behavioral dysfunction. Epilepsy Behav 7:336-44 [Journal] [PubMed]

Maglóczky Z, Freund TF (2005) Impaired and repaired inhibitory circuits in the epileptic human hippocampus. Trends Neurosci 28:334-40 [Journal] [PubMed]

Manganotti P, Miniussi C, Santorum E, Tinazzi M, Bonato C, Marzi CA, Fiaschi A, Dalla Bernard (1998) Influence of somatosensory input on paroxysmal activity in benign rolandic epilepsy with 'extreme somatosensory evoked potentials'. Brain 121 ( Pt 4):647-58 [PubMed]

McAllister AK (2000) Cellular and molecular mechanisms of dendrite growth. Cereb Cortex 10:963-73 [PubMed]

Middleton S, Jalics J, Kispersky T, Lebeau FE, Roopun AK, Kopell NJ, Whittington MA, Cunningh (2008) NMDA receptor-dependent switching between different gamma rhythm-generating microcircuits in entorhinal cortex. Proc Natl Acad Sci U S A 105:18572-7 [PubMed]

Navarro Mora G, Bramanti P, Osculati F, Chakir A, Nicolato E, Marzola P, Sbarbati A, Fabene P (2009) Does pilocarpine-induced epilepsy in adult rats require status epilepticus? PLoS One 4:e5759 [Journal] [PubMed]

Neymotin SA, Lazarewicz MT, Sherif M, Contreras D, Finkel LH, Lytton WW (2011) Ketamine disrupts theta modulation of gamma in a computer model of hippocampus Journal of Neuroscience 31(32):11733-11743 [Journal] [PubMed]

   Ketamine disrupts theta modulation of gamma in a computer model of hippocampus (Neymotin et al 2011) [Model]

Ren H, Shi YJ, Lu QC, Liang PJ, Zhang PM (2014) The role of the entorhinal cortex in epileptiform activities of the hippocampus. Theor Biol Med Model 11:14 [Journal] [PubMed]

Rutecki PA, Yang Y (1998) Ictal epileptiform activity in the CA3 region of hippocampal slices produced by pilocarpine. J Neurophysiol 79:3019-29 [PubMed]

Seddigh S, Thömke F, Vogt TH (1999) Complex partial seizures provoked by photic stimulation. J Neurol Neurosurg Psychiatry 66:801-2 [PubMed]

Sloviter RS, Zappone CA, Harvey BD, Bumanglag AV, Bender RA, Frotscher M (2003) "Dormant basket cell" hypothesis revisited: relative vulnerabilities of dentate gyrus mossy cells and inhibitory interneurons after hippocampal status epilepticus in the rat. J Comp Neurol 459:44-76

Stewart M, Fox SE (1990) Do septal neurons pace the hippocampal theta rhythm? Trends Neurosci 13:163-8 [PubMed]

Stoop R, Pralong E (2000) Functional connections and epileptic spread between hippocampus, entorhinal cortex and amygdala in a modified horizontal slice preparation of the rat brain. Eur J Neurosci 12:3651-63

Sylwestrak EL, Ghosh A (2012) Elfn1 regulates target-specific release probability at CA1-interneuron synapses. Science 338:536-40 [Journal] [PubMed]

Whittington MA, Traub RD, Jefferys JG (1995) Erosion of inhibition contributes to the progression of low magnesium bursts in rat hippocampal slices. J Physiol 486 ( Pt 3):723-34 [PubMed]

Witter MP (2007) Intrinsic and extrinsic wiring of CA3: indications for connectional heterogeneity. Learn Mem 14:705-13 [PubMed]

Wittner L, Eross L, Czirják S, Halász P, Freund TF, Maglóczky Z (2005) Surviving CA1 pyramidal cells receive intact perisomatic inhibitory input in the human epileptic hippocampus. Brain 128:138-52 [Journal] [PubMed]

Zhang W, Buckmaster PS (2009) Dysfunction of the dentate basket cell circuit in a rat model of temporal lobe epilepsy. J Neurosci 29:7846-56 [PubMed]

Ziburkus J, Cressman JR, Barreto E, Schiff SJ (2006) Interneuron and pyramidal cell interplay during in vitro seizure-like events. J Neurophysiol 95:3948-54 [PubMed]

(46 refs)