back=0
//////// load needed templates////////////
if(!back){ load_file("nrngui.hoc") }
if(!back){ load_file("template/ObliquePath.hoc") }
if(!back){ load_file("template/BasalPath.hoc" ) }
objref econ,f1,f2,f3,ss,cvode
f1= new File()
f2= new File()
f3= new File()
ss=new SaveState()
cvode = new CVode(1)
x=cvode.active(1)
restart=0
v_init=-70
strdef morphology_location, morpho_path, ObliqueTrunkSection, BasalTrunkSection
objref vRP, vAPEX
proc xopen_morphology(){
sprint(morpho_path,"%s/%s",morphology_location,$s1)
xopen(morpho_path)
}
// Carmen
morphology_location = "pc2b"
ObliqueTrunkSection = "trunk[17]"
BasalTrunkSection = "trunk[7]"
xopen_morphology("cell.hoc") //reads morpholofy from the file
xopen_morphology("cell-analysis-simple.hoc") //reads simplified version of CA
// --------------- Creating lists-----------------
xopen("lib/TP-lib.hoc")
Tip_sections(apical_non_trunk_list,apical_trunk_list,"Apical")
objref apical_tip_list
apical_tip_list=TP_list // Apical Tip list
print "apical_tip_list"
apical_tip_list.printnames()
print "END apical_tip_list"
objref tmp_pl[num_tips],pl[num_tips],opl[num_tips],degree_apical_tip,peri_trunk_list
objref bl[num_tips],obl[num_tips],degree_basal_tip
xopen("lib/Oblique-lib.hoc")
oblique_sections(apical_tip_list,apical_trunk_list,num_tips) // apical dendrite path lists and degree of tips
xopen("lib/vector-distance.hoc")
//-----------------------------------------------------------------------------------------------------
printf("Setting up cell\n") // load cell-setup to
xopen("cell_setup_pc2b_CCh.hoc")
//load_file("atolscalekd.ses") // specify all mechanisms, membrane properties etc
///////////////////Load File//////////////////////
if(!back) { load_file("w_soma_cap.ses") }
/*cvode_active(1)*/
////// Spike counter//////////
objref apc, v1
proc insert_APC() {
apc = new APCount(0.5)
apc.thresh = $1
v1 = new Vector()
apc.record(v1)
}
proc init() {
if(restart){
f1.ropen("statekdsoma")
ss.fread(f1)
f1.close
finitialize(v_init)
ss.restore()
t=0
fcurrent()
cvode.re_init()
} else {
finitialize(v_init)
fcurrent()
}
}
////////////////////Main///////////////////
nsyn=10
objref s[nsyn], rsyn[nsyn], nc[nsyn]
objref rsynmda[nsyn], ncnmda[nsyn]
objref rect,recv,reci,savv,savi,savt
objref tvec,ampvec,iclamp
objref savtotcurr, savtotna16a, savtottrpm4, totcurr, totna16a, tottrpm4
strdef cmd, filename
i=0
forall{
for(x){
sprint(cmd,"%s%d","objref totcurrentpart",i)
execute(cmd)
if(ismembrane("ican")){
sprint(cmd,"%s%d","objref tottrpm4apart",i)
execute(cmd)
sprint(cmd,"%s%d","objref savtrpm4apart",i)
execute(cmd)
}
if(ismembrane("na16a")){
sprint(cmd,"%s%d","objref totna16apart",i)
execute(cmd)
}
i=i+1
}
}
proc main(){
recv =new Vector()
rect =new Vector()
reci =new Vector()
i=0
forall{
for(x){
sprint(cmd,"%s%d%s","totcurrentpart",i,"=new Vector()")
execute(cmd)
if(ismembrane("ican")){
sprint(cmd,"%s%d%s","tottrpm4apart",i,"=new Vector()")
execute(cmd)
