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

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We developed a 3-layer sensorimotor cortical network of consisting of 704 spiking model-neurons, including excitatory, fast-spiking and low-threshold spiking interneurons. Neurons were interconnected with AMPA/NMDA, and GABAA synapses. We trained our model using spike-timing-dependent reinforcement learning to control a virtual musculoskeletal human arm, with realistic anatomical and biomechanical properties, to reach a target. Virtual arm position was used to simultaneously control a robot arm via a network interface.
1 . 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 [PubMed]
2 . Dura-Bernal S, Li K, Neymotin SA, Francis JT, Principe JC, Lytton WW (2016) Restoring behavior via inverse neurocontroller in a lesioned cortical spiking model driving a virtual arm. Front. Neurosci. Neuroprosthetics 10:28
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s): Neocortex M1 pyramidal pyramidal tract L5B cell; Neocortex M1 pyramidal intratelencephalic L2-6 cell; Neocortex M1 interneuron basket PV cell; Neocortex fast spiking (FS) interneuron; Neostriatum fast spiking interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON; Python (web link to model);
Model Concept(s): Synaptic Plasticity; Learning; Reinforcement Learning; STDP; Reward-modulated STDP; Sensory processing; Motor control;
Implementer(s): Neymotin, Sam [samn at]; Dura, Salvador [ salvadordura at];
Search NeuronDB for information about:  Neocortex M1 pyramidal intratelencephalic L2-6 cell; Neocortex M1 pyramidal pyramidal tract L5B cell; Neocortex M1 interneuron basket PV cell; GabaA; AMPA; NMDA; Gaba; Glutamate;
boxes.hoc *
bpf.h *
colors.hoc *
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
filtutils.hoc *
hinton.hoc *
infot.hoc *
intfsw.hoc *
local.hoc *
misc.h * *
network.hoc *
nqs.hoc *
nqsnet.hoc *
pywrap.hoc *
samutils.hoc *
setup.hoc *
simctrl.hoc *
stats.hoc *
syncode.hoc *
units.hoc *
xgetargs.hoc *
print "Loading col.hoc..."

//* globals
{declare("UNIF",0)}    //use roughly uniform prob. distrib for div
{declare("NEGEXP",1)}  //use neg exp. with mean=div prob. distrib in setdvi
{declare("PARETO",2)}  //use pareto (scalefree) distrib with mean=div prob., shape=2
{declare("NORM",3)}    //use normal distrib with mean=div, stdev=div/5
{declare("DVFIXED",4)} //use fixed divergence ( no variability )
{declare("PARETOSH",4.5)}//shape for pareto (scalefree) distrib -- low value will produce fatter/higher tails

//* template CSTIM
begintemplate CSTIM

double wmatex[1][1],ratex[1][1],EIBalance[1]
public wmatex,ratex,setwm,vq,col,sgrhzdel,sgrdur,setspks,pushspks,savewt,restorewt,turnoff,mulwts,sgrdel,EIBalance,shock
external CTYP,CTYPi,STYPi,AM,AM2,NM,NM2,GA,GA2,case,nil,allocvecs,dealloc,nqsdel
objref this,vq,col,vsgrpp,vsgrsidx,vwt
double iseed[1],sgrhzdel[1],sgrdur[1],sgrdel[1],usens[1],sseed[1]
objref ncl,nsl,rsl,vrse // <-- objects for external inputs via NetCon(ncl)+NetStim(nsl) 
// with Random(rsl), Random sead(vrse)
public ncl,nsl,rsl,vrse,usens,sgrcells,initrands,jitterspks,sseed,iseed

//** clrwm - reset wmatex to 0
proc clrwm () { local ct,sy
  for ct=0,CTYPi-1 for sy=0,STYPi-1 wmatex[ct][sy]=0
//** new CSTIM(COLUMN,iseed,sgrdur[,sgrhzdel,EIBalance,usens])
// iseed = seed for random # generator, sgrdur = duration of persistent stims
// sgrhzdel = variability of stim rates, EIBalance = make E,I inputs balanced
// usens = whether to use NetStim instead of vq for persistent stims
proc init () { 
  double wmatex[CTYPi][STYPi]
  double ratex[CTYPi][STYPi]
  double EIBalance[1]
  clrwm() col=$o1 col.cstim=this
  if(numarg()>1) iseed=$2 else iseed=1234
  sgrdur=$3 sgrdel=0
  vsgrpp=new Vector(CTYPi) //% X 100 of cells of a type to stim, used in stim,sgrcells
  vsgrsidx=new Vector(CTYPi) //startind index of cell to stim when using topstim
  vq=new NQS("ind","time","wt","sy")
  if(numarg()>3)sgrhzdel=$4 else sgrhzdel=0.2
  if(numarg()>4)EIBalance=$5 else EIBalance=0
  if(numarg()>5)usens=$6 else usens=0

