load_file("nrngui.hoc")
objref b,b2,s1,f,b3,b4,b5,tr,tr1,tr2,tr3,e,final,ats1,ats2,ats4,b6,b7
objref tracetime,tracemt0,tracegc0,tracegc33,tracemt0dend066
objref outfile1, outfile2, outfile4, outtrace1, outtrace2,outtrace3,outtrace4,outtrace5
objref index1,index2,index4,times1,times2,times4,timespikeints1,timespikeints2,timespikeints4,sinweights1,sinweights2,sinweights4,sigmoidmt0,sigmoidmt1,sigmoid,sigmoida
objref distrs1,distrs2,distrs4,distryf,distrx,distrxs1, distrys1, distrxs2, distrys2, distrxs4, distrys4,distrts1,distrts2,distrts4
objref sinindex,sinie,sintime,sin1,sin2,sin4,temp,temp1
double nc[300],nc1[300],nct1[300],nct2[300],nct3[300],nct4[300]
objref distrs1,distrs2,distrs4
objref temptime,tracetimetemp,tracemt0temp,tracegc0temp,tracemt0d66temp,tracegc33temp
objref obj
obj=new StringFunctions()
outfile1 = new File()
outfile2 = new File()
outfile4 = new File()
outtrace1 = new File()
outtrace2 = new File()
outtrace3 = new File()
outtrace4 = new File()
outtrace5 = new File()
index1 = new Vector()
index2 = new Vector()
index4 = new Vector()
times1 = new Vector()
times2 = new Vector()
times4 = new Vector()
timespikeints1 =new Vector()
timespikeints2 =new Vector()
timespikeints4 =new Vector()
sigmoidmt0=new Vector()
sigmoidmt1=new Vector()
sigmoid=new Vector()
sinweights1= new Vector()
sinweights2= new Vector()
sinweights4= new Vector()
distrx = new Vector(50)
distryf = new Vector()
distrs1 = new Vector(50)
distrs2 = new Vector(50)
distrs4 = new Vector(50)
distrxs1 = new Vector()
distrys1 = new Vector()
distrxs2 = new Vector()
distrys2 = new Vector()
distrxs4 = new Vector()
distrys4 = new Vector()
distrts1 = new Vector()
distrts2 = new Vector()
distrts4 = new Vector()
func plast() {
return (1-(1/(1+exp(($1-25)/3))))
}
proc loadsyn(){
strdef pt,pths1,pths2,pths4,ptht1,ptht2,ptht3,ptht4,ptht5,sig,pthin,pthres,pths1r,pths2r,pths4r,ptht1r,ptht2r,ptht3r,ptht4r,ptht5r
sig="sig"
for (k=0;k<50;k=k+1){
nc1[1+k*6]=0
nc1[2+k*6]=0
nc1[4+k*6]=0
nc[1+k*6]=0
nc[2+k*6]=0
nc[4+k*6]=0
}
pthres=$s1
obj.right($s1,7)
obj.left($s1,obj.len($s1)-4)
pt=$s1
if(obj.substr(pthres,"r.") != -1){
print "restart"
obj.left($s1,obj.len($s1)-1)
}
print $s1
sprint(pths1,"2mt-s1-%s.txt",$s1)
sprint(pths2,"2mt-s2-%s.txt",$s1)
sprint(pths4,"2mt-s4-%s.txt",$s1)
sprint(ptht1,"trace-time-%s.txt",$s1)
sprint(ptht2,"trace-mt0soma05-%s.txt",$s1)
sprint(ptht3,"trace-gc0dend0-%s.txt",$s1)
sprint(ptht4,"trace-mt0dend066-%s.txt",$s1)
sprint(ptht5,"trace-gc33dend0-%s.txt",$s1)
if(obj.substr($s1,"sig") != -1){
print "sig"
sprint(pthin,"%sinit.txt",$s1)
dispin(pthin)
doNotify()
}
trace(ptht1,ptht2,ptht3,ptht4,ptht5)
load(pths1,pths2,pths4)
}
proc trace(){
outtrace1.ropen($s1)
outtrace2.ropen($s2)
outtrace3.ropen($s3)
outtrace4.ropen($s4)
outtrace5.ropen($s5)
print "reading"
tracesize=outtrace1.scanvar()
temptime= new Vector()
tracetimetemp= new Vector()
tracemt0temp= new Vector()
tracegc0temp=new Vector()
tracemt0d66temp=new Vector()
tracegc33temp=new Vector()
tracetime = new Vector(tracesize)
tracemt0 = new Vector(tracesize)
