// This is a fully wired network that functions with 500 GCs and 1 PP input
//With spike raster and write to file
// Auto init and run
load_file("nrngui.hoc")
secondorder=2
tstep=0
period=2
dt=0.1
tstop=2000 //1500
// define network size
ngcell = 1000 //500
nbcell = 12 //6
nmcell = 30 //15
nhcell = 12
npp = 1 //1024
sync= ngcell+nbcell+nmcell+nhcell
sproutNumber = 20
InhNet = 1
TC=0.5
IPSCmod=1 //0.7
Spr=1
mcKILL=4
hcKILL=2
//BCinput =0.5 // decreses GC to BC conductance to avoid BC depol block
// Define EPSCs---- using:
//- an Exp2Syn object (parameters tau1 -rise, tau2 -decay,
// time constant [ms] and e - rev potential [mV]
// delay [ms] and weight -variablr betw 0 and 1 [1 corresponding to 1 'S]
create acell_home_
access acell_home_
//***********************************************************************************************
//Defining granule cell
objref Gcell[ngcell]
begintemplate GranuleCell
ndend1=4
ndend2=4
public pre_list, connect_pre, subsets, is_art, is_connected
public vbc2gc, vmc2gc, vhc2gc, vgc2bc, vbc2bc, vmc2bc, vhc2bc, vgc2mc, vbc2mc, vmc2mc, vhc2mc, vgc2hc, vmc2hc
public soma, gcdend1, gcdend2
public all, gcldend, pdend, mdend, ddend, ngcld
//nst=10
//objectvar stim[nst]
//double stimdur[nst], stimdel[nst], stimamp[nst]
public stim, stimdur, stimamp, stimdel
objref stim, stimdur, stimamp, stimdel
create soma, gcdend1[ndend1], gcdend2[ndend2]
objref syn, pre_list, fl, vcl, fl_list
public fl, E_i, fl_list
proc init() {
pre_list = new List()
fl_list = new List()
subsets()
gctemp()
synapse()
}
objref all, gcldend, pdend, mdend, ddend, ngcld
proc subsets(){ local i
objref all, gcldend, pdend, mdend, ddend, ngcld
all = new SectionList()
soma all.append()
for i=0, 3 gcdend1 [i] all.append()
for i=0, 3 gcdend2 [i] all.append()
gcldend = new SectionList()
gcdend1 [0] gcldend.append()
gcdend2 [0] gcldend.append()
pdend = new SectionList()
gcdend1 [1] pdend.append()
gcdend2 [1] pdend.append()
mdend = new SectionList()
gcdend1 [2] mdend.append()
gcdend2 [2] mdend.append()
ddend = new SectionList()
gcdend1 [3] ddend.append()
gcdend2 [3] ddend.append()
ngcld = new SectionList()
gcdend1 [1] ngcld.append()
gcdend2 [1] ngcld.append()
gcdend1 [2] ngcld.append()
gcdend2 [2] ngcld.append()
gcdend1 [3] ngcld.append()
gcdend2 [3] ngcld.append()
}
proc gctemp() {
soma {nseg=1 L=16.8 diam=16.8} // changed L & diam
gcdend1 [0] {nseg=1 L=50 diam=3}
for i = 1, 3 gcdend1 [i] {nseg=1 L=150 diam=3}
gcdend2 [0] {nseg=1 L=50 diam=3}
for i = 1, 3 gcdend2 [i] {nseg=1 L=150 diam=3}
forsec all {
insert ccanl
catau_ccanl = 10
caiinf_ccanl = 5.e-6
Ra=210
}
soma {insert ichan2 //ildikos ichan
gnatbar_ichan2=0.12 //original 0.030 to .055
gkfbar_ichan2=0.016 //original 0.015
gksbar_ichan2=0.006
insert borgka
gkabar_borgka=0.012
insert nca // HAV-N- Ca channel
gncabar_nca=0.002 // check to modify- original 0.004
insert lca
glcabar_lca=0.005
insert cat
gcatbar_cat=0.000037
insert gskch
gskbar_gskch=0.001