//** setwm - set weights of external inputs to INTF6s
proc setwm () {  local i,sz,ct,sy localobj nq,vct,vsy,vw,vr
  {nq=$o1 nq.tog("DB") vct=nq.getcol("ct")}
  {vsy=nq.getcol("sy") vw=nq.getcol("w") vr=nq.getcol("rate")}
  for ct=0,CTYPi-1 for sy=0,STYPi-1 wmatex[ct][sy]=ratex[ct][sy]=0
  for i=0,nq.v.size-1 {
//** setspks([checkdup]) - set time of the external inputs to cells, can still call shock later
// optional checkdup arg specifies whether to check for & correct consecutive duplicate spike times
// checkdup only makes sense when vq is not empty (i.e. when NOT using NetStim)
proc setspks () { local cd,se,ndx localobj rdm,ce,intf
  ce=col.ce if(numarg()>0) cd=$1 else cd=0
  if(ce.count<=0) { //need INTFs to stim
    printf("CSTIM: no cells to stim!\n")
  intf=ce.o(0) rdm=new Random() rdm.ACG(iseed) //initialize Random object
  if(vq==nil) vq=new NQS("ind","time","wt","sy") else vq.clear() //NQS storing INTF6 spike times
  intf.clrvspks() //clear INTF6 spike times
  if(sgrdur>0) {
    if(usens) nsstim(rdm) else popstim(rdm) //add random firing of INTF6 cells
  if(vq.v.size>0) pushspks(cd)
//** checkcdups - checks for consecutive duplicate spike times
proc checkcdups () { local a,ii,lastval localobj v1
  v1.copy(vq.getcol("time")) // get the times to allow checks
  lastval = -1.0
  for ii=0,v1.size()-1 {
    if (v1.x(ii) == lastval) {
      printf("ERROR: spike time duplicate at %f (row #%d)\n", v1.x(ii), ii)
      // If we can, change the spike time to the average of the current one and the one just ahead.
      if (v1.x(ii+1) > v1.x(ii)) v1.x(ii) = (v1.x(ii) + v1.x(ii+1)) / 2.0
    lastval = v1.x(ii)
  vq.v[1].copy(v1)        // copy the fixed time vector back
//** pushspks([checkdup]) - finalize spike times to INTF6 cells
// (useful, since after calls to shock/pulsestim, vq is modified)
// optional checkdup arg specifies whether to check for & correct consecutive duplicate spike times
proc pushspks () { local cd localobj ce,intf
  if(numarg()>0) cd=$1 else cd=0
  ce=col.ce intf=ce.o(0)
  vq.sort("time") vq.sort("ind") //finalize INTF6 spike times
  if(cd) checkcdups()
  intf.initvspks(vq.v,vq.v[1],vq.v[2],vq.v[3]) // single global call
//** jitterspks([jmin,jmax,seed]) - add jitter to spike times to avoid redundant spikes
// jmin,jmax are min,max jitters to add, seed is random # seed
proc jitterspks () { local a,jmin,jmax,seed localobj v1,rdm
  if(numarg()>0) jmin=$1 else jmin=0
  if(numarg()>1) jmax=$2 else jmax=1e-6
  if(numarg()>2) seed=$3 else seed=1234
  rdm=new Random()
//** savewt - initialize temporary storage space to allow modifications to vq weight column
proc savewt () {
  if(vwt==nil) vwt=new Vector(vq.v.size)  
//** restorewt - restore weights in vq to original values
proc restorewt () {
  if(vwt==nil) return
//** mulwts(celltype,synapsetype,scaling factor,[skippush]) - scale weights of cell and synapse type by factor
proc mulwts () { local ct,sy,fctr,i,j localobj ce
  ct=$1 sy=$2 fctr=$3 ce=col.ce,"sy",sy)
  for i=0,vq.ind.size-1 {j=vq.ind.x(i) 
    if(ce.o(vq.v[0].x(j)).type==ct) vq.v[2].x(j)*=fctr
  if(numarg()>3) { if(!$4) pushspks() } else pushspks()
//** turnoff(celltype,synapsetype,[skippush]) - turn off spikes by setting weights to 0
proc turnoff () { 
  if(numarg()>2) mulwts($1,$2,0,$3) else mulwts($1,$2,0)
//** pulsestim(rate[,maxt,clear,seed]) - stim using pulses @ specified rate - doesn't work correctly now
proc pulsestim () { local nspk,tt,i,j,nrate,ti,maxt localobj rdp,vqtmp
  rdp=new Random()   nrate=$1
  if(numarg()>1) maxt=$2 else maxt=tstop
  if(numarg()>2) {
    if($3) vq.clear() 
  } else vq.clear()  
  if(numarg()>3) rdp.ACG($4) else rdp.ACG(1234)
  vqtmp=new NQS()
  tt=1 rdp.poisson(1000/nrate)
  while(tt<=maxt) {
    while(ti <= 0) ti=rdp.repick()    
    if(vqtmp.size(-1)==0) vqtmp.cp(vq) else vqtmp.append(vq)
    print tt
    tt += ti
  vq.cp(vqtmp) nqsdel(vqtmp)
  vq.sort("time") vq.sort("ind")

//** initrands() - initialize Random # objects used by NetCon/NetStim for external inputs
// this function should be called in init -- at the start of each run to ensure same random # stream each time
proc initrands () { local i,se localobj rds
  if(vrse==nil) return  
  for i=0,vrse.size-1 {
    rds = rsl.o(i)       // go thru Random objects 
    se = vrse.x(i)       // seed previously used
    rds.MCellRan4(se,se) // initialize MCellRan4 Random # generator
    rds.negexp(1)        // must be called this way 

//** nsstim(Random) - setup random external inputs via NetStims
proc nsstim () { local a,sy,sdx,idx,sglo,sghi,hzlo,hzhi,ct,se localobj rdm,vsy,vhz,nc,ns,rds
  rdm=$o1  vsy.append(GA) vsy.append(GA2) vsy.append(AM2) vsy.append(NM2)
  sglo=1-sgrhzdel sghi=1+sgrhzdel if(sglo<0) sglo=0
  {nsl=new List() ncl=new List() rsl=new List() vrse=new Vector() se=iseed}
  for sdx=0,vsy.size-1 { sy=vsy.x(sdx) // go through synapse types
    for ct=0,CTYPi-1 if(col.numc[ct] && wmatex[ct][sy] && ratex[ct][sy]) {//go through cell types, check weights,rates of inputs
      vhz.resize(col.numc[ct]) //set vector to # of cells of type ct
      {hzlo=MAXxy(ratex[ct][sy]*sglo,1) hzhi=MAXxy(ratex[ct][sy]*sghi,1)}//find min,max frequencies
      rdm.discunif(hzlo,hzhi) //set random # generator to frequency btwn hzlo,hzi
      vhz.setrand(rdm) //set rate of inputs to each synapse
      for idx=col.ix[ct],col.ixe[ct] { // for each cell of type ct (idx is id of the cell)

