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

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Accession:186768
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.
Reference:
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;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s): HCN1; HCN2;
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Activity Patterns; Oscillations; Pathophysiology; Epilepsy; Brain Rhythms;
Implementer(s): Neymotin, Sam [samn at neurosim.downstate.edu]; Sanjay, M [msanjaycmc at gmail.com];
Search NeuronDB for information about:  Hippocampus CA3 pyramidal cell; Hippocampus CA3 basket cell; GabaA; AMPA; NMDA;
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SanjayEtAl2015
readme.html
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 *
stats.mod
vecst.mod *
wrap.mod *
aux_fun.inc *
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
Epileptic Activity.png
geom.hoc *
geom.py *
grvec.hoc *
init.hoc *
labels.hoc *
local.hoc *
misc.h *
mosinit.py
network.py *
networkmsj.py
nqs.hoc *
nqs_utils.hoc *
nrnoc.hoc *
params.py
pyinit.py *
run.py
simctrl.hoc *
stats.hoc *
syncode.hoc *
xgetargs.hoc *
xtmp
                            
// $Id: drline.hoc,v 1.41 2011/02/15 14:05:02 billl Exp $

// load_file("drline.hoc")

// click and drag left button to draw lines on top of a figure interactively
// select graph to draw on with setdrl(Graph[])
// set color with clr, line width with lne
// select 'Draw curve' for continuous drawing
// select 'Arrow' to place an arrow pointing according to direction of drag

drlflush=1 //whether to flush line drawings each drline call

//* drline(x0,y0,x1,y1,OPT graph or color) 
proc drline () { local color,line
  if (numarg()==0) { print "drline(x0,y0,x1,y1[,g,col,line])"
    return }
  if (numarg()>4) { 
    if (argtype(5)==0) { color=$5 
                         if (numarg()>5) line=$6
    } else {             graphItem = $o5 
                         if (numarg()>5) color=$6
                         if (numarg()>6) line=$7      }}
  graphItem.beginline(color,line)
  graphItem.line($1,$2)
  graphItem.line($3,$4)
  if(drlflush) graphItem.flush()
}

//* set to drawlines on top of fig
proc setdrl () {
  g=$o1 // select this graph for further drawing
  xpanel("")
  $o1.menu_tool("Draw line","drl")
  $o1.menu_tool("Draw curve","drc")
  $o1.menu_tool("Label","drw")
  $o1.menu_tool("Arrow","dra")
  $o1.menu_tool("Circle","drci")
  $o1.menu_tool("Rectangle","drr")
  xvalue("Color","clr",1,"",1)
  xvalue("Line","lne",1,"",1)
  xbutton("Erase","g.erase_all()")
  xpanel()
  $o1.exec_menu("Draw line")
}

//* draw line interactively on top of fig
// interesting that this should work at all since x0,y0 local but still preserving their
// values across multiple calls
proc drl ()  { local x0,y0,type,x,y,keystate
  type=$1 x=$2 y=$3 keystate=$4
  if (type==2) {x0=x y0=y}
  if (type==3) drline(x0,y0,x,y,clr,lne)
}

//* draw circle interactively on top of fig
// drci(2,0,0,0) drci(3,1,0,0)
proc drci ()  { local a,x0,y0,type,x,y,keystate,ii,rad localobj xv,yv
  type=$1 x=$2 y=$3 keystate=$4
  if (type==2) {x0=x y0=y}
  if (type==3) { rad=sqrt((x-x0)^2+(y-y0)^2) 
    a=allocvecs(xv,yv) vrsz(360,xv,yv)
    print "Circle: ",x0,y0,rad
    yv.circ(xv,x0,y0,rad)
    yv.line(g,xv,clr,lne)
    dealloc(a)
  }
}

//* draw retangle interactively on top of fig
proc drr ()  { local x0,y0,type,x,y,keystate
  type=$1 x=$2 y=$3 keystate=$4
  if (type==2) {x0=x y0=y}
  if (type==3) { drline(x0,y0,x0,y,clr,lne)
    drline(x,y0,x,y,clr,lne) drline(x,y,x0,y,clr,lne) drline(x,y0,x0,y0,clr,lne) }
}