insert cagk
gkbar_cagk=0.0006
gl_ichan2 = 0.00004
cm=1
}
forsec gcldend {insert ichan2
gnatbar_ichan2=0.018 //original 0.015
gkfbar_ichan2=0.004
gksbar_ichan2=0.006
insert nca // HAV-N- Ca channel
gncabar_nca=0.003 // check to modify- original 0.004
insert lca
glcabar_lca=0.0075
insert cat
gcatbar_cat=0.000075
insert gskch
gskbar_gskch=0.0004
insert cagk
gkbar_cagk=0.0006
gl_ichan2 = 0.00004
cm=1}
forsec pdend {insert ichan2
gnatbar_ichan2=0.013
gkfbar_ichan2=0.004
gksbar_ichan2=0.006
insert nca // HAV-N- Ca channel
gncabar_nca=0.001 // check to modify- original 0.004
insert lca
glcabar_lca=0.0075
insert cat
gcatbar_cat=0.00025
insert gskch
gskbar_gskch=0.0002
insert cagk
gkbar_cagk=0.001
gl_ichan2 = 0.000063
cm=1.6
}
forsec mdend {insert ichan2
gnatbar_ichan2=0.008
gkfbar_ichan2=0.001
gksbar_ichan2=0.006
insert nca // HAV-N- Ca channel
gncabar_nca=0.001 // check to modify- original 0.004
insert lca
glcabar_lca=0.0005
insert cat
gcatbar_cat=0.0005
insert gskch
gskbar_gskch=0.0
insert cagk
gkbar_cagk=0.0024
gl_ichan2 = 0.000063
cm=1.6}
forsec ddend {insert ichan2
gnatbar_ichan2=0.0
gkfbar_ichan2=0.001
gksbar_ichan2=0.008
insert nca // HAV-N- Ca channel
gncabar_nca=0.001 // check to modify- original 0.004
insert lca
glcabar_lca=0.0
insert cat
gcatbar_cat=0.001
insert gskch
gskbar_gskch=0.0
insert cagk
gkbar_cagk=0.0024
gl_ichan2 = 0.000063
cm=1.6}
connect gcdend1[0](0), soma(1)
connect gcdend2[0](0), soma(1)
for i=1,3 {
connect gcdend1[i](0), gcdend1[i-1](1)
}
for i=1,3 {
connect gcdend2[i](0), gcdend2[i-1](1)
}
forsec all {enat = 45 ekf = -90 eks = -90 ek=-90 elca=130 etca=130 esk=-90
el_ichan2 =-70
cao_ccanl=2 } // make catau slower70e-3 cao=2 cai=50.e-6
}
proc connect_pre() { // $o1 target point process, $o2 returned NetCon
soma $o2 = new NetCon (&v(1), $o1)
//alternative statement $o1.soma pre_list.append(new NetCon(soma.v(1),syn,0,Delsyn,0))
}
objref syn
proc synapse() {
gcdend1[3] syn = new Exp2Syn(0.5) // PP syn based on Greg and Staley 0
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend2[3] syn = new Exp2Syn(0.5) // PPsyn based on Greg and Staley 1
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend1[1] syn = new Exp2Syn(0.5) // MC syn *** Estimated 2
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend2[1] syn = new Exp2Syn(0.5) // MC syn *** Estimated 3
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend1[3] syn = new Exp2Syn(0.5) // HIPP syn based on Harney and Jones corrected for temp 4
syn.tau1 = 0.5 syn.tau2 = 6 syn.e = -70
pre_list.append(syn)
gcdend2[3] syn = new Exp2Syn(0.5) // HIPP syn based on Harney and Jones corrected for temp 5
syn.tau1 = 0.5 syn.tau2 = 6 syn.e = -70
pre_list.append(syn)
soma syn = new Exp2Syn(0.5) // BC syn syn based on Bartos 6
syn.tau1 = 0.26 syn.tau2 = 5.5 syn.e = -70
pre_list.append(syn)
gcdend1[1] syn = new Exp2Syn(0.5) // Sprouted Syn************* 7
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend2[1] syn = new Exp2Syn(0.5) // Sprouted Syn********* 8