        nsl.append( ns = new NetStim(0.5) ) // NetStim is source
        ns.number = int( 0.5 + vhz.x(idx-col.ix[ct]) * sgrdur / 1e3 ) // # of inputs
        ns.start = sgrdel // approx start of first input
        ns.noise = 1 // make it fully random
        ns.interval = 1e3 / vhz.x(idx-col.ix[ct]) // avg interval btwn the inputs

        rsl.append( rds = new Random() )
        rds.negexp(1) // set random # generator using negexp(1) - avg interval in NetStim.interval
        rds.MCellRan4(se,se)  // seeds are in order, shouldn't matter
        ns.noiseFromRandom(rds) // use random # generator for this NetStim
        vrse.append(se) // save random # seed

        ncl.append( nc = new NetCon(ns,col.ce.o(idx)) ) // set the connection (netstim->postsynaptic INTF6 cell)
        nc.delay = 0
        nc.weight(sy) = wmatex[ct][sy]

        se += 10 // increment seed for NetStim random # generator

//** popstim(Random) - setup random external synaptic inputs 
proc popstim () { local a,se,sy,sz,sdx,idx,jdx,pos,sglo,sghi,hzlo,hzhi,nspk,ct,mxr localobj rdm,vsy,vnspks,vtmp,vfctr
  rdm=$o1  vsy.append(GA) vsy.append(GA2) vsy.append(AM2) vsy.append(NM2)
  pos=mxr=0 sglo=1-sgrhzdel sghi=1+sgrhzdel if(sglo<0) sglo=0
  for ct=0,CTYPi-1 for sy=0,STYPi-1 mxr=MAXxy(mxr,ratex[ct][sy])
  if(EIBalance) { vfctr.resize(col.allcells) // flag for excit/inhib inputs to be balanced
    {rdm.uniform(sglo,sghi) vfctr.setrand(rdm) jdx=pos=0}
    for idx=0,col.allcells-1 { ct=col.ce.o(idx).type
      for sdx=0,vsy.size-1 { sy=vsy.x(sdx)
        if(wmatex[ct][sy] && ratex[ct][sy]) {
          if((nspk=int(ratex[ct][sy]*vfctr.x(idx)*sgrdur/1e3))<1) {nspk=1}
          if(sy==GA||sy==GA2) {
          } else vq.v[2].fill(wmatex[ct][sy],pos,pos+nspk-1)
          pos += nspk
  } else { // default here
    for sdx=0,vsy.size-1 { sy=vsy.x(sdx) // go through synapse types
      for ct=0,CTYPi-1 if(col.numc[ct] && wmatex[ct][sy] && ratex[ct][sy]) {//go through cell types, check weights,rates of inputs
        vnspks.resize(col.numc[ct]) //set vector to # of cells of type ct
        {hzlo=MAXxy(ratex[ct][sy]*sglo,1) hzhi=MAXxy(ratex[ct][sy]*sghi,1)}//find min,max frequencies
        rdm.discunif(hzlo,hzhi) //set random # generator to frequency btwn hzlo,hzi
        {vnspks.setrand(rdm) vnspks.mul(sgrdur/1e3) vnspks.apply("int")} //set # of spikes per intf in vnspks
        jdx = 0 // pointer into vnspks
        for idx=col.ix[ct],col.ixe[ct] { // for each cell of type ct (idx is id of the cell)
          vq.v[0].fill(idx,pos,pos+vnspks.x(jdx)-1) //fill vq.v[0] with ID of cell
          if(sy==GA||sy==GA2) { //is synapse inhibitory? if so, use negative weights
          } else vq.v[2].fill(wmatex[ct][sy],pos,pos+vnspks.x(jdx)-1) //use positive weights for excit. synapses
          vq.v[3].fill(sy,pos,pos+vnspks.x(jdx)-1)//fill corresponding entries in vq.v[3] with synapse type
          pos += vnspks.x(jdx) //increment pointer into vq row
          jdx += 1 //move jdx to next cell
  vq.pad(pos)//set all vq vectors to right size
  rdm.uniform(sgrdel,sgrdel+sgrdur) vq.v[1].setrand(rdm) // set times of inputs in vq.v[1]

//** shock(duration,percent,type[,time,seed,sy,wt])
// shock random % of cells
// single shock so duration means it spreads it out over eg 5 ms in terms of delivery to different cells
// % > 100 means multiple stime eg 200% will stim each cell 2 times in that interval
// sy specifies which synapse to stim, default is AM2
// wt specifies weight of inputs -- default is 1e9 for guaranteed spiking @ AM2 synapses. otherwise
// will provide a wt-dependent stim
proc shock () { local ct,startt,sy,wt
  if(numarg()>3) startt=$4 else startt=0
  if(numarg()>4) mc4seed_stats(sseed=$5) else mc4seed_stats(sseed=59743)
  if(numarg()==7) {
    {sy=$6    wt=$7   sgrcells($1,$2,$3,startt,1,0,sy,wt)}
  } else sgrcells($1,$2,$3,startt)