tracegc0 = new Vector(tracesize)
tracemt0dend066 = new Vector(tracesize)
tracegc33= new Vector(tracesize)
tracetime.scanf(outtrace1,tracesize)
print "loaded trace1"
tracemt0.scanf(outtrace2,tracesize)
print "loaded trace2"
tracegc0.scanf(outtrace3,tracesize)
print "loaded trace3"
tracemt0dend066.scanf(outtrace4,tracesize)
print "loaded trace4"
tracegc33.scanf(outtrace5,tracesize)
print "loaded trace5"
print "loaded"
start=0
}
proc load(){
print " reading ...\n",$s1,"...\n",$s2,"...\n",$s3,"...\n"
outfile1.ropen($s1)
outfile2.ropen($s2)
outfile4.ropen($s3)
if (!outfile1.eof()){
outfile1.ropen($s1)
index1.scanf(outfile1, 1, 5)
outfile1.close()
outfile1.ropen($s1)
times1.scanf(outfile1, 2, 5)
outfile1.close()
outfile1.ropen($s1)
timespikeints1.scanf(outfile1, 3, 5)
outfile1.close()
outfile1.ropen($s1)
sigmoidmt0.scanf(outfile1, 4, 5)
outfile1.close()
outfile1.ropen($s1)
sinweights1.scanf(outfile1, 5, 5)
sigmoidmt0.apply("plast")
sigmoidmt0.mul(1.e-3)
sigmoidmt0.mul(synstr)
sigmoidmt0.div(2e-3)
print "loaded syn1"
} else {
index1.resize(0)
times1.resize(0)
timespikeints1.resize(0)
sinweights1.resize(0)
sigmoidmt0.resize(0)
}
if (!outfile2.eof()){
outfile2.ropen($s2)
index2.scanf(outfile2, 1, 5)
outfile2.close()
outfile2.ropen($s2)
times2.scanf(outfile2, 2, 5)
outfile2.close()
outfile2.ropen($s2)
timespikeints2.scanf(outfile2, 3, 5)
outfile2.close()
outfile2.ropen($s2)
sigmoid.scanf(outfile2, 4, 5)
outfile2.close()
outfile2.ropen($s2)
sinweights2.scanf(outfile2, 5, 5)
sigmoid.apply("plast")
sigmoid.mul(1.e-3)
sigmoid.mul(inh)
sigmoid.div(3e-3)
print "loaded syn2"
}else {
index2.resize(0)
times2.resize(0)
timespikeints2.resize(0)
sinweights2.resize(0)
sigmoid.resize(0)
}
if (!outfile4.eof()){
outfile4.ropen($s3)
index4.scanf(outfile4, 1, 5)
outfile4.close()
outfile4.ropen($s3)
times4.scanf(outfile4, 2, 5)
outfile4.close()
outfile4.ropen($s3)
timespikeints4.scanf(outfile4, 3, 5)
outfile4.close()
outfile4.ropen($s3)
sigmoidmt1.scanf(outfile4, 4, 5)
outfile4.close()
outfile4.ropen($s3)
sinweights4.scanf(outfile4, 5, 5)
sigmoidmt1.apply("plast")
sigmoidmt1.mul(1.e-3)
sigmoidmt1.mul(synstr)
print "loaded syn4"
} else {
index4.resize(0)
times4.resize(0)
timespikeints4.resize(0)
sinweights4.resize(0)
sigmoidmt1.resize(0)
}
sinsize=index1.size()+index2.size()+index4.size()
sin1=new Vector(index1.size())
sin2=new Vector(index2.size())
sin4=new Vector(index4.size())
sinie=new Vector()
sin1.add(1)
sin2.add(2)
sin4.add(4)
sinie.append(sin1)
sinie.append(sin2)
sinie.append(sin4)
sigmoida=new Vector()
sigmoida.append(sigmoidmt0)
sigmoida.append(sigmoid)
sigmoida.append(sigmoidmt1)
sinindex= new Vector()
sintime= new Vector()
sinindex.append(index1)
sinindex.append(index2)
sinindex.append(index4)
sintime.append(times1)
sintime.append(times2)
sintime.append(times4)
temp=new Vector(sinsize)
temp=sintime.sortindex()
temp1=new Vector()
ind=0
for(i=0;i<temp.size();i=i+1){
while (tracetime.x[ind]<=sintime.x[temp.x[i]]){
ind=ind+1
}
temp1.append(ind)
}
print "loaded"
}
proc disp(){
closeAll()
distrys1.resize(0)
distrxs1.resize(0)