//* draw arrow interactively on top of fig
proc dra ()  { local xsz,ysz,type,x,y,keystate,rot
  type=$1 x=$2 y=$3 keystate=$4
  xsz=0.1*(g.size(2)-g.size(1)) // 10% of size
  ysz=0.1*(g.size(4)-g.size(3))
  if (type==2) {x0=x y0=y}
  if (type==3) {
    if (y==y0) {
      if (x>x0) rot=-90 else rot=90
    } else {
      rot=-atan((x-x0)/(y-y0))/2/PI*360
      if ((y-y0)<=0) rot+=180
    }
    g.glyph(arrow(),x,y,xsz,ysz,rot)
  }
}

//* draw curve interactively on top of fig
proc drc ()  { local x0,y0,type,x,y,keystate
  type=$1 x=$2 y=$3 keystate=$4
  if (type==2) { x0=x y0=y
  } else if (type==1) {
    drline(x0,y0,x,y,clr,lne)
    x0=x y0=y
  } else if (type==3) drline(x0,y0,x,y,clr,lne)
}

//* write label
proc drw ()  { local x0,y0,type,x,y,keystate
  type=$1 x=$2 y=$3 keystate=$4
  if (type==2) { 
   string_dialog("Label: ",tstr) 
   g.label(x,y,tstr,1,1,0.5,0.5,clr)
  }
}

obfunc arrow () { localobj o
  o=new Glyph()
  o.m(0,0)  o.l(0,2) o.s(1,4) // draw vertical line
  o.m(0,0)  o.l(0,-2) o.s(1,4) // draw vertical line
  o.m(0,-2) o.l(-2,0) o.s(1,4)
  o.m(0,-2) o.l(2,0) o.s(1,4)
  return o
}

//* hist(g,vec,min,max,bins)
{clr=1 hflg=1 ers=1 sym=1 pflg=0 lin=4 hbup=0} 
declared("hfunc")
// clr:color, hflg=1 draw lines; 2 draw boxes; 3 fill in; ers=erase; 
// pflg=1 normalize hist by size of $o2, so will be probability instead of count
// pflg=2 turn hist upside down
// pflg=3 operate on values with hfunc()
// style determined by hflg
// hflg==0 lines with dots
// hflg==0.x offset lines with dots
// hflg==1 outlines but not down to zero
// hflg==2 outlines with lines down to zero
// hflg==3 just dots
// hflg==3.x lines between dots
// hbup=1 // move baseline up by this amount
func hist () { local a,b,c,min,max,wid,bins,ii,jj,offset,x,y
  if (numarg()==0) { printf("hist(g,vec,min,max,bins)\n") return 0}
  if ($o2.size<2)  { printf("hist: $o2 too small\n",$o2) return -1}
  if ($o2.min==$o2.max)  { printf("hist: %s all one value: %g\n",$o2,$o2.min) return -1}
  if (numarg()==5) {min=$3 max=$4 bins=$5 
  } else if (numarg()==4) { min=0 max=$3 bins=$4 
  } else if (numarg()<=3) { 
    if ((min=0.95*$o2.min)<0) min=1.05*$o2.min
    if ((max=1.05*$o2.max)<0) max=0.95*$o2.max
    bins=100
    if (min>0) min*=0.9 else min*=1.1
    if (max>0) max*=1.1 else max*=0.9
    if (numarg()==3) bins=$3
  }
  wid=(max-min)/bins
  // print min,max,max-wid,wid
  a=b=c=allocvecs(3) b+=1 c+=2
  offset=0 x=-1
  if (ers) $o1.erase_all()
  mso[c].hist($o2,min,bins,wid) // c has values
  if(pflg==1) mso[c].div(mso[c].sum) // normalize to sum to 1
  if(pflg==2) mso[c].mul(-1)
  if(pflg==3) hfunc(mso[c])
  mso[a].resize(2*mso[c].size())
  mso[a].indgen(0.5) 
  mso[a].apply("int") 
  mso[b].index(mso[c], mso[a]) 
  mso[a].mul(wid) mso[a].add(min)
  mso[b].rotate(1)
  mso[b].x[0] = 0 
  mso[b].append(mso[b].x[mso[b].size-1],0)
  mso[b].add(hbup)
  mso[a].append(max,max)
  if (hflg==1 || hflg==2) { 
    mso[b].line($o1, mso[a],clr,lin)
    if (hflg==2) for vtr(&x,mso[a]) drline(x,0,x,mso[b].x[i1],$o1,clr,lin)
  } else if (int(hflg)==0 || hflg>=3) { 
    if (hflg%1!=0) offset=hflg*wid // use eg -0.5+ii/8 to move back to integer
    mso[a].indgen(min,max-wid,wid)
    mso[a].add(wid/2+offset)
    // print mso[a].min,mso[a].max
    // mso[c].mark($o1,mso[a],"O",6,clr,2) // this will place points where 0 count
    for jj=0,mso[a].size-1 if (mso[c].x[jj]!=0) {
      if (hflg!=3 && hflg%1!=0) drline(mso[a].x[jj],0,mso[a].x[jj],mso[c].x[jj],$o1,clr,lin)
      if (hflg==4) {
        if (x!=-1) drline(x,y,mso[a].x[jj],mso[c].x[jj],$o1,clr,lin)
        x=mso[a].x[jj] y=mso[c].x[jj]
      }
      $o1.mark(mso[a].x[jj],mso[c].x[jj],sg(sym).t,10,clr,2) // don't place points with 0 count
    }
  }
  $o1.flush()
  $o1.size(min,max,0,mso[b].max)
  dealloc(a)
  return 1
}