//** sgrcells(dur,percent,stimcelltype,starttime[,burst#,ISI,sy,wt]) - stim the cells
//  sgrcells(dur,percent,stimcelltype,starttime[,burst#,ISImin,ISImax])
// if numarg == 8, uses specified sy,wt for sub-threshold stim
proc sgrcells () { local ii,sgrdur,sgrpp,sgrpsz,stimcc,startt,a,bst,sy,wt localobj v1,v2,v3,vqtmp,dnq,vid,str
  if (vq==nil) vq=new NQS("ind","time","wt","sy")
  sgrdur=$1 sgrpp=$2 stimcc=$3 startt=$4 str=new String()
  bst=1 v3.resize(bst) // number of spikes/cell -- default 1
  if (argtype(5)==0) { 
    bst=$5 v3.resize(bst) 
    if (argtype(7)==0) { v3.setrnd(4.5,$6,$7,sseed) // interval of intervals
    } else if (argtype(6)==0) { v3.fill($6)
    } else v3.fill(4) // default 250 Hz without randomization
  if(numarg()==8) {sy=$7 wt=$8 } else {sy=AM2 wt=1e9} // use specified wt,sy?
  v3.x[0]=0.0 // so first one delivered at start time
  vqtmp=new NQS("ind","time","wt","sy")
      v1.setrnd(6,col.ix[stimcc],col.ixe[stimcc],sseed)//unique random ints in range
    } else v1.setrnd(5,col.ix[stimcc],col.ixe[stimcc],sseed)//nonunique since >= 100 %
  } else {
    if(col.div[stimcc][stimcc][0]>0)sprint(str.s,"to%s",CTYP.o(stimcc).s) else str.s="toE4"
    {"type",stimcc) dnq.sort(str.s) vid=dnq.getcol("id")}
    } else v1.copy(vid,0,sgrpsz-1)
  v2.resize(v1.size) // same size as v1
  v2.setrnd(4.5,startt,startt+sgrdur,sseed)// at some random time between startt and startt+sgrdur
  for ii=1,bst {vqtmp.v[0].append(v1) vqtmp.v[1].append(v2.add(v3.x[ii-1]))}
  {vqtmp.pad() vqtmp.v[2].fill(wt) vqtmp.v[3].fill(sy) } 
  vq.append(vqtmp) // need to call pushspks after call to shock/sgrcells

endtemplate CSTIM

//* template COLUMN
begintemplate COLUMN

external CTYPi,STYPi,ice,DEND,SOMA,IsLTS,CTYP,STYP,allocvecs,vrsz,dealloc,nil,NM,NM2,AM,AM2,GA,GA2,vlk,nqsdel

double numc[50]
double ix[50],ixe[50] //start,end IDs of types in a column
double div[50][50]//div[i][j]==# of outputs from type i->j
double wmat[50][50][25] // wmat[i][j][k]==weight from type i->j for synapse k
double wd0[50][50][25] // wmat[i][j][k]==weight from type i->j for synapse k
double delm[50][50]//avg. delay from type i->j
double deld[50][50]//delay variance from type i->j
double conv[50][50]
double pmat[50][50]
double synloc[50][50]//location of synapses
double allcells[1],ecells[1],icells[1],setdviPT[1],dgcor[1],xpos[1],ypos[1],wseed[1],verbose[1]
double syty1[50][50] //synapse type lookup table
double syty2[50][50] //synapse type lookup table
double cside[1] // column diameter, in swire
double pseed[1] // positioning seed, in swire
double zvar[1] // z variance, when using swire

public id,wmat,wd0,pmat,wire,wirenq,div,delm,deld,conv,numc,setdviPT,allcells,ecells,icells,xpos,ypos,wire2col
public setwmat,setpmat,setdelmats,setsynloc,ix,ixe,cstim,defsynloc,wseed,verbose,syty1,syty2,synloc
public mknetnqss,version
objref this,ce,intf,cstim
objref cellsnq,connsnq,xcolconnsnq
strdef name
public ce,intf,allwtsoff,allwtson,inhibon,inhiboff,name
public ctt,cttr,stt,prdiv
public cellsnq,connsnq,xcolconnsnq,mkcellsnq
public cside,pseed,zvar
public setcellpos,swire,swire2col

proc setstim () {

//** allwtson -- turn all internal weights on
proc allwtson () { local i,j,s
  if(wsetting_INTF6 == 1) {
    print "allwtson ERR: can't return weights with wsetting_INTF6==1 !"
  } else for i=0,CTYPi-1 for j=0,CTYPi-1 for s=0,STYPi-1 if(wmat[i][j][s]>0) wd0[i][j][s]=1

//** allwtsoff -- turn all internal weights off
proc allwtsoff () { local i,j,s,a localobj vwt,cel
  if(wsetting_INTF6 == 1) {
    print "allwtsoff WARN: will lose sywv values, wsetting_INTF6==1 !"
    for i=0,ce.count-1 { cel=ce.o(i)
  } else for i=0,CTYPi-1 for j=0,CTYPi-1 for s=0,STYPi-1 wd0[i][j][s]=0

// ** inhiboff -- turn inhibition off -- only call after setting up network
proc inhiboff () { local i,from,to
  for i=0,allcells-1 if(ice(ce.o(i).type)) ce.o(i).prune(1) //prune all inhib cells
  for from=0,CTYPi-1 if(ice(from)) for to=0,CTYPi-1 wd0[from][to][GA]=0

// ** inhibon -- turn inhibition on
proc inhibon () { local i,from,to
  for i=0,allcells-1 if(ice(ce.o(i).type)) ce.o(i).prune(0) //unprune all inhib cells
  for from=0,CTYPi-1 if(ice(from)) for to=0,CTYPi-1 wd0[from][to][GA]=1

//** getNdv - gets # of outputs based on divergence settings, always returns at least 1
// $o1 = random object, $2 = avg. # of outputs
func getNdv () { local dv,N localobj rdm
  rdm=$o1 dv=$2
  if(setdviPT==PARETO) {
    rdm.avg=dv N=int(rdm.pick+0.5)
  } else if(setdviPT==NEGEXP) {
  } else if(setdviPT==UNIF) {
  } else if(setdviPT==NORM) {
  } else if(setdviPT==DVFIXED) {
    return dv
  return N

