load_file("nrngui.hoc")
secondorder=2
tstep=0
period=2
dt=0.1
tstop=2000
nbcell = 200
TC=0.4
objref Bcell[nbcell]
begintemplate BasketCell
ndend1=4
ndend2=4
ndend3=4
ndend4=4
public pre_list, connect_pre, subsets, is_connected, is_art, stim
public soma, bcdend1, bcdend2, bcdend3, bcdend4
public all, adend, bdend, cdend, ddend
create soma, bcdend1[ndend1], bcdend2[ndend2], bcdend3[ndend3], bcdend4[ndend4]
objref syn, pre_list, stim
objref syn
proc init() {
pre_list = new List()
subsets()
temp()
synapse()
}
objref all, adend, bdend, cdend, ddend
proc subsets() { local i
objref all, adend, bdend, cdend, ddend
all = new SectionList()
soma all.append()
bcdend1[0] all.append()
bcdend2[0] all.append()
bcdend3[0] all.append()
bcdend4[0] all.append()
bcdend1[1] all.append()
bcdend2[1] all.append()
bcdend3[1] all.append()
bcdend4[1] all.append()
bcdend1[2] all.append()
bcdend2[2] all.append()
bcdend3[2] all.append()
bcdend4[2] all.append()
bcdend1[3] all.append()
bcdend2[3] all.append()
bcdend3[3] all.append()
bcdend4[3] all.append()
adend = new SectionList()
for i=0,3{
bcdend1 [i] adend.append()}
bdend = new SectionList()
for i=0,3{
bcdend2 [i] adend.append()}
cdend = new SectionList()
for i=0,3{
bcdend3 [i] adend.append()}
ddend = new SectionList()
for i=0,3{
bcdend4 [i] adend.append()}
}
proc temp() {
soma {nseg=1 L=20 diam=15} // changed L & diam
bcdend1 [0] {nseg=1 L=75 diam=4}
bcdend2 [0] {nseg=1 L=75 diam=3}
bcdend3 [0] {nseg=1 L=75 diam=2}
bcdend4 [0] {nseg=1 L=75 diam=1}
bcdend1 [1] {nseg=1 L=75 diam=4}
bcdend2 [1] {nseg=1 L=75 diam=3}
bcdend3 [1] {nseg=1 L=75 diam=2}
bcdend4 [1] {nseg=1 L=75 diam=1}
bcdend1 [2] {nseg=1 L=50 diam=4}
bcdend2 [2] {nseg=1 L=50 diam=3}
bcdend3 [2] {nseg=1 L=50 diam=2}
bcdend4 [2] {nseg=1 L=50 diam=1}
bcdend1 [3] {nseg=1 L=50 diam=4}
bcdend2 [3] {nseg=1 L=50 diam=3}
bcdend3 [3] {nseg=1 L=50 diam=2}
bcdend4 [3] {nseg=1 L=50 diam=1}
forsec all {
insert ccanl
catau_ccanl = 10
caiinf_ccanl = 5.e-6
insert borgka
gkabar_borgka=0.00015
insert nca // HAV-N- Ca channel
gncabar_nca=0.0008 //check to modify- original 0.004
insert lca
glcabar_lca=0.005
insert gskch
gskbar_gskch=0.000002
insert cagk
gkbar_cagk=0.0002
insert tonic
g_tonic = 0.000008 //0.001
e_tonic = -74
}
soma {insert ichan2 //ildikos ichan
gnatbar_ichan2=0.12
gkfbar_ichan2=0.013
gl_ichan2 = 0.00014
cm=1.4
}
forsec adend {insert ichan2
gnatbar_ichan2=0.12
gkfbar_ichan2=0.013
gl_ichan2 = 0.00012
cm=1.4
}
forsec bdend {insert ichan2
gnatbar_ichan2=0.0
gkfbar_ichan2=0.00
gl_ichan2 = 0.00012
cm=1.4}
forsec cdend {insert ichan2
gnatbar_ichan2=0.0
gkfbar_ichan2=0.00
gl_ichan2 = 0.00012
cm=1.4}
forsec ddend {insert ichan2
gnatbar_ichan2=0.0
gkfbar_ichan2=0.00
gl_ichan2 = 0.00012
cm=1.4}
connect bcdend1[0](0), soma(1)
connect bcdend1[1](0), soma(1)
connect bcdend1[2](0), soma(0)
connect bcdend1[3](0), soma(0)
connect bcdend2[0](0), bcdend1[0](1)
connect bcdend2[1](0), bcdend1[1](1)
connect bcdend2[2](0), bcdend1[2](1)
connect bcdend2[3](0), bcdend1[3](1)
connect bcdend3[0](0), bcdend2[0](1)
connect bcdend3[1](0), bcdend2[1](1)
connect bcdend3[2](0), bcdend2[2](1)
connect bcdend3[3](0), bcdend2[3](1)
connect bcdend4[0](0), bcdend3[0](1)
connect bcdend4[1](0), bcdend3[1](1)
connect bcdend4[2](0), bcdend3[2](1)
