// CN model used in Saak V Ovsepian, Volker Steuber, Marie Le
// Berre, Liam O'Hara, Valerie B O'Leary, and J. Oliver Dolly
// (2013). A Defined Heteromeric KV1 Channel Stabilizes the
// Intrinsic Pacemaking and Regulates the Efferent Code of Deep
// Cerebellar Nuclear Neurons to Thalamic Targets. Journal of
// Physiology (epub ahead of print).
//
// written by Johannes Luthman, modified by Volker Steuber
//
// main simulation script that replicates Figure 9A,B
// in Ovsepian et al. (2013)
strdef strFilePrefix
Kdrblock = 1 // will be overwritten
strFilePrefix = "Kdr60"
load_file("nrngui.hoc")
load_file("model2_params_highgain.hoc")
load_file("DCN_morph.hoc")
load_file("DCN_mechs2.hoc")
objref oRndInh, oRndExc,CurrentClamp,ra,VoltageClamp,Vol1,Edata,Edata1
objref gammaStimPC[INHTOTALSYNAPSES]
objref netconPC[INHTOTALSYNAPSES],spikecount,spiketimes,Vol,GABAsyn,vdata_ex,vtemp_ex,vlength_ex,Vect_list_ex
// Declare instances of the GammaStim objects for excitatory synapses
// (1 GammaStim activates 1 AMPA + 1 fNMDA + 1 sNMDA) and the corresponding
// NetCon objects (=1 each for AMPA, fNMDA, and sNMDA).
objref gammaStimExc[EXCTOTALSYNAPSES],filed,filed1
objref filed3,filed4,filed5
objref netconExc[3 * EXCTOTALSYNAPSES]
num=1
if (name_declared("x")==5) { // x has been assigned a numerical value
num = x
}
print "num is ", num
strdef PCdata, MFdata, ext,PCfilename,MFfilename
PCdata = "datasp"
MFdata = "datasp_ex"
ext = ".dat"
sprint(PCfilename,"%s%d%s",PCdata,num,ext)
sprint(MFfilename,"%s%d%s",MFdata,num,ext)
print PCfilename
print MFfilename
strdef PCl, MFl, ext,PClname,MFlname
PCl = "l"
MFl = "l_ex"
ext = ".dat"
sprint(PClname,"%s%d%s",PCl,num,ext)
sprint(MFlname,"%s%d%s",MFl,num,ext)
print PClname
print MFlname
objref fdata,vtemp,vdata,Vect_list,fdata1,vlength
vdata=new Vector()
vtemp=new Vector()
vlength = new Vector()
Vect_list=new List()
fdata = new File() //datasp
fdata1 = new File() //datasp
Vol1=new Vector()
Edata = new File()
Edata1=new File()
vdata_ex=new Vector()
vtemp_ex=new Vector()
vlength_ex = new Vector()
Vect_list_ex=new List()
objref NaFcurrent,NaPcurrent,fKdrcurrent,sKdrcurrent,SKcurrent,TNCcurrent, hcurrent,CaLVAcurrent,CaHVAcurrent,trialtorecord
objref vectmp,vectmp1,fnmdalist,snmdalist
NaFcurrent = new Vector()
NaPcurrent = new Vector()
fKdrcurrent = new Vector()
sKdrcurrent = new Vector()
SKcurrent = new Vector()
TNCcurrent = new Vector()
hcurrent = new Vector()
CaLVAcurrent = new Vector()
CaHVAcurrent = new Vector()
trialtorecord = new Vector()
//trialtorecord.append(1,9,11,13,21,23,33,35,49,43,52,53,61,68,72,78,87,88,99,91)
trialtorecord.indgen(1,100,1)
fnmdalist =new List()
snmdalist =new List()
for i=0, EXCTOTALSYNAPSES-1 {
vectmp = new Vector()
vectmp1 = new Vector()
fnmdalist.append(vectmp)
snmdalist.append(vectmp1)
}
// model vecstim for inhibitory input
fdata.ropen(PCfilename)
fdata1.ropen(PClname)
vtemp = new Vector()
vdata.scanf(fdata)
vlength.scanf(fdata1)
fdata.close()
fdata1.close()
numspikespercell = int(vdata.size()/INHTOTALSYNAPSES)
src_start = 0
for i = 0, INHTOTALSYNAPSES-1 {
vtemp = new Vector()
src_tmp = vlength.x[i]
vtemp.copy(vdata,0,src_start,src_start+src_tmp-1)
src_start=src_start+src_tmp
Vect_list.append(vtemp)