// barplot(g,yvec,xvec[,bar_width]) 
// barplot(g,yvec,xvec[,bar_width,color_vec]) -- for multicolored bars -- each point has a color
// barplot(g,yvec,xvec[,bar_width,color_vec,error_vec]) -- error_vec plots the error
scribble=0
func barplot () { local a,sz,wid,ii,jj,x,y,mulcol localobj go,vx,vy,v1,vcol
  if (numarg()==0) {
    printf("barplot(g,yvec,xvec[,bar_width]), scribble=1 to 'fill in'\n") 
    printf("set scribble=1 to fill in with single color (based on clr)\n")
    printf("barplot(g,yvec,xvec[,bar_width,color_vec]):multicolored bars-each point has a color\n")
    printf("barplot(g,yvec,xvec[,bar_width,color_vec,error_vec]):add +/- error to each bar\n")
    return 0}
  if ((sz=$o2.size)!=$o3.size)  { printf("barplot: x,y vectors differ in size\n") return -1}
  go=$o1 $o3.sort
  if (argtype(4)==0)  wid=$4 else wid=1
  if (argtype(5)==1)  {vcol=$o5 mulcol=-1
    if (sz!=vcol.size) { printf("barplot: color vec wrong size: %d %d\n",sz,vcol.size) return -1}  
  } else if (argtype(5)==0) mulcol=$5 else mulcol=0
  wid/=2
  // print min,max,max-wid,wid
  a=allocvecs(vx,vy,v1)
  if (ers) go.erase_all()
  for vtr2(&x,&y,$o3,$o2,&ii)  { 
    vx.append(x-wid,x-wid,x+wid,x+wid)
    vy.append(0,y,y,0)
  }
  if (mulcol) {
    for vtr2(&x,&y,$o3,$o2,&jj)  { 
      if (mulcol==-1) clr=vcol.x[jj] else clr=mulcol
      vrsz(0,vx,vy)
      vx.append(x-wid,x-wid)
      vy.append(0,y)
      for (ii=0;ii<2*wid;ii+=(wid/100)) { 
        vx.add(wid/100) 
        vy.line(go, vx, clr, 4)
      }
    }
    vy.line(go, vx, clr, 4)
  } else if (scribble) {
    vrsz(0,vx,vy)
    for vtr2(&x,&y,$o3,$o2,&ii)  { 
      vx.append(x-wid,x-wid,x-wid)
      vy.append(0,y,0)
    }
    for (ii=0;ii<2*wid;ii+=(wid/100)) { 
      vx.add(wid/100) 
      vy.line(go, vx, clr, 4)
    }
    vy.line(go, vx, clr, 4)
  } else vy.line(go, vx, clr, lne)
  if(numarg()>5) $o2.ploterr(go, $o3, $o6, 15, 1, 3)
  go.flush()
  go.size(vx.min-wid,vx.max+wid,0,vy.max)
  dealloc(a)
  return 1
}