connect bcdend4[3](0), bcdend3[3](1)
forsec all {Ra=100}
forsec all {enat = 55 ekf = -90 ek=-90 elca=130 esk=-90
el_ichan2 =-75
cao_ccanl=2 } // make catau slower70e-3 cao=2 cai=50.e-6
}
objref syn
proc synapse() {
bcdend4 [0] syn = new Exp2Syn(0.5)
syn.tau1 = 2 syn.tau2 = 6.3 syn.e = 0 //2 and 6.3
pre_list.append(syn)
bcdend2 [1] syn = new Exp2Syn(0.5) //BC(GABA) syn to apical IML dend Bartos
syn.tau1 = 0.16 syn.tau2 = 1.8 syn.e = -74 //0.16 and 1.8
pre_list.append(syn)
//******************************Tonic GABA synapses**************
bcdend3[0] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum 2
syn.tau1 = 7 syn.tau2 = 200 syn.e = -74
pre_list.append(syn)
bcdend3[1] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum 3
syn.tau1 = 7 syn.tau2 = 200 syn.e = -74
pre_list.append(syn)
bcdend3[2] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum 4
syn.tau1 = 7 syn.tau2 = 200 syn.e = -74
pre_list.append(syn)
bcdend3[3] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum 5
syn.tau1 = 7 syn.tau2 = 200 syn.e = -74
pre_list.append(syn)
bcdend2[0] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum 6
syn.tau1 = 7 syn.tau2 = 200 syn.e = -74
pre_list.append(syn)
bcdend1[2] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum 7
syn.tau1 = 7 syn.tau2 = 200 syn.e = -74
pre_list.append(syn)
bcdend2[2] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum 8
syn.tau1 = 7 syn.tau2 = 200 syn.e = -74
pre_list.append(syn)
bcdend2[3] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum 9
syn.tau1 = 7 syn.tau2 = 200 syn.e = -74
pre_list.append(syn)
}
proc connect_pre() { // $o1 target point process, $o2 returned NetCon
soma $o2 = new NetCon (&v(1), $o1)
}
func is_art() { return 0 }
endtemplate BasketCell
//**********************************************************************************
//********************************************************************
// NETWORK SPECIFICATION INTERFACE
for i=0, nbcell-1 {Bcell[i] = new BasketCell(i)}
//*********************************************************************
objref nclist, netcon, cells, net_c, net_bc
{ cells = new List()
nclist = new List()
}
func cell_append() {cells.append($o1)
return cells.count -1}
func nc_append() {
if ($3 >= 0 ) {
cells.object($1).connect_pre(cells.object($2).pre_list.object($3),netcon)
netcon.weight = $4 netcon.delay = $5 netcon.threshold = $6
}
nclist.append(netcon)
return nclist.count-1
}
func is_connected() {local i, c
c=0
for i=0, nclist.count-1 {
net_c= nclist.object(i)
if (($o1 == net_c.postcell()) && ($o2 == net_c.precell())) {c=1}
}
return c
}
objref vbc2bc
{
vbc2bc = new Vector(nbcell, 0)
}
//initiating randm number generator
objref rdsyna, rdbc2bc, rdgap, rddend
ropen("/proc/uptime") // get a seed that is changing based on the processing time
{
rseed = fscan() // so simulation will not start with the same seed
ropen()
}
//rseed=12345
rdgap = new Random(rseed)
proc new_rdgap() {rdgap.discunif(-20,20)} // use for gap junc
new_rdgap()
rddend = new Random(rseed)
proc new_rddend() {rddend.discunif(0,3)}
new_rddend()
rdbc2bc = new Random(rseed) // use for syn.connections
proc new_rdbc2bc() {rdbc2bc.discunif(-15, 15)}
new_rdbc2bc()
rdsyna = new Random(rseed) // initialize random distr.