//** defsynloc - set default values in synloc
proc defsynloc () { local from,to
  for from=0,CTYPi-1 for to=0,CTYPi-1 {
    if(ice(from)) {
      if(IsLTS(from)) {
        synloc[from][to]=DEND // distal [GA2] - from LTS
      } else {
        synloc[from][to]=SOMA // proximal [GA] - from FS
    } else synloc[from][to]=DEND // E always distal. use AM2,NM2

//** setsynloc - sets synapse location - not modifiable for now
proc setsynloc () { local i,sz,from,to,sy localobj nq,vfrom,vto,vloc
  if(numarg()==0) {
  } else {
    {nq=$o1 nq.verbose=0"dist",0)}
    {vfrom=nq.getcol("from") vto=nq.getcol("to") vloc=nq.getcol("loc")}
    for i=0,sz-1 synloc[vfrom.x(i)][vto.x(i)]=vloc.x(i)
    {nq.tog("DB") nq.verbose=1}

//** prdiv - prints div info
proc prdiv () { local i,j,k
  for i=0,CTYPi-1 for j=0,CTYPi-1 for k=0,STYPi-1 if(wmat[i][j][k]>0) if(div[i][j]) {

//** scalepmat - scales entries in pmat by $1
proc scalepmat () { local fctr,from,to
  for from=0,CTYPi-1 for to=0,CTYPi-1 pmat[from][to] *= fctr

//** clrpmat - sets pmat entries to 0
proc clrpmat () { local from,to
  for from=0,CTYPi-1 for to=0,CTYPi-1 pmat[from][to]=0 // clear it

//** setpmat(nqs with from,to,pij columns) - from=presynaptic type,
// to=postsynaptic type, pij=connection probability
proc setpmat () { local i,sz,from,to localobj nq,vfrom,vto,vpij
  {nq=$o1 nq.verbose=0"dist",0)}
  clrpmat() // clear it
  {vfrom=nq.getcol("from") vto=nq.getcol("to") vpij=nq.getcol("pij")}
  for i=0,sz-1 pmat[vfrom.x(i)][vto.x(i)]=vpij.x(i)
  setdivmat() // set divergence vectors based on pmat
  {nq.tog("DB") nq.verbose=1}

//** setdivmat - sets div/conv based on values in pmat
proc setdivmat () { local from,to,cl
  for from=0,CTYPi-1 for to=0,CTYPi-1 if(pmat[from][to]) {
    div[from][to] =  ceilg(pmat[from][to]*numc[to])
    conv[from][to] = int(0.5 + pmat[from][to]*numc[from])

//** clrwmat - sets wmat entries to 0
proc clrwmat () { local from,to,sy
  for from=0,CTYPi-1 for to=0,CTYPi-1 for sy=0,STYPi-1 wmat[from][to][sy]=0
//** clrwmd0 - sets wd0 entries to 0
proc clrwd0 () { local from,to,sy
  for from=0,CTYPi-1 for to=0,CTYPi-1 for sy=0,STYPi-1 wd0[from][to][sy]=0

//** clrsyty - sets syty1,sty2 entries to -1
proc clrsyty () { local from,to
  for from=0,CTYPi-1 for to=0,CTYPi-1 syty1[from][to]=syty2[from][to]=-1

//** setwmat(nqs with from,to,sy,w columns) - from=presynaptic type,
// to=postsynaptic type, sy=synapse type, w=weight
proc setwmat () { local i,sz,from,to,sy localobj nqwm,vfrom,vto,vsy,vw
  {nqwm=$o1 nqwm.verbose=0"dist",0) clrwmat() clrwd0()}
  {vfrom=nqwm.getcol("from") vto=nqwm.getcol("to")}
  {vsy=nqwm.getcol("sy") vw=nqwm.getcol("w") sz=vfrom.size}
  for i=0,sz-1 { 
    {sy=vsy.x(i) from=vfrom.x(i) to=vto.x(i)}
    {wmat[from][to][sy]=vw.x(i) wd0[from][to][sy]=1}
    if(sy==NM2) syty2[from][to]=sy else syty1[from][to]=sy
  {nqwm.tog("DB") nqwm.verbose=1}

//** setdelmats(nqs with from,to,delm,deld columns) - from=presynaptic type,
// to=postsynaptic type, sy=synapse type, delm=avg. delay, deld=variation in delay
proc setdelmats () {  local i,sz,from,to localobj nq,vfrom,vto,vdelm,vdeld
  {nq=$o1 nq.verbose=0"dist",0)}
  {vfrom=nq.getcol("from") vto=nq.getcol("to") vdelm=nq.getcol("delm") vdeld=nq.getcol("deld")}
  for i=0,sz-1 {delm[vfrom.x(i)][vto.x(i)]=vdelm.x(i) deld[vfrom.x(i)][vto.x(i)]=vdeld.x(i)}
  {nq.tog("DB") nq.verbose=1}

//** clrnqss - clear nqs objects used for storing cell/connectivity info
proc clrnqss () {
  {nqsdel(cellsnq) cellsnq=nil}
  {nqsdel(connsnq) connsnq=nil}
  {nqsdel(xcolconnsnq)  xcolconnsnq=nil}

