// Double-click on this file to run the code
load_file("nrngui.hoc") // neuron main menu and some key parameter init (must come first)
xopen("ri06.nrn") // geometry
xopen("spinegeom.nrn")
//Generate 10um segments
ii = 0
tot_nsegs = 0
forall {
if (ii != 0) {
mynseg = int((L/10 + 0.9)/2)*2 + 1
if (mynseg == 0) {
mynseg = 1 }
nseg = mynseg
}
tot_nsegs = tot_nsegs + nseg
ii = ii + 1
}
//load simulated axon and count segments
xopen("simulated_axon.nrn")
hill {
tot_nsegs = tot_nsegs + nseg
}
iseg {
tot_nsegs = tot_nsegs + nseg
}
for jj = 0,1 node[jj] {
tot_nsegs = tot_nsegs + nseg
}
for jj = 0,2 inode[jj] {
tot_nsegs = tot_nsegs + nseg
}
naslopebasal=0 //constant Na conductance along basal dendrites
dslopebasal=0 //constant K conductance along basal disconnect
synwait=1000 //time to wait for membrane voltage to equilibrate
tstop = 100+synwait //simulation endtime
init_routine = 1 // 1 for using initialization routine
usecvode = 0 // 1 for using cvode
xopen("code_point_processes.hoc") // point processes (original)
xopen("code_objects.hoc") // additional objects (specific to geometry)
xopen("code_membrane.hoc") // membrane mechanisms (was init)
xopen("code_routine_for_runs.hoc") // contains regular run procedure
// these next few lines correct for the fact that the soma is elliptical rather than cylindrical
// due to an idiosyncrasy of NEURON, you have to do the area call first
access somaA
area(0.5)
correctsoma()
// This procedure initializes the active properties when called from the init() routine
init_params()
forall {insert dv}
insert_pass()
init_props()
// Create spine object, single synapse, and output files
objref spinearray[1]
spinehead spinearray[0] = new SectionRef()
objref ampasyn, nmdasyn
ampasyn = new synampa()
nmdasyn = new synnm()
objref scalefile
scalefile=new File()
//set spine neck resistance
spineneck {Ra=200.00}
spinehead {Ra=200.00}
spinehead {
insert h
insert pas
insert kdr
insert kap
insert kad
insert nafast2
insert naslowcond2
}
spineneck {
insert h
insert pas
insert kdr
insert kap
insert kad
insert nafast2
insert naslowcond2
}
xopen("code_synapse_setup.hoc")
//start parallel instance
objref pc
pc = new ParallelContext()
print "number of hosts: ", pc.nhost(), "\thost id: ", pc.id()
//function farmed out to slave nodes
func distscale() {local key, errval localobj parvec, returnvec
key = $1
parvec = $o2
returnvec = new Vector(35)
returnvec = calc_EPSP_single(parvec.x[0],parvec.x[1],parvec.x[2],parvec.x[3])
pc.pack(returnvec)
pc.post(key)
return key
}
obfunc calc_EPSP_single() {localobj outvec, currecord
//function to calculate the max deflection due to a single synapse
dendval=$1
seg=$2
useperfa=$3
useperfn=$4
outvec=new Vector(35)
currecord = new Vector()
//connect spine to section
dend[dendval].sec connect spineneck(0), seg
spinearray[0].sec {
g_pas=dend[dendval].sec.g_pas(seg)
cm=dend[dendval].sec.cm(seg)
gbar_nafast2=0
gbar_naslowcond2=0
//gbar_nafast2=dend[dendval].sec.gbar_nafast2(seg) //Uncomment for active spines
//gbar_naslowcond2=dend[dendval].sec.gbar_naslowcond2(seg) //Uncomment for active spines
gbar_kdr=0
gbar_kap=0
gbar_kad=0
gbar_h=0
}
soma.sec() distance()
spineneck {
g_pas=dend[dendval].sec.g_pas(seg)
cm=dend[dendval].sec.cm(seg)
gbar_nafast2=0
gbar_naslowcond2=0
//gbar_nafast2=dend[dendval].sec.gbar_nafast2(seg) //Uncomment for active spines
//gbar_naslowcond2=dend[dendval].sec.gbar_naslowcond2(seg) //Uncomment for active spines
gbar_kdr=0
gbar_kap=0
gbar_kad=0
gbar_h=0
}
//Run simulations in the following order:
//AMPA only, no scaling
//AMPA and NMDA, no scaling
//AMPA no scaling, NMDA scaling
//AMPA only, scaling
//AMPA scaling, NMDA no scaling
//AMPA and NMDA, scaling
dend[dendval].sec {
distloc=distance(seg)
noscaledAMPAcond=NA
noscaledNMDAcond=NN
scaledAMPAcond=NA
scaledNMDAcond=NN
if (useperfa==1) {
noscaledAMPAcond=calc_syn_strength(1,50)
scaledAMPAcond=calc_syn_strength(1,distloc)
}
if (useperfn==1) {
noscaledNMDAcond=calc_syn_strength(2,50)
scaledNMDAcond=calc_syn_strength(2,distloc)
}
if ((useperfa==1) || (useperfn==1)) {
//no scale AMPA only
syn_cc(dendval,seg,noscaledAMPAcond,2)
syn_nmdacc(dendval,seg,0,1)
currecord.record(&nmdasyn.i)
run()
print currecord.min()
outvec.x[0]=distloc
outvec.x[1]=dvmax_dv(seg)
outvec.x[2]=somaA.dvmax_dv(0.5)
outvec.x[3]=spinearray[0].sec.dvmax_dv(0.5)
outvec.x[4]=currecord.min()
outvec.x[5]=currecord.sum()*dt
//no scale AMPA + no scale NMDA
syn_nmdacc(dendval,seg,noscaledNMDAcond,2)
run()
outvec.x[6]=dvmax_dv(seg)
outvec.x[7]=somaA.dvmax_dv(0.5)
outvec.x[8]=spinearray[0].sec.dvmax_dv(0.5)
outvec.x[9]=currecord.min()
outvec.x[10]=currecord.sum()*dt
//no scale AMPA + scale NMDA
syn_nmdacc(dendval,seg,scaledNMDAcond,2)
run()
outvec.x[11]=dvmax_dv(seg)
outvec.x[12]=somaA.dvmax_dv(0.5)
outvec.x[13]=spinearray[0].sec.dvmax_dv(0.5)
outvec.x[14]=currecord.min()
outvec.x[15]=currecord.sum()*dt
//scale AMPA only
syn_cc(dendval,seg,scaledAMPAcond,2)
syn_nmdacc(dendval,seg,0,1)
run()
outvec.x[16]=dvmax_dv(seg)
outvec.x[17]=somaA.dvmax_dv(0.5)
outvec.x[18]=spinearray[0].sec.dvmax_dv(0.5)
outvec.x[19]=currecord.min()
outvec.x[20]=currecord.sum()*dt
//scale AMPA + no scale NMDA
syn_nmdacc(dendval,seg,noscaledNMDAcond,2)
run()
outvec.x[21]=dvmax_dv(seg)
outvec.x[22]=somaA.dvmax_dv(0.5)
outvec.x[23]=spinearray[0].sec.dvmax_dv(0.5)
outvec.x[24]=currecord.min()
outvec.x[25]=currecord.sum()*dt
//scale AMPA + scale NMDA
syn_nmdacc(dendval,seg,scaledNMDAcond,2)
run()
outvec.x[26]=dvmax_dv(seg)
outvec.x[27]=somaA.dvmax_dv(0.5)
outvec.x[28]=spinearray[0].sec.dvmax_dv(0.5)
outvec.x[29]=currecord.min()
outvec.x[30]=currecord.sum()*dt
outvec.x[31]=noscaledAMPAcond
outvec.x[32]=scaledAMPAcond
outvec.x[33]=noscaledNMDAcond
outvec.x[34]=scaledNMDAcond
} else { //only nonperf, so no synaptic saling
//AMPA only
syn_cc(dendval,seg,noscaledAMPAcond,2)
syn_nmdacc(dendval,seg,0,1)
currecord.record(&nmdasyn.i)
run()
outvec.x[0]=distloc
outvec.x[1]=dvmax_dv(seg)
outvec.x[2]=somaA.dvmax_dv(0.5)
outvec.x[3]=spinearray[0].sec.dvmax_dv(0.5)
outvec.x[4]=currecord.min()
outvec.x[5]=currecord.sum()*dt
//AMPA + NMDA
syn_nmdacc(dendval,seg,noscaledNMDAcond,2)
run()
outvec.x[6]=dvmax_dv(seg)
outvec.x[7]=somaA.dvmax_dv(0.5)
outvec.x[8]=spinearray[0].sec.dvmax_dv(0.5)
outvec.x[9]=currecord.min()
outvec.x[10]=currecord.sum()*dt
outvec.x[11]=0
outvec.x[12]=0
outvec.x[13]=0
outvec.x[14]=0
outvec.x[15]=0
outvec.x[16]=0
outvec.x[17]=0
outvec.x[18]=0
outvec.x[19]=0
outvec.x[20]=0
outvec.x[21]=0
outvec.x[22]=0
outvec.x[31]=noscaledAMPAcond
outvec.x[32]=scaledAMPAcond
outvec.x[33]=noscaledNMDAcond
outvec.x[34]=scaledNMDAcond
}
}
spineneck disconnect()
return outvec
}
pc.runworker()
//objects for input/output
objref parvec, threshvec
parvec=new Vector(4)
threshvec=new Vector(35)
proc calcEPSPs() {
scalefile.wopen("basal_EPSP_spines_record.dat")
scalefile.printf("Dendrite\tSegment\tAMPA_perf(1)_or_nonperf(0)\tNMDA_perf(1)_or_nonperf(0)\tDistance_from_soma\tdV_dendritic_segment\tdV_soma\tdV_spine\tMax_current\tTotal_charge\tAMPA_conductance\tNMDA_conductance\tAMPA_scaling\tNMDA_scaling\n")
somaA distance()
for m=1,basalno-1 {
dend[m].sec() {
for p=0,nseg+1 {
checkdist=distance(p/(nseg+1))
if (checkdist>50) {
for nn=0,1 {
parvec.x[0]=m //dendrite number
parvec.x[1]=p/(nseg+1) //section
parvec.x[2]=nn //perf or nonperf
parvec.x[3]=nn
mmtag=1000000*m+10000*p+100*nn+nn
pc.submit("distscale",mmtag,parvec) //send out the error calculations
}
}
}
}
}
//collect error values
while (pc.working()) {
key = pc.retval() //retrieve the tag
pc.look_take(key) //remove the tag/job from the bulletin
threshvec = pc.upkvec() //unpack the error value associated with the tag
print "received key ",key
dno=int(key/1000000)
sno=int((key-dno*1000000)/10000)
nno=int((key-dno*1000000-sno*10000)/100)
mmo=key-dno*1000000-sno*10000-nno*100
scalefile.printf("%d\t%d\t%d\t%d\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\tAMPA no scale NMDA no scale\n",dno,sno,nno,mmo,threshvec.x[0],threshvec.x[6],threshvec.x[7],threshvec.x[8],threshvec.x[9],threshvec.x[10],threshvec.x[31],threshvec.x[33])
if (nno==1) {
scalefile.printf("%d\t%d\t%d\t%d\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\tAMPA no scale NMDA scale\n",dno,sno,nno,mmo,threshvec.x[0],threshvec.x[11],threshvec.x[12],threshvec.x[13],threshvec.x[14],threshvec.x[15],threshvec.x[31],threshvec.x[34])
scalefile.printf("%d\t%d\t%d\t%d\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\tAMPA scale NMDA no scale\n",dno,sno,nno,mmo,threshvec.x[0],threshvec.x[21],threshvec.x[22],threshvec.x[23],threshvec.x[24],threshvec.x[25],threshvec.x[32],threshvec.x[33])
scalefile.printf("%d\t%d\t%d\t%d\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\tAMPA scale NMDA scale\n",dno,sno,nno,mmo,threshvec.x[0],threshvec.x[26],threshvec.x[27],threshvec.x[28],threshvec.x[29],threshvec.x[30],threshvec.x[32],threshvec.x[34])
}
scalefile.flush()
}
scalefile.close()
}
calcEPSPs()