proc new_rdsyna() {rdsyna.discunif(1, 1)}
new_rdsyna()
// NETWORK INITIATION
for i = 0, nbcell-1 {cell_append(Bcell[i])}
//*********************************************************************************
//**********************************************************************************
objref randomVector
randomVector = new Vector(nbcell)
proc initBcell() { local i,j
for i=0, nbcell-1 {
randomVector.resize(nbcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 30) {
Gauz3 = rdbc2bc.repick()
dist = abs(Gauz3)
axdel = dist/5*0.2
if (Gauz3==0){Gauz3 = rdbc2bc.repick()}
if (i+Gauz3==i){Gauz3 = rdbc2bc.repick()}
if (Gauz3==0){Gauz3 = rdbc2bc.repick()}
if (i+Gauz3==i){Gauz3 = rdbc2bc.repick()}
if (i+Gauz3 > nbcell-1) {npost = i+Gauz3-nbcell }
if (i+Gauz3 < 0) {npost = i+Gauz3+nbcell}
if ((i+Gauz3 >-1) && (i+Gauz3 < nbcell)) {npost = i+Gauz3}
if ((randomVector.x[npost] == 0) && (vbc2bc.x[npost] < 31)) {
randomVector.x[npost] += 1
vbc2bc.x[npost] += 1
}
dbr = rdsyna.repick()
}
for k = 0, randomVector.size-1 {
if (randomVector.x[k] == 1) {
nc_append(i, k, dbr, 7.6e-3, 0.8+axdel, 0)
u=k
v=u+1
w=u-1
r=0.4*TC
if (v > 199) {v = v-1}
if (w < 0) {w = w+1}
nc_append(i, v, 8, r*0.0125e-3, 8, 10)
nc_append(i, v, 9, r*0.0125e-3, 8, 10)
nc_append(i, u, 8, TC*0.0125e-3, 8, 10)
nc_append(i, u, 9, TC*0.0125e-3, 8, 10)
nc_append(i, w, 8, r*0.0125e-3, 8, 10)
nc_append(i, w, 9, r*0.0125e-3, 8, 10)
}
}
}
}
objref gaps[20000]
for i=0,19999{
gaps[i] = new Gap(0.5)
gaps[i].r = 100000}
n=0
for i=0,199{
d = rddend.repick()
pre=i //for bcells
for j=1,50{
post = j+i
n +=2
if (post == pre){post =pre-post}
if (post>199) {post = post-200}
Bcell[pre].bcdend3[d] gaps[n-2].loc(0.5)
Bcell[post].bcdend3[d] gaps[n-1].loc(0.5)
setpointer gaps[n-2].vgap, Bcell[post].bcdend3[d].v(0.5)
setpointer gaps[n-1].vgap, Bcell[pre].bcdend3[d].v(0.5)
//print "Bcell", pre, "gap pre", n-2, "is connected post Bcell", post, "post gap", n-1
}
}
//******************************************
objref rddelay,rdamp
rddelay= new Random()
rddelay.uniform(-20,50)
rdamp= new Random()
rdamp.normal(0.6, 0.0006) //0.5% het Iinj and mean Iinj is 0.6nA
objref stim [200]
for i=0,199{
r=rddelay.repick()
a=abs(rdamp.repick())
//print i, "delay this time is ", r, "amplitude is ",a
Bcell[i].soma stim[i] = new IClamp(0.5)
stim[i].del = r
stim[i].dur = 1000
stim[i].amp = a
}
//*******************************************************************************************************
//*********************************Print out Net cons***************************************************
strdef strvar
objref nfile
nfile = new File()
proc saveNet(){ local i
nfile.wopen("N_connect_50GJ_30syn_74mV tonicspill.txt")
nfile.printf("Precell \tps.tcell \t Synapse \n")
for i=0, nclist.count-1 {
nfile.printf("%s\t%s\t%s\n", nclist.object[i].precell, nclist.object[i].postcell, nclist.object[i].syn)}