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
// Total of 7 synapses per GC 0,1 PP; 2,3 MC; 4,5 HIPP and 6 BC 7,8 Sprout
}
func is_art() { return 0 }
endtemplate GranuleCell
// ************************************************************************************************************
objref Bcell[nbcell]
begintemplate BasketCell
ndend1=4
ndend2=4
ndend3=4
ndend4=4
public pre_list, connect_pre, subsets, is_art, is_connected
public vbc2gc, vmc2gc, vhc2gc, vgc2bc, vbc2bc, vmc2bc, vhc2bc, vgc2mc, vbc2mc, vmc2mc, vhc2mc, vgc2hc, vmc2hc
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, fl, vcl, fl_list
public fl, E_i, fl_list
nst=10
objectvar stim[nst]
double stimdur[nst], stimdel[nst], stimamp[nst]
public stim, stimdur, stimamp, stimdel
objref syn
proc init() {
pre_list = new List()
fl_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 = 0.00001 //10uS
e_tonic = -74
}
soma {insert ichan2 //ildikos ichan
gnatbar_ichan2=0.12 //original 0.030 to .055
gkfbar_ichan2=0.013 //original 0.015
gl_ichan2 = 0.00018
cm=1.4
}
forsec adend {insert ichan2
gnatbar_ichan2=0.12 //original 0.015
gkfbar_ichan2=0.013
gl_ichan2 = 0.00018
cm=1.4
}
forsec bdend {insert ichan2
gnatbar_ichan2=0.0
gkfbar_ichan2=0.00
gl_ichan2 = 0.00018
cm=1.4}
forsec cdend {insert ichan2
gnatbar_ichan2=0.0
gkfbar_ichan2=0.00
gl_ichan2 = 0.00018
cm=1.4}
forsec ddend {insert ichan2
gnatbar_ichan2=0.0
gkfbar_ichan2=0.00
gl_ichan2 = 0.00018
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) //PP(AMPA) syn to apical dist dend Dingledine '95 0
syn.tau1 = 2 syn.tau2 = 6.3 syn.e = 0 // *** check Tau rise 2ms is the rise time
pre_list.append(syn)
bcdend4 [1] syn = new Exp2Syn(0.5) //PP(AMPA) syn to apical dist dend Dingledine '95 1
syn.tau1 = 2 syn.tau2 = 6.3 syn.e = 0 // *** check Tau rise 2ms is the rise time
pre_list.append(syn)
bcdend1 [0] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend Geiger '97 2
syn.tau1 = .3 syn.tau2 = .6 syn.e = 0 // original syn.e = 0
pre_list.append(syn)
bcdend1 [1] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend Geiger '97 3
syn.tau1 = .3 syn.tau2 = .6 syn.e = 0 // original syn.e = 0
pre_list.append(syn)
bcdend1 [3] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend Geiger '97 4
syn.tau1 = .3 syn.tau2 = .6 syn.e = 0 // original syn.e = 0
pre_list.append(syn)
bcdend1 [2] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend Geiger '97 5
syn.tau1 = .3 syn.tau2 = .6 syn.e = 0 // original syn.e = 0
pre_list.append(syn)
bcdend2 [0] syn = new Exp2Syn(0.5) //MC(AMPA) syn to apical IML dend 6
syn.tau1 = 0.9 syn.tau2 = 3.6 syn.e = 0 // *** Estimated based on CA3>BC min stim Dingledine '95
pre_list.append(syn)
bcdend2 [1] syn = new Exp2Syn(0.5) //MC(AMPA) syn to apical IML dend 7
syn.tau1 = 0.9 syn.tau2 = 3.6 syn.e = 0 // *** Estimated based on CA3>BC min stim Dingledine '95
pre_list.append(syn)
bcdend2 [0] syn = new Exp2Syn(0.5) //BC(GABA) syn to apical IML dend Bartos 8
syn.tau1 = 0.16 syn.tau2 = 1.8 syn.e = -74
pre_list.append(syn)
bcdend2 [1] syn = new Exp2Syn(0.5) //BC(GABA) syn to apical IML dend Bartos 9
syn.tau1 = 0.16 syn.tau2 = 1.8 syn.e = -74
pre_list.append(syn)
bcdend4 [0] syn = new Exp2Syn(0.5) //HIPP(GABA) syn to apical distal dend 10
syn.tau1 = 0.4 syn.tau2 = 5.8 syn.e = -74 // *** Estimated as HIPP>GC
pre_list.append(syn)
bcdend4 [1] syn = new Exp2Syn(0.5) //HIPP(GABA) syn to apical distal dend 11
syn.tau1 = 0.4 syn.tau2 = 5.8 syn.e = -74 // *** Estimated as HIPP>GC
pre_list.append(syn)
//******************************Tonic GABA synapses**************
bcdend3[0] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum 12
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 13
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 14
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 15
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 16
syn.tau1 = 7 syn.tau2 = 200 syn.e = -74
pre_list.append(syn)
bcdend2[1] syn = new Exp2Syn(0.5) // TONIC GABA synapse based on Rossi evoked data from cerebellum 17
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 18
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 19
syn.tau1 = 7 syn.tau2 = 200 syn.e = -74
pre_list.append(syn)
// Total of 12 synapses 0,1 PP; 2-5 GC; 6,7 MC; 8,9 BC; 10,11 HIPP
}
proc connect_pre() { // $o1 target point process, $o2 returned NetCon
soma $o2 = new NetCon (&v(1), $o1)
//$o1.soma pre_list.append(new NetCon(soma.v(1),syn,0,Delsyn,0)) alternative statement
}
func is_art() { return 0 }
endtemplate BasketCell
//***********************************************************************************************************
objref Mcell[nmcell]
begintemplate MossyCell
ndend1=4
ndend2=4
ndend3=4
ndend4=4
public pre_list, connect_pre, subsets, is_art, is_connected
public vbc2gc, vmc2gc, vhc2gc, vgc2bc, vbc2bc, vmc2bc, vhc2bc, vgc2mc, vbc2mc, vmc2mc, vhc2mc, vgc2hc, vmc2hc
public soma, mcdend1, mcdend2, mcdend3, mcdend4
create soma, mcdend1[ndend1], mcdend2[ndend2], mcdend3[ndend3], mcdend4[ndend4]
public all, adend, bdend, cdend, ddend
objref syn, pre_list, fl
nst=10
objectvar stim[nst]
double stimdur[nst], stimdel[nst], stimamp[nst]
public stim, stimdur, stimamp, stimdel
objref syn
proc init() {
pre_list = new List()
subsets()
temp()
synapse()
}
objref all, pdend, ddend
proc subsets() { local i
objref all, pdend, ddend
all = new SectionList()
soma all.append()
for i=0, 3 mcdend1 [i] all.append()
for i=0, 3 mcdend2 [i] all.append()
for i=0, 3 mcdend3 [i] all.append()
for i=0, 3 mcdend4 [i] all.append()
pdend = new SectionList()
mcdend1 [0] pdend.append()
mcdend2 [0] pdend.append()
mcdend3 [0] pdend.append()
mcdend4 [0] pdend.append()
ddend = new SectionList()
for i=1, 3 mcdend1 [i] ddend.append()
for i=1, 3 mcdend2 [i] ddend.append()
for i=1, 3 mcdend3 [i] ddend.append()
for i=1, 3 mcdend4 [i] ddend.append()
}
proc temp() {
soma {nseg=1 L=20 diam=20} // changed L & diam
mcdend1 [0] {nseg=1 L=50 diam=5.78}
mcdend1 [1] {nseg=1 L=50 diam=4}
mcdend1 [2] {nseg=1 L=50 diam=2.5}
mcdend1 [3] {nseg=1 L=50 diam=1}
mcdend2 [0] {nseg=1 L=50 diam=5.78}
mcdend2 [1] {nseg=1 L=50 diam=4}
mcdend2 [2] {nseg=1 L=50 diam=2.5}
mcdend2 [3] {nseg=1 L=50 diam=1}
mcdend3 [0] {nseg=1 L=50 diam=5.78}
mcdend3 [1] {nseg=1 L=50 diam=4}
mcdend3 [2] {nseg=1 L=50 diam=2.5}
mcdend3 [3] {nseg=1 L=50 diam=1}
mcdend4 [0] {nseg=1 L=50 diam=5.78}
mcdend4 [1] {nseg=1 L=50 diam=4}
mcdend4 [2] {nseg=1 L=50 diam=2.5}
mcdend4 [3] {nseg=1 L=50 diam=1}
forsec all {
insert ccanl
catau_ccanl = 10
caiinf_ccanl = 5.e-6
insert borgka
gkabar_borgka=0.00001
insert nca // HAV-N- Ca channel
gncabar_nca=0.00008 // check to modify- original 0.004
insert lca
glcabar_lca=0.0006
insert gskch
gskbar_gskch=0.016
insert cagk
gkbar_cagk=0.0165
insert hyperde3
ghyfbar_hyperde3=0.000005
ghysbar_hyperde3=0.000005
}
soma {insert ichan2 //ildikos ichan
gnatbar_ichan2=0.12 //original 0.030 to .055
gkfbar_ichan2=0.0005 //original 0.015
gl_ichan2 = 0.000011
cm=0.6}
forsec pdend {insert ichan2
gnatbar_ichan2=0.12 //original 0.015
gkfbar_ichan2=0.0005
gl_ichan2 = 0.000044
cm=2.4}
forsec ddend {insert ichan2
gnatbar_ichan2=0.0
gkfbar_ichan2=0.00
gl_ichan2 = 0.000044
cm=2.4}
connect mcdend1[0](0), soma(1)
connect mcdend2[0](0), soma(1)
connect mcdend3[0](0), soma(0)
connect mcdend4[0](0), soma(0)
for i=1,3 {connect mcdend1[i](0), mcdend1[i-1](1)}
for i=1,3 {connect mcdend2[i](0), mcdend2[i-1](1)}
for i=1,3 {connect mcdend3[i](0), mcdend3[i-1](1)}
for i=1,3 {connect mcdend4[i](0), mcdend4[i-1](1)}
forsec all {Ra=100}
forsec all {enat = 55 ekf = -90 ek=-90 esk=-90 elca=130
ehyf=-40 ehys=-40
el_ichan2 =-59
cao_ccanl=2 } // make catau slower70e-3 cao=2 cai=50.e-6
}
objref syn
proc synapse() {
mcdend1 [3] syn = new Exp2Syn(0.7) //PP(AMPA) syn to dist dend similar to PP to GC
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
mcdend2 [3] syn = new Exp2Syn(0.7) //PP(AMPA) syn to dist dend similar to PP to GC
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
mcdend3 [3] syn = new Exp2Syn(0.7) //PP(AMPA) syn to dist dend similar to PP to GC
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
mcdend4 [3] syn = new Exp2Syn(0.7) //PP(AMPA) syn to dist dend similar to PP to GC
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
mcdend1 [0] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend similar to GC>CA3 Jonas '93
syn.tau1 = 0.5 syn.tau2 = 6.2 syn.e = 0
pre_list.append(syn)
mcdend2 [0] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend similar to GC>CA3 Jonas '93
syn.tau1 = 0.5 syn.tau2 = 6.2 syn.e = 0
pre_list.append(syn)
mcdend3 [0] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend similar to GC>CA3 Jonas '93
syn.tau1 = 0.5 syn.tau2 = 6.2 syn.e = 0
pre_list.append(syn)
mcdend4 [0] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend similar to GC>CA3 Jonas '93
syn.tau1 = 0.5 syn.tau2 = 6.2 syn.e = 0
pre_list.append(syn)
mcdend1 [0] syn = new Exp2Syn(0.5) //MC(AMPA) syn to prox dend similar to CA#>CA3 Aaron
syn.tau1 = 0.45 syn.tau2 =2.2 syn.e = 0
pre_list.append(syn)
mcdend2 [0] syn = new Exp2Syn(0.5) //MC(AMPA) syn to prox dend similar to CA#>CA3 Aaron
syn.tau1 = 0.45 syn.tau2 = 2.2 syn.e = 0
pre_list.append(syn)
mcdend3 [0] syn = new Exp2Syn(0.5) //MC(AMPA) syn to prox dend similar to CA#>CA3 Aaron
syn.tau1 = 0.45 syn.tau2 = 2.2 syn.e = 0
pre_list.append(syn)
mcdend4 [0] syn = new Exp2Syn(0.5) //MC(AMPA) syn to prox dend similar to CA#>CA3 Aaron
syn.tau1 = 0.45 syn.tau2 = 2.2 syn.e = 0
pre_list.append(syn)
soma syn = new Exp2Syn(0.5) //BC(GABA) syn to prox dend based on BC>CA3 Bartos PNAS (mice)
syn.tau1 = 0.3 syn.tau2 = 3.3 syn.e = -70
pre_list.append(syn)
mcdend1 [2] syn = new Exp2Syn(0.5) //HIPP(GABA) syn to prox dend based on Hilar>GC Harney&Jones
syn.tau1 = .5 syn.tau2 = 6 syn.e = -70
pre_list.append(syn)
mcdend2 [2] syn = new Exp2Syn(0.5) //HIPP(GABA) syn to prox dend based on Hilar>GC Harney&Jones
syn.tau1 = .5 syn.tau2 = 6 syn.e = -70
pre_list.append(syn)
mcdend3 [2] syn = new Exp2Syn(0.5) //HIPP(GABA) syn to prox dend based on Hilar>GC Harney&Jones
syn.tau1 = .5 syn.tau2 = 6 syn.e = -70
pre_list.append(syn)
mcdend4 [2] syn = new Exp2Syn(0.5) //HIPP(GABA) syn to prox dend based on Hilar>GC Harney&Jones
syn.tau1 = .5 syn.tau2 = 6 syn.e =-70
pre_list.append(syn)
// Total of 17 synapses 0-3 PP; 4-7 GC; 8-11 MC; 12 BC; 13-16 HIPP
}
proc connect_pre() { // $o1 target point process, $o2 returned NetCon
soma $o2 = new NetCon (&v(1), $o1)
}
func is_art() { return 0 }
endtemplate MossyCell
//**************************************************************************************************
objref Hcell[nhcell]
begintemplate HIPPCell
ndend1=3
ndend2=3
ndend3=3
ndend4=3
public pre_list, connect_pre, subsets, is_art, is_connected
public vbc2gc, vmc2gc, vhc2gc, vgc2bc, vbc2bc, vmc2bc, vhc2bc, vgc2mc, vbc2mc, vmc2mc, vhc2mc, vgc2hc, vmc2hc
public soma, hcdend1, hcdend2, hcdend3, hcdend4
create soma, hcdend1[ndend1], hcdend2[ndend2], hcdend3[ndend3], hcdend4[ndend4]
public all, pdend, ddend
objref syn, pre_list
nst=10
objectvar stim[nst]
double stimdur[nst], stimdel[nst], stimamp[nst]
public stim, stimdur, stimamp, stimdel
objref syn
proc init() {
pre_list = new List()
subsets()
temp()
synapse()
}
objref all, pdend, ddend
proc subsets() { local i
objref all, pdend, ddend
all = new SectionList()
soma all.append()
for i=0, 2 hcdend1 [i] all.append()
for i=0, 2 hcdend2 [i] all.append()
for i=0, 2 hcdend3 [i] all.append()
for i=0, 2 hcdend4 [i] all.append()
pdend = new SectionList()
hcdend1 [0] pdend.append()
hcdend2 [0] pdend.append()
hcdend3 [0] pdend.append()
hcdend4 [0] pdend.append()
ddend = new SectionList()
for i=1, 2 hcdend1 [i] ddend.append()
for i=1, 2 hcdend2 [i] ddend.append()
for i=1, 2 hcdend3 [i] ddend.append()
for i=1, 2 hcdend4 [i] ddend.append()
}
proc temp() {
soma {nseg=1 L=20 diam=10} // changed L & diam
hcdend1 [0] {nseg=1 L=75 diam=3}
hcdend1 [1] {nseg=1 L=75 diam=2}
hcdend1 [2] {nseg=1 L=75 diam=1}
hcdend2 [0] {nseg=1 L=75 diam=3}
hcdend2 [1] {nseg=1 L=75 diam=2}
hcdend2 [2] {nseg=1 L=75 diam=1}
hcdend3 [0] {nseg=1 L=50 diam=3}
hcdend3 [1] {nseg=1 L=50 diam=2}
hcdend3 [2] {nseg=1 L=50 diam=1}
hcdend4 [0] {nseg=1 L=50 diam=3}
hcdend4 [1] {nseg=1 L=50 diam=2}
hcdend4 [2] {nseg=1 L=50 diam=1}
forsec all {
insert ccanl
catau_ccanl = 10
caiinf_ccanl = 5.e-6
insert borgka
gkabar_borgka=0.0008
insert nca // HAV-N- Ca channel
gncabar_nca=0.0 //0005 check to modify- original 0.004
insert lca
glcabar_lca=0.0015
insert gskch
gskbar_gskch=0.003
insert cagk
gkbar_cagk=0.003
insert hyperde3
ghyfbar_hyperde3=0.000015
ghysbar_hyperde3=0.000015
}
soma {insert ichan2 //ildikos ichan
gnatbar_ichan2=0.2 //original 0.030 to .055
gkfbar_ichan2=0.006 //original 0.015
gl_ichan2 = 0.000036
cm=1.1}
forsec pdend {insert ichan2
gnatbar_ichan2=0.2 //original 0.015
gkfbar_ichan2=0.006
gl_ichan2 = 0.000036
cm=1.1}
forsec ddend {insert ichan2
gnatbar_ichan2=0.0
gkfbar_ichan2=0.00
gl_ichan2 = 0.000036
cm=1.1}
connect hcdend1[0](0), soma(1)
connect hcdend2[0](0), soma(1)
connect hcdend3[0](0), soma(0)
connect hcdend4[0](0), soma(0)
for i=1,2 {connect hcdend1[i](0), hcdend1[i-1](1)}
for i=1,2 {connect hcdend2[i](0), hcdend2[i-1](1)}
for i=1,2 {connect hcdend3[i](0), hcdend3[i-1](1)}
for i=1,2 {connect hcdend4[i](0), hcdend4[i-1](1)}
forsec all {Ra=100}
forsec all {enat = 55 ekf = -90 ek=-90 esk=-90 elca=130
el_ichan2 =-70.45 ehyf=-40 ehys=-40
cao_ccanl=2 } // make catau slower70e-3 cao=2 cai=50.e-6
}
objref syn
proc synapse() {
hcdend1 [0] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend similar to GC>BC
syn.tau1 = .3 syn.tau2 = .6 syn.e = 0
pre_list.append(syn)
hcdend2 [0] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend similar to GC>BC
syn.tau1 = .3 syn.tau2 = .6 syn.e = 0
pre_list.append(syn)
hcdend3 [0] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend similar to GC>BC
syn.tau1 = .3 syn.tau2 = .6 syn.e = 0
pre_list.append(syn)
hcdend4 [0] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend similar to GC>BC
syn.tau1 = .3 syn.tau2 = .6 syn.e = 0
pre_list.append(syn)
hcdend1 [1] syn = new Exp2Syn(0.5) //MC(AMPA) syn to mid dend similar to CA3>int Aaron
syn.tau1 = .9 syn.tau2 = 3.6 syn.e = 0 //*** Assumed data at physio temp
pre_list.append(syn)
hcdend2 [1] syn = new Exp2Syn(0.5) //MC(AMPA) syn to mid dend similar to CA3>int Aaron
syn.tau1 = 0.9 syn.tau2 = 3.6 syn.e = 0 //*** Assumed data at physio temp
pre_list.append(syn)
hcdend3 [1] syn = new Exp2Syn(0.5) //MC(AMPA) syn to mid dend similar to CA3>int Aaron
syn.tau1 = 0.9 syn.tau2 = 3.6 syn.e = 0 //*** Assumed data at physio temp
pre_list.append(syn)
hcdend4 [1] syn = new Exp2Syn(0.5) //MC(AMPA) syn to mid dend similar to CA3>int Aaron
syn.tau1 = 0.9 syn.tau2 = 3.6