//** new COLUMN(ID,vnumc,[nqwiring,wiringseed,xpos,ypos,setdviPT,mknetnqss,skipwire]])
proc init () { local skipwire
  if (numarg()==0) { 
    print "WARN: skipping default COLUMN init"
  {id=$1 dgcor=0 setdviPT=DVFIXED wseed=1234 verbose=0}
  {pseed=4321 cside=300 zvar=25} // swire-based params
  if(numarg()>=9) skipwire=$9 else skipwire=0 // whether to skip wiring , so can save time & wire directly from NQS
  if(numarg()>=8) mknetnqss=$8 else mknetnqss=0
  double numc[CTYPi],ix[CTYPi],ixe[CTYPi],div[CTYPi][CTYPi]
  double wmat[CTYPi][CTYPi][STYPi],wd0[CTYPi][CTYPi][STYPi],delm[CTYPi][CTYPi],deld[CTYPi][CTYPi]
  double conv[CTYPi][CTYPi],pmat[CTYPi][CTYPi],synloc[CTYPi][CTYPi],syty1[CTYPi][CTYPi],syty2[CTYPi][CTYPi]
  {clrsyty() mkcells($o2) sprint(name,"C%d",id) clrnqss()}
  if(mknetnqss) mkcellsnq()  // make cellsnq and connsnq
  if(numarg()>2) {
    {setpmat($o3) setwmat($o3) setsynloc($o3) setdelmats($o3)}
    if(numarg()>=6) {xpos=$5 ypos=$6 sprint(name,"C%d_X%d_Y%d",id,xpos,ypos)} // position in 2D grid
    if(numarg()>=7) setdviPT=$7 // wiring scheme
    if(numarg()>3) wseed=$4
    if(!skipwire) wire(wseed)

//** initdivrnd(seed) - initializes random object for wiring
obfunc initdivrnd () { local s localobj rd
  if(setdviPT==PARETO) rd=new rdmpareto(1,PARETOSH,s) else {rd=new Random() rd.ACG(s)}
  return rd

//** wirenq(nqs) - wires the column using connections in NQS
proc wirenq () {local ii,jj,a,flag localobj nq,vid2,vid1,vdel,vdist,vwt1,vwt2,vpre
  nq=$o1 nq.verbose=0
  if (numarg()>1) flag=$2 else flag=1
  if (verbose) printf("wiring COLUMN %d from %s...",id,nq)
  nq.tog("DB") // get the master vectors
  if (wsetting_INTF6==1) {
    vid1=nq.getcol("id1")   vid2=nq.getcol("id2")  vdel=nq.getcol("del")
    vdist=nq.getcol("dist") vwt1=nq.getcol("wt1")  vwt2=nq.getcol("wt2")
    ce.o(0).setdviv(vid1,vid2,vdel,vdist,vwt1,vwt2) // do all of them
  } else { // setting singly does not set the wt1,wt2
    nq.getcol("id1").uniq(vpre) // all presynaptic IDs
    nq.tog("SEL") // get the output vectors
    vid2=nq.getcol("id2")   vdel=nq.getcol("del") vdist=nq.getcol("dist") vwt1=nq.getcol("wt1")  vwt2=nq.getcol("wt2")
    for ii=0,vpre.size-1 { jj=vpre.x(ii)
      if ("id1",jj)) ce.o(jj).setdvi(vid2,vdel,vdist,flag)
  if(verbose) printf("done\n")

//** xydistm -- return x,y distance in milli-meters btwn ce.o($1) and ce.o($2)
func xydistmm () { localobj c1,c2
  return sqrt( (c1.xloc-c2.xloc)^2 + (c1.yloc-c2.yloc)^2 ) / 1e3

//** swire2col - spatial wiring btwn columns
proc swire2col () {
  print "WARNING: swire2col not implemented yet!"

//** swire([seed,maxfall]) - spatial wiring: wires the column using pmat and cell positions
//                   (wiring probability effected by distance btwn cells)
// seed is random # seed, maxfall is a number (0,1) that specifies maximum fall-off in
// probability at opposite side of column where dx^2+dy^2==2*cside^2
proc swire () { local x,y,z,ii,jj,a,del,prid,poid,prty,poty,dv,dvt,lseed,dvrand,szo,sc,h,prob,maxfall\
               localobj v1,v2,v3,v4,v5,v6,v7,vidx,vdel,vdist,vwt1,vwt2,vtmp,opr,opo,st,l,rdm
  if(verbose) printf("wiring COLUMN %d",id)
  a=allocvecs(v1,v2,v3,v4,v5,v6,v7,vidx,vdel,vtmp,vdist,vwt1,vwt2) z=0 l=new List() l.append(v1) l.append(v4)
  if (argtype(1)==0) lseed=$1 else lseed=1234
  if(numarg()>1) maxfall=$2 else maxfall=0.1  
  if(maxfall<0 || maxfall>=1) {
    printf("swire WARN: invalid maxfall=%g, setting maxfall to 0.1\n",maxfall)
  rdm=initdivrnd(lseed)//initialize random # generator
  sd = 2*cside^2 / log(maxfall) // this is negative
  // Create the connectivity NQS table.
  if(mknetnqss) {nqsdel(connsnq) connsnq=new NQS("id1","id2","del","dist","wt1","wt2")}
  for y=0,ce.count-1 { opr=ce.o(y)
    if(verbose) if(y%100==0)printf(".") prty=opr.type
    for poty=0,CTYPi-1 if (numc[poty]!=0 && (h=pmat[prty][poty])>0) {
      for poid=ix[poty],ixe[poty] if(prid!=poid) { // go thru postsynaptic cells
        opo = ce.o(poid)
        dx = abs(opr.xloc - opo.xloc)
        dy = abs(opr.yloc - opo.yloc)
        prob = h * E^((dx^2+dy^2)/sd) // probability of connect
        //print h,dx,dy,sd,prob
        if( prob >= rdm.uniform(0,1) ) {
          del = rdm.uniform(delm[prty][poty]-deld[prty][poty],delm[prty][poty]+deld[prty][poty])
          //if(dlayer[idx]==dlayer[jdx]){ //add intra-layer conduction delay
          //  if(ex1) del += xydistmm(idx,jdx) else del += xydistmm(idx,jdx) / 0.4
          if(synloc[prty][poty]==DEND) vdist.append(1) else vdist.append(0)