nfile.printf("TO BC\tBC")
for i= 0, nbcell-1 {nfile.printf("%d\t \n", vbc2bc.x[i])}
//print "BCout"
nfile.close("N_connect_50GJ_30syn_74mV tonicspill.txt")
}
//**************************************************************************
objref VmT
objref VmMat[nbcell]
VmT = new Vector()
for i=0, nbcell-1 {
VmMat[i] = new Vector()
}
proc VecMx() { local i
VmT.append(t)
for i=0, nbcell-1 {
VmMat[i].append( cells.object[i].soma.v(0.5))
}
}
objref Spike[nbcell]
for i=0, nbcell-1 {
Spike[i] = new Vector()
}
strdef Spkstr
objref dfile
dfile = new File()
proc SpkMx() { local i, j
k = 0
for i=0, nbcell-1 {
Spike[i].spikebin(VmMat[i], 0)
}
dfile.wopen("Spike50gaps_30syn_74mV tonicspill.txt")
while(k < VmT.size) {
for j = 0, nbcell-1 {
if(Spike[j].x[k] != 0) {
dfile.printf("%f\t%d\n", VmT.x[k], j)}
}
k +=1 }
dfile.close("Spike50gaps_30syn_74mV tonicspill.txt")
}
strdef strmat
objref efile
efile = new File()
efile.wopen("Mempot50gaps_30syn_74mV tonicspill.txt")
efile.printf("t\t")
for i = 0, 199 {
efile.printf("%s\t", Bcell[i])}
efile.printf("\n")
efile.close("Mempot50gaps_30syn_74mV tonicspill.txt")
proc sMatrix(){ local i
efile.aopen("Mempot50gaps_30syn_74mV tonicspill.txt")
efile.printf("%f\t", t)
for i = 0, 199 {
efile.printf("%f\t", Bcell[i].soma.v(0.5))}
efile.printf("\n")
efile.close("Mempot50gaps_30syn_74mV tonicspill.txt")
}
strdef strmat
objref gfile
gfile = new File()
gfile.wopen("gapctesthz_50GJ_30syn_74mV tonicspill.txt")
gfile.printf("t\t")
for i = 50, 100 {
gfile.printf("%s\t", Gap[i])}
gfile.printf("\n")
gfile.close("gapctesthz_50GJ_30syn_74mV tonicspill.txt")
proc gMatrix(){ local i
gfile.aopen("gapctesthz_50GJ_30syn_74mV tonicspill.txt")
gfile.printf("%f\t", t)
for i=50, 100 {
gfile.printf("%f\t", Gap[i].i)}
gfile.printf("\n")
gfile.close("gapctesthz_50GJ_30syn_74mV tonicspill.txt")
}
objref r_plt
proc initrPlt() {
r_plt = new Graph(0)
r_plt.size(0, tstop,0, cells.count)
r_plt.label(0.95, 0.02, "ms")
r_plt.label(0.01, 0.82, "neu")
r_plt.view(0,0, tstop, cells.count,320,20,300,230)
}
initrPlt()
proc plotAP() { local i, a
a=1
r_plt.erase()
while(j < cells.count-1) {
for i = 0, VmT.size-1 {
if (Spike[j].x[i] == 1) {
r_plt.mark(VmT.x[i], j, "T", 5, a, 1)}}
j+=1}
r_plt.flush()
}
proc init() { local dtsav, temp, secsav
finitialize(v_init)
t = -1000
dtsav = dt
secondorder =0
dt= 10
// if cvode is on, turn it off to do large fixed step
temp= cvode.active()
if (temp!=0) {cvode.active(0)}
while(t<-100) { fadvance() print t}
//restore cvode if reqd
if (temp!=0) {cvode.active(1)}
dt = dtsav
secondorder =2
t = 0
if (cvode.active()){
cvode.re_init()
}else{
fcurrent()
}
//frecord_init()
}
proc continuerun() {local rt
eventcount =0
eventslow =1
stoprun =0
if (using_cvode_) {
cvode.event($1)
}
while(t < $1 && stoprun == 0) {
step()