distrts1.resize(0)
distrys2.resize(0)
distrxs2.resize(0)
distrts2.resize(0)
distrys4.resize(0)
distrxs4.resize(0)
distrts4.resize(0)
b2= new VBox()
b2.intercept(1)
xpanel("")
xvalue("synapse")
xbutton("display synapse", "disp1()")
xpanel()
//xpanel("",1)
s1 = new Graph()
b2.intercept(0)
b2.map(pt, 0, 0, 240, 620)
disp1()
}
proc disp1(){
s1.erase()
distrys1.resize(0)
distrxs1.resize(0)
distrts1.resize(0)
distrys2.resize(0)
distrxs2.resize(0)
distrts2.resize(0)
distrys4.resize(0)
distrxs4.resize(0)
distrts4.resize(0)
s1.size(0,10000, 0,1)
s1.xaxis(1)
s1.exec_menu("10% Zoom out")
s1.label(0.5,0.75," mitral->GC (exc)",2,1,0.4,0.4,1)
s1.label(0.5,0.70," GC->mitral (inh)",2,1,0.4,0.4,3)
for (i=0;i<index1.size();i=i+1){
if (index1.x[i] == synapse){
distrys1.append(sigmoidmt0.x[i])
distrxs1.append(times1.x[i])
}
}
for (i=0;i<index2.size();i=i+1){
if (index2.x[i] == synapse){
distrys2.append(sigmoid.x[i])
distrxs2.append(times2.x[i])
}
}
for (i=0;i<index4.size();i=i+1){
if (index4.x[i] == synapse){
distrys4.append(sigmoidmt1.x[i])
distrxs4.append(times4.x[i])
}
}
distrys1.line(s1,distrxs1,1,2)
distrys2.line(s1,distrxs2,3,2)
// distrys4.mark(s1,distrxs4,"O",6,2)
s1.flush()
}
proc evolution(){
closeAll()
for k=0,49{
distrs1.x[k]=nc1[1+k*6]
distrs2.x[k]=nc1[2+k*6]
distrs4.x[k]=nc1[4+k*6]
distrx.x[k]=k*10
}
go=0
bool=0
bool1=0
start=0
skip=30
b4=new VBox()
b4.intercept(1)
tr=new Graph()
b4.intercept(0)
b4.map("mt soma (Fig.2b)",0,0,300,200)
b6=new VBox()
b6.intercept(1)
tr2=new Graph()
b6.intercept(0)
b6.map("mt0 dend (Fig.2c)",820,0,300,200)
b3 = new VBox()
b3.intercept(1)
tr.size(0,10000,-70, 50)
xpanel("",1)
e = new Graph()
e.size(0,50,0,1)
e.erase()
interval=500
time=0
xvalue("time")
xvalue("skip")
xvalue("time window", "interval")
xbutton("play", "play()")
xbutton("pause", "pause()")
xbutton("close", "closeEvol()")
xpanel()
b3.intercept(0)
b3.map(pt)
b5=new HBox()
b5.intercept(1)
tr1=new Graph()
b5.intercept(0)
b5.map("gc (Fig.2b)",0,540,300,200)
b7=new HBox()
b7.intercept(1)
tr3=new Graph()
b7.intercept(0)
b7.map("gc (Fig.2c)",820,540,300,200)
tr1.size(0,10000,-70, 50)
tr.label(5000, 30, "mt0")
tr2.label(5000, 30, "mt0dend66")
tr1.label(5000, 30, "gc0")
tr3.label(5000, 30, "gc33")
tr2.size(0,10000,-70, 50)
tr3.size(0,10000,-70, 50)
tr.xaxis(3)
tr1.xaxis(3)
tr2.xaxis(3)
tr3.xaxis(3)
distrs1.mark(e,distrx,"S",9,1)
distrs2.mark(e,distrx,"O",6,3)
play()
}
proc pause(){
bool=1
bool1=0
}
proc play(){
bool1=bool1+1
if (bool1 < 2 && bool == 0){
for (i=go;i<sintime.size();i=i+1){
time=sintime.x[temp.x[i]]
if (sinie.x[temp.x[i]]==1){
index=sinindex.x[temp.x[i]]
peso=sigmoida.x[temp.x[i]]
distrs1.x[index]=peso
}
if (sinie.x[temp.x[i]]==2){
index=sinindex.x[temp.x[i]]
peso=sigmoida.x[temp.x[i]]
distrs2.x[index]=peso
}
if (sinie.x[temp.x[i]]==4){
index=sinindex.x[temp.x[i]]
peso=sigmoida.x[temp.x[i]]
distrs4.x[index]=peso
}
if ((i-(int(i/skip)*skip)) == 0 ){
tracedisp(i)
dispevol()
doNotify()
}
if(i==sintime.size()-1){
dispevol()
doNotify()
for k=0,49{
distrs1.x[k]=nc1[1+k*6]
distrs2.x[k]=nc1[2+k*6]