          if(mknetnqss || wsetting_INTF6==1) {
            if(syty1[prty][poty]>=0) vwt1.append(wmat[prty][poty][syty1[prty][poty]]) else vwt1.append(0)
            if(syty2[prty][poty]>=0) vwt2.append(wmat[prty][poty][syty2[prty][poty]]) else vwt2.append(0)
    if(vidx.size>0) {
      if(wsetting_INTF6==1) opr.setdvi(vidx,vdel,vdist,1,vwt1,vwt2) else opr.setdvi(vidx,vdel,vdist,1)
      if(mknetnqss) for ii=0,vidx.size-1 connsnq.append(prid,vidx.x(ii),vdel.x(ii),vdist.x(ii),vwt1.x(ii),vwt2.x(ii))
  if(ce.count>0) {
  if(verbose) printf("\n")

//** wire([seed]) - wires the column using div matrix
// optional 2nd arg "NOWIRE" just set up the NQS table
proc wire () { local x,y,z,ii,jj,a,del,prid,prty,poty,dv,dvt,lseed,dvrand,szo\
               localobj v1,v2,v3,v4,v5,v6,v7,vdvd,vidx,vdel,vdist,vwt1,vwt2,vtmp,opr,opo,st,l,rdm,rdmDV
  if(verbose) printf("wiring COLUMN %d",id)
  a=allocvecs(v1,v2,v3,v4,v5,v6,v7,vidx,vdel,vdvd,vtmp,vdist,vwt1,vwt2) z=0 l=new List() l.append(v1) l.append(v4)
  if (argtype(1)==0) lseed=$1 else lseed=1234
  if (argtype(2)==2) if (strcmp($s2,"NOWIRE")==0) {nowire=1 mknetnqss=1 print "WARNING: wire(NOWIRE)"}
  {rdm=new Random() rdm.MCellRan4(lseed,lseed)}
  if(dgcor){dvrand=0.2 rdm.uniform(.8,1.2) vdvd.setrand(rdm)}// div variability of 20% when dgcor==1
  rdmDV=initdivrnd(lseed)//initialize random # generator for use when dgcor==0
  // Create the connectivity NQS table.
  if(mknetnqss) {nqsdel(connsnq) connsnq=new NQS("id1","id2","del","dist","wt1","wt2")
    for prty=0,CTYPi-1 for poty=0,CTYPi-1 if (numc[prty]!=0 && numc[poty]!=0 && (dv=int(div[prty][poty]))>0) sz+=MAXxy(2*dv,4*numc[poty])
    for prty=0,CTYPi-1 if (numc[prty]!=0) cnt+=1
    connsnq.clear(cnt) // presized
  for y=0,ce.count-1 { opr=ce.o(y)
    if(verbose) if(y%100==0)printf(".") prty=opr.type
    for poty=0,CTYPi-1 if (numc[poty]!=0 && (dv=int(div[prty][poty]))>0) {      
      if(!dgcor) dv=getNdv(rdmDV,dv) else dv*=(1+vdvd.x[y])
      {rdm.discunif(ix[poty],ixe[poty]) v3.setrand(rdm)}
      if(prty==poty) {v1.cull(v3,prid) v3.copy(v1) v2.resize(v3.size)} // get rid of self connect      
      if( (cnt=v3.uniq(l,1)) > dv){ cnt = dv } // puts unsorted uniq vals into v4
      vrsz(cnt,v2,v4,v5,v6,v7) // v4 has poids
      v2.abs() // no negative delays
      if(synloc[prty][poty]==DEND) v5.fill(1) else v5.fill(0)
      vidx.append(v4) vdel.append(v2) vdist.append(v5) // vidx.append(v1) will give sorted bug
      if(mknetnqss || wsetting_INTF6==1) {
        if(syty1[prty][poty]>=0) v6.fill(wmat[prty][poty][syty1[prty][poty]]) else v6.fill(0)
        if(syty2[prty][poty]>=0) v7.fill(wmat[prty][poty][syty2[prty][poty]]) else v7.fill(0)
        vwt1.append(v6) vwt2.append(v7)
    }//end poty
    if(vidx.size>0) {
      if (!nowire) {if(wsetting_INTF6==1) opr.setdvi(vidx,vdel,vdist,1,vwt1,vwt2) else opr.setdvi(vidx,vdel,vdist,1)}
      if(mknetnqss) for ii=0,vidx.size-1 connsnq.append(prid,vidx.x(ii),vdel.x(ii),vdist.x(ii),vwt1.x(ii),vwt2.x(ii))
  }//end cell loop
  if(ce.count>0 && !nowire) {
  if(verbose) printf("\n")

//** wire2col(targetcol,nq,distance,ncl) - connect this COLUMN to another COLUMN
func wire2col () { local d,from,to,sz,dvm,dv,pij,dlym,dlyd,w1,w2,sy1,sy2,loc,i,idx,jdx,kdx,gid1,gid2,cnt,a\
                  localobj tcol,nq,ncl,vfrom,vto,vdelm,vdeld,vw,vsy,vpij,vloc,rdm,vidx,vdel,v1,v2,v3,v4,l,nc,prx,pox,rdmDV
  {tcol=$o1 nq=$o2 d=$3 ncl=$o4 nq.verbose=0}
  if(verbose) print "wiring COLUMN ", id, " to COLUMN ",
  if(!"dist",d)) {nq.verbose=1 printf("wire2col WARNA: none found @ d=%d!\n",d) nq.tog("DB") return 0}
  a=allocvecs(vidx,vdel,v1,v2,v3,v4) l=new List() l.append(v1) l.append(v4)
  {vfrom=nq.getcol("from") vto=nq.getcol("to") vsy=nq.getcol("sy")}
  {vdelm=nq.getcol("delm") vdeld=nq.getcol("deld") vw=nq.getcol("w")}
  {vpij=nq.getcol("pij") vloc=nq.getcol("loc")}
  if(verbose) print "tcol.wseed = ",tcol.wseed, " vfrom.size = ",vfrom.size
  rdmDV=initdivrnd(tcol.wseed)//initialize random # generator
  {rdm=new Random() rdm.MCellRan4(tcol.wseed,tcol.wseed)}
  if (mknetnqss && xcolconnsnq==nil) xcolconnsnq=new NQS("id1","col2","id2","del","wt1","wt2")
  while(i<vfrom.size) {
    {from=vfrom.x(i) to=vto.x(i) dlym=vdelm.x(i) dlyd=vdeld.x(i)}
    {w1=vw.x(i) sy1=vsy.x(i) sy2=w2=-1 pij=vpij.x(i) loc=vloc.x(i)}
    dvm = ceilg(pij*tcol.numc[to]) // divergence
    if((sy1==AM || sy1==AM2) && i+1<vfrom.size) { // check for NMDA, which follows AMPA
      if(vfrom.x(i+1)==from && vto.x(i+1)==to && (vsy.x(i+1)==NM || vsy.x(i+1)==NM2)) {
        sy2=vsy.x(i+1) w2=vw.x(i+1)
    for idx=ix[from],ixe[from] { // go thru presynaptic cells
      {rdm.discunif(tcol.ix[to],tcol.ixe[to]) v3.setrand(rdm)}
      if(verbose && v3.size<1) print "dv=",dv," from ",CTYP.o(from).s, " to ",CTYP.o(to).s," numc=",tcol.numc[to]," ix=",tcol.ix[to]
      if((cnt=v3.uniq(l,1))>dv) cnt=dv 
      {vrsz(cnt,v2,v4) rdm.uniform(dlym-dlyd,dlym+dlyd) v2.setrand(rdm)}
      v2.abs() // no negative delays
      if(verbose>1) {
        print CTYP.o(from).s, " -> ", CTYP.o(to).s, ": pij ", pij, ", dvm ", dvm, ", dv ", dv, ", v4.size ", v4.size
        printf("v4: ") vlk(v4)
        printf("v2: ") vlk(v2)
      ce.o(idx).flag("out",1) // make sure NetCon events enabled from this cell
      for jdx=0,v4.size-1 {
        prx = ce.o(idx)
        pox = tcol.ce.o(v4.x(jdx))
        ncl.append(nc=new NetCon(prx,pox))
        if(sy2!=-1) nc.weight(sy2)=w2
        if(mknetnqss) {
          if(sy2!=-1) {
          } else {
    if(sy2!=-1) i+=2 else i+=1 // if used NMDA, skip it
  {nq.verbose=1 nq.tog("DB") dealloc(a) return 1}

//** setarrs(vector of num per type) - sets  up arrays/numc/cell counts
proc setarrs () { local ct,cnt,cl,ii localobj vnumc
  {vnumc=$o1 cnt=allcells=icells=ecells=0}
  for ct=0,CTYPi-1 if (vnumc.x(ct)>0) { numc[ct]=vnumc.x(ct)
    ix[ct]=cnt ixe[ct]=cnt+numc[ct]-1 cnt+=numc[ct]
    if(ice(ct))icells+=numc[ct] else ecells+=numc[ct]
  } else numc[ct]=0

//** setcellpos(vector of z values by type[,z variance,pseed,columndiameter in microns])
proc setcellpos () { local i,z,x,y,zvar,c localobj rdm,vz
  if(numarg()>1) zvar=$2 
  if(numarg()>2) pseed=$3
  if(numarg()>3) cside=$4
  {rdm=new Random() rdm.ACG(pseed)}
  for i=0,allcells-1 {
    if(c!=-1) {

//** mkcells(vector of num per type) - make the cells
proc mkcells () { local ct,idx,jdx,ty,nc,ic localobj vnumc,xo,st
  st=new String()
  if(ce==nil) ce=new List()
  {vnumc=$o1 setarrs(vnumc)  }
  idx=0 // starting ID for cells in column - assumes all columns same size
  for ct=0,CTYPi-1 if(vnumc.x(ct)>0) { ic=ice(ct)
    for jdx=ix[ct],ixe[ct] {
      ce.append(xo=new INTF6(jdx,ct,ic,
  if(!ce.count) return  
  if(verbose) print st.s
  {sprint(st.s,"%s.intf.flag(\"jcn\",1,1)",this) execute(st.s)}
  if(verbose) print " finished mkcells "

//** mkcellsnq() -- make NQS table for all of the cells in the column
proc mkcellsnq () { local ii localobj xo 
  cellsnq=new NQS("gid","id","col","ty","ice","xloc","yloc","zloc")
  for ii=0,ce.count - 1 {
    xo = ce.o(ii)

//*** ctt(&i) - iterate over cell types in increasing CTYPi order
iterator ctt () { local i
  for i=0,CTYPi-1 if(numc[i]>0) {
//*** cttr(&i) - iterate over cell types in decreasing CTYPi order
iterator cttr () { local i
  for(i=CTYPi-1;i>=0;i-=1) if(numc[i]>0) {
//*** stt(&i,&j,&k) - iterate over active synapses types in order
iterator stt () { local i,j,k
  for i=0,CTYPi-1 if(numc[i]>0) for j=0,CTYPi-1 if(numc[j]>0 && div[i][j]>0) {
    for k=0,STYPi-1 if(wmat[i][j][k]>0) {
      $&1=i $&2=j $&3=k

proc version () { print "$Id: col.hoc,v 1.107 2012/10/02 14:25:45 billl Exp $" }

endtemplate COLUMN

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