proc smgs () { local a,b,c,min,max,wid,bins,ii,jj,offset,x,y localobj v1
  if ($o2.size<2)  { printf("smgs: $o2 too small\n",$o2) return -1}
  if ($o2.min==$o2.max)  { printf("smgs: %s all one value: %g\n",$o2,$o2.min) return -1}
  if (numarg()==5) {min=$3 max=$4 bins=$5 
  } else if (numarg()==4) { min=0 max=$3 bins=$4 
  } else if (numarg()<=3) { 
    if ((min=0.95*$o2.min)<0) min=1.05*$o2.min
    if ((max=1.05*$o2.max)<0) max=0.95*$o2.max
    bins=100
    if (min>0) min*=0.9 else min*=1.1
    if (max>0) min*=1.1 else max*=0.9
    if (numarg()==3) bins=$3
  }
  wid=(max-min)/bins
  // print min,max,max-wid,wid
  a=b=c=allocvecs(3,1e4) b+=1 c+=2
  offset=0 x=-1
  if (ers) $o1.erase_all()
  mso[a].indgen(min,max,wid)
  if (0) {
    mso[c].smgs($o2,min,max,wid,wid*wid/4) // c has values
    mso[c].line($o1, mso[a],clr,4)
  } else {
    v1=$o2.sumgauss(min,max,wid,wid/2) // c has values
    v1.line($o1, mso[a],clr,4)
  }
}

//* a few drawing utilities from sam (not too spectacular)
 
//** drawhticks(ticksz,minx,maxx,linewidth,$5-$numarg() == y position of horizontal ticks)
// draw horizontal ticks of a view box along left/right of box
proc drawhticks () { local ticksz,minx,maxx,lw,i
  ticksz=$1 minx=$2 maxx=$3 lw=$4
  for i=5,numarg() {
    drline(minx,$i,minx+ticksz,$i,g,1,lw)    drline(maxx,$i,maxx-ticksz,$i,g,1,lw)
  }
}

//** drawvticks(ticksz,miny,maxy,linewidth,$5-$numarg() == x position of vertical ticks)
// draw vertical ticks of a view box along top/bottom of box
proc drawvticks () { local ticksz,miny,maxy,lw,i
  ticksz=$1 miny=$2 maxy=$3 lw=$4
  for i=5,numarg() {
    drline($i,miny,$i,miny+ticksz,g,1,lw)    drline($i,maxy,$i,maxy-ticksz,g,1,lw)
  }
}

//** drawbox(minx,maxx,miny,maxy[,line,graph]) - draw box
proc drawbox () { local minx,maxx,miny,maxy,ln localobj myg
  minx=$1 maxx=$2 miny=$3 maxy=$4
  if(numarg()>4)ln=$5 else ln=3
  if(numarg()>5)myg=$o6 else myg=g
  drline(minx,miny,minx,maxy,myg,1,ln) //bottom
  drline(minx,miny,maxx,miny,myg,1,ln) //left
  drline(minx,maxy,maxx,maxy,myg,1,ln) //top
  drline(maxx,miny,maxx,maxy,myg,1,ln) //right
}

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