sMatrix()
gMatrix()
VecMx()
rt = stopsw()
if (rt > realtime) {
realtime = rt
if (!stdrun_quiet) fastflushPlot()
doNotify()
if (realtime == 2 && eventcount > 50) {
eventslow = int(eventcount/50)+1
}
eventcount = 0
}else{
eventcount = eventcount +1
if ((eventcount%eventslow) == 0) {
doEvents()
}
}
}
flushPlot()
}
objectvar save_window_, rvp_
objectvar scene_vector_[4]
objectvar ocbox_, ocbox_list_, scene_, scene_list_
{ocbox_list_ = new List() scene_list_ = new List()}
{
xpanel("RunControl", 0)
v_init = -60
xvalue("Init","v_init", 1,"stdinit()", 1, 1 )
xbutton("Init & Run","run()")
xbutton("Stop","stoprun=1")
runStopAt = 5
xvalue("Continue til","runStopAt", 1,"{continuerun(runStopAt) stoprun=1}", 1, 1 )
runStopIn = 1
xvalue("Continue for","runStopIn", 1,"{continuerun(t + runStopIn) stoprun=1}", 1, 1 )
xbutton("Single Step","steprun()")
t = 0
xvalue("t","t", 2 )
tstop = 1000 //1500
xvalue("Tstop","tstop", 1,"tstop_changed()", 0, 1 )
dt = 0.1
xvalue("dt","dt", 1,"setdt()", 0, 1 )
steps_per_ms = 10 //40
xvalue("Points plotted/ms","steps_per_ms", 1,"setdt()", 0, 1 )
xpanel(544,121)
}
{
save_window_ = new Graph(0)
save_window_.size(0,tstop,-80,40)
scene_vector_[2] = save_window_
{save_window_.view(0, -80, tstop, 120, 290, 470, 579.84, 208)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addexpr("Bcell[1].soma.v(0.5)",1,1)
save_window_.addexpr("Bcell[10].soma.v(0.5)",2,1)
save_window_.addexpr("Bcell[20].soma.v(0.5)",3,1)
save_window_.addexpr("Bcell[30].soma.v(0.5)",4,1)
save_window_.addexpr("Bcell[40].soma.v(0.5)",5,1)
save_window_.addexpr("Bcell[50].soma.v(0.5)",6,1)
save_window_.addexpr("Bcell[60].soma.v(0.5)",7,1)
save_window_.addexpr("Bcell[70].soma.v(0.5)",8,1)
save_window_.addexpr("Bcell[80].soma.v(0.5)",9,1)
save_window_.addexpr("Bcell[90].soma.v(0.5)",2,1)
save_window_.addexpr("Bcell[100].soma.v(0.5)",3,1)
save_window_.addexpr("Bcell[120].soma.v(0.5)",4,1)
save_window_.addexpr("Bcell[140].soma.v(0.5)",5,1)
save_window_.addexpr("Bcell[160].soma.v(0.5)",6,1)
save_window_.addexpr("Bcell[180].soma.v(0.5)",7,1)
save_window_.addexpr("Bcell[199].soma.v(0.5)",8,1)
}
save_window_ = new Graph(0)
save_window_.size(0,1000,-2,2)
scene_vector_[3] = save_window_
{save_window_.view(0, -2, tstop, 120, 290, 470, 579.84, 208)}
graphList[1].append(save_window_)
save_window_.save_name("graphList[1].")
save_window_.addexpr("Gap[10].i",2,1)
save_window_ = new Graph(0)
save_window_.size(0,1000,-2,2)
scene_vector_[3] = save_window_
{save_window_.view(0, -2, tstop, 120, 290, 470, 579.84, 208)}
graphList[1].append(save_window_)
save_window_.save_name("graphList[1].")
save_window_.addexpr("Bcell[10].bcdend4[0].igaba_tonic",2,1)
save_window_.addexpr("Bcell[10].soma.igaba_tonic",3,1)
proc rrun(){
initBcell()
saveNet()
run()
SpkMx()
}
rrun()
plotAP()
objectvar scene_vector_[1]
{doNotify()}