}
if(ismembrane("na16a")){
sprint(cmd,"%s%d%s","totna16apart",i,"=new Vector()")
execute(cmd)
}
i=i+1
}
}
//tol=cvode.atolscale(&soma.v(0.5),1e-5)
period=95.75
phase0=67.8234
dur=3
amp2=0.0
tstop= 16000
in=0
th=-14
access soma
insert_APC(th)
f3.wopen("spike.dat")
current=0.0 // 0.18
del=50
npulse = 10
pulsdur = 1000
pulsamp = 0.18//
starttime = 13000
curbase = 0.09
soma {
iclamp = new IClamp( 0.5 )
tvec = new Vector(5 )
ampvec = new Vector(5 )
}
iclamp.del = 0
iclamp.dur = 1e9
tvec.x[0 ] = 0
tvec.x[1 ] = starttime
tvec.x[2 ] = starttime + pulsdur
tvec.x[3 ] = starttime + 2*pulsdur
tvec.x[4 ] = tstop
ampvec.x[0 ] = curbase
ampvec.x[1 ] = curbase
ampvec.x[2 ] = curbase + pulsamp
ampvec.x[3 ] = curbase
ampvec.x[4 ] = curbase
ampvec.play(&iclamp.amp,tvec,1)
access soma[0]
recv.record(&v(0.5))
rect.record(&t)
reci.record(&iclamp.i)
i=0
forall{
for(x){
sprint(cmd,"%s%d%s%s%s%f%s","totcurrentpart",i,".record(&",secname(),".i_cap(",x,"))")
execute(cmd)
if(ismembrane("ican")){
sprint(cmd,"%s%d%s%s%s%f%s","tottrpm4apart",i,".record(&",secname(),".can_ican(",x,"))")
execute(cmd)
}
if(ismembrane("na16a")){
sprint(cmd,"%s%d%s%s%s%f%s","totna16apart",i,".record(&",secname(),".ina_na16a(",x,"))")
execute(cmd)
}
i=i+1
}
}
//////////////run////////////////////////
run()
/////////////////////////////////////
savv= new File()
savt= new File()
savi = new File()
savv.wopen("v.txt")
savt.wopen("time.txt")
savi.wopen("i.txt")
recv.printf(savv)
rect.printf(savt)
reci.printf(savi)
savv.close
savt.close
savi.close
totcurr=new Vector(rect.size())
totna16a=new Vector(rect.size())
//tottrpm4=new Vector(rect.size())
i=0
forall{
for(x){
sprint(cmd,"%s%d%s%f%s","totcurrentpart",i,".mul(area(",x,")*1e-8)")
execute(cmd)
sprint(cmd,"%s%d%s","totcurr.add(totcurrentpart",i,")")
execute(cmd)
if(ismembrane("ican")){
sprint(cmd,"%s%d%s","savtrpm4apart",i,"= new File()")
execute(cmd)
sprint(filename,"%s%d%s","nanodomain_data/can",i,".txt")
sprint(cmd,"%s%d%s","savtrpm4apart",i,".wopen(filename)")
execute(cmd)
sprint(cmd,"%s%d%s%d%s","tottrpm4apart",i,".printf(savtrpm4apart",i,")")
print cmd
execute(cmd)
sprint(cmd,"%s%d%s","savtrpm4apart",i,".close")
execute(cmd)
}
if(ismembrane("na16a")){
sprint(cmd,"%s%d%s%f%s","totna16apart",i,".mul(area(",x,")*1e-8)")
execute(cmd)
sprint(cmd,"%s%d%s","totna16a.add(totna16apart",i,")")
execute(cmd)
}
i=i+1
}
}
savtotcurr= new File()
savtotna16a= new File()
//savtottrpm4 = new File()
savtotcurr.wopen("totcurr.txt")
savtotna16a.wopen("totna16a.txt")
//savtottrpm4.wopen("tottrpm4.txt")
totcurr.printf(savtotcurr)
totna16a.printf(savtotna16a)
//tottrpm4.printf(savtottrpm4)
savtotcurr.close
savtotna16a.close
//savtottrpm4.close
// print the spike number
if(!back) printf("\n Current: %.4f nA | # Spikes: %d\n", current, apc.n)
if(!back) printf("___________________\n")
v1.printf(f3)
f3.close
f2.wopen("state.new")
ss.save
ss.fwrite(f2)
f2.close
}
main()
/******** end file ******/