distrs4.x[k]=nc1[4+k*6]
start=0
tracetimetemp.resize(0)
tracemt0temp.resize(0)
tracemt0temp.resize(0)
tracegc0temp.resize(0)
tracemt0d66temp.resize(0)
tracegc33temp.resize(0)
}
go=0
bool1=0
print go
}
if(bool==1){
bool=0
go=i
i=sintime.size()-1
print go
}
}
}
}
proc tracedisp() {
tr.size(tracetime.x[start]-interval,tracetime.x[temp1.x[$1]], -70,50)
tr1.size(tracetime.x[start]-interval,tracetime.x[temp1.x[$1]], -70,50)
tr2.size(tracetime.x[start]-interval,tracetime.x[temp1.x[$1]], -70,50)
tr3.size(tracetime.x[start]-interval,tracetime.x[temp1.x[$1]], -70,50)
tr.flush
tr1.flush
tr2.flush
tr3.flush
tracetimetemp=tracetime.at(start,temp1.x[$1])
tracemt0temp=tracemt0.at(start,temp1.x[$1])
tracetimetemp=tracetime.at(start,temp1.x[$1])
tracemt0temp=tracemt0.at(start,temp1.x[$1])
tracegc0temp=tracegc0.at(start,temp1.x[$1])
tracemt0d66temp=tracemt0dend066.at(start,temp1.x[$1])
tracegc33temp=tracegc33.at(start,temp1.x[$1])
tracemt0temp.line(tr,tracetimetemp,1,0)
tracegc0temp.line(tr1,tracetimetemp,1,0)
tracemt0d66temp.line(tr2,tracetimetemp,1,0)
tracegc33temp.line(tr3,tracetimetemp,1,0)
start=temp1.x[$1]
}
proc dispevol() {
e.size(0,500,0,1)
e.erase()
e.mark(0,0.0005, "T", 15, 2, 2)
// e.mark(500,0.0005, "T", 15, 2, 2)
e.color(2)
e.beginline()
e.line(0, 0.0005)
e.line(500, 0.2)
// e.beginline()
// e.line(500, 0.0005)
// e.line(-5, 0.001)
distrs1.mark(e,distrx,"S",9,1)
distrs2.mark(e,distrx,"O",6,3)
e.flush
}
proc dispfinal(){
closeAll()
j=0
end=0
end1=0
end2=0
end3=0
while(end<3){
if(j<index1.size()){
nc[1+index1.x[j]*6]=sigmoidmt0.x[j]
}else{
end1=1
}
if (j<index2.size()){
nc[2+index2.x[j]*6]=sigmoid.x[j]
}else{
end2=1
}
if (j<index4.size()){
nc[4+index4.x[j]*6]=sigmoidmt1.x[j]
}else{
end3=1
}
end=end1+end2+end3
j=j+1
}
final = new Graph()
final.size(0,500,0,1)
final.erase()
final.mark(0,0.0005, "T", 15, 2, 2)
final.mark(500,0.0005, "T", 15, 2, 2)
final.color(2)
final.beginline()
final.line(0, 0.0005)
final.line(500, 0.2)
final.beginline()
final.line(500, 0.0005)
final.line(-5, 0.001)
distryf.resize(0)
for k=0, 49 {
distryf.append(nc[1+k*6])
distrx.x[k]=k*10
}
distryf.mark(final,distrx,"S",9,1)
final.flush()
distryf.resize(0)
for k=0, 49 {distryf.append(nc[4+k*6]) }
distryf.mark(final,distrx,"O",6,2)
final.flush()
distryf.resize(0)
for k=0, 49 {distryf.append(nc[2+k*6])}
distryf.mark(final,distrx,"O",6,3)
final.flush()
}
proc closeAll(){
objref b2,b3,b4,b5,b6,b7,final
}
proc closeEvol(){
b3.unmap()
b4.unmap()
b5.unmap()
b6.unmap()
b7.unmap()
}
func max(){
if ($1 >= $2){
return ($1)
}else{
return ($2)
}
}
weight=0.5
amp=.03
rel=0.2
inh=3
synstr=2
nmdafactor=0.0035
tracesize=0
b = new VBox()
b.intercept(1)
strdef path1
loadsyn("2mt-s1-w05-w00-e2i3-int220.txt")
xpanel("")
xvarlabel(pths1)
xvarlabel(pths2)
xvarlabel(pths4)
go=0
synapse=33
box=-1
xvalue("synapse")
xbutton("synapse time course ", "disp()")
xbutton("traces and weights, Fig. 2b-c","evolution()")
xbutton("final weights", "dispfinal()")
xpanel()
b.intercept(0)
b.map(pt)
//evolution()
outfile1.close()
outfile2.close()
outfile4.close()
Simulation Platform