}
// model netstim for inhibitory input
Edata.ropen(MFfilename)
Edata1.ropen(MFlname)
vtemp_ex = new Vector()
vdata_ex.scanf(Edata)
vlength_ex.scanf(Edata1)
Edata.close()
Edata1.close()
//numspikespercell = int(vdata_ex.size()/EXCTOTALSYNAPSES)
src_start_ex = 0
for i = 0, EXCTOTALSYNAPSES-1 {
vtemp_ex = new Vector()
src_tmp_ex = vlength_ex.x[i]
vtemp_ex.copy(vdata_ex,0,src_start_ex,src_start_ex+src_tmp_ex-1)
src_start_ex=src_start_ex+src_tmp_ex
Vect_list_ex.append(vtemp_ex)
}
///////////////////////////////////////////////////////////////
/// for ploting Vm using hoc
objectvar save_window_, rvp_
objectvar scene_vector_[8]
objectvar ocbox_, ocbox_list_, scene_, scene_list_
{ocbox_list_ = new List() scene_list_ = new List()}
{
save_window_ = new Graph(0)
save_window_.size(0,1000,-80,40)
scene_vector_[5] = save_window_
{save_window_.view(500, -80,500, 120,1071, 66, 300.48, 300.32)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addexpr("soma.v(.5)", 1, 1, 0.8, 0.9, 2)
save_window_.label(0.629393, 0.392971, "voltage axis", 2, 1, 0, 0, 1)
}
objectvar scene_vector_[1]
{doNotify()}
proc DCNloop() {
DCNmechs()
tstop=totsimtime
runSimulation()
run(tstop)
spiketimes.printf()
//quit()
}
proc runSimulation() {
// Set up the excitatory synapses
oRndExc = new Random()
oRndExc.ACG(randomiserSeed)
spiketimes=new Vector()
Vol=new Vector()
soma spikecount=new APCount(0.5)
spikecount.thresh=-20
spikecount.record(spiketimes)
Vol.record(&soma.v(0.5))
soma CurrentClamp = new IClamp(0.5)
CurrentClamp.amp = 0//-0.15
CurrentClamp.dur = 0//1500
CurrentClamp.del = 500
soma VoltageClamp = new SEClamp(0.5)
VoltageClamp.amp1 = -60
VoltageClamp.dur1 = 0
ra=new Random()
for (c=0; c < EXCTOTALSYNAPSES; c+=1) {
gammaStimExc[c] = new VecStim(0.5)
gammaStimExc[c].play(Vect_list_ex.object[c])
}
ncIndex = 0
for (c=0; c < EXCTOTALSYNAPSES; c+=1) {
netconExc[ncIndex] = new NetCon(gammaStimExc[c], ampa[c])
netconExc[ncIndex].threshold = 0 //mV
netconExc[ncIndex].weight = gAMPA
netconExc[ncIndex+1] = new NetCon(gammaStimExc[c], fnmda[c])
netconExc[ncIndex+1].threshold = 0 //mV
netconExc[ncIndex+1].weight = gfNMDA
netconExc[ncIndex+2] = new NetCon(gammaStimExc[c], snmda[c])
netconExc[ncIndex+2].threshold = 0 //mV
netconExc[ncIndex+2].weight = gsNMDA
ncIndex = ncIndex + 3
}
oRndInh = new Random()
oRndInh.ACG(randomiserSeed)
for (c=0; c<INHTOTALSYNAPSES; c+=1) {
gammaStimPC[c] = new VecStim(0.5)
gammaStimPC[c].play(Vect_list.object[c])
}
// Set up the GABA NetCons.
gsIndex = 0
counterOfNetCons = 0
for (cGABA=0; cGABA < INHTOTALSYNAPSES; cGABA=cGABA+1) {
s=ra.discunif(0,INHTOTALSYNAPSES)
netconPC[cGABA] = new NetCon(gammaStimPC[cGABA], gaba[s])
netconPC[cGABA].weight = gGABA
}
} // end of "proc runSimulation()".
DCNloop()
strdef file1, file2, ext,filename1,filename2
file1 = "m2_a"
file2 = "m2_b"
ext = ".bin"
sprint(filename1,"%s%d%s",file1,num,ext)
sprint(filename2,"%s%d%s",file2,num,ext)
print filename1
print filename2
filed = new File()
filed.wopen(filename1)
filed.close(filename1)
filed.aopen(filename1)
Vol.vwrite(filed)
filed.close()
filed1 = new File()
filed1.wopen(filename2)
filed1.close(filename2)
filed1.aopen(filename2)
spiketimes.vwrite(filed1)
filed1.close()
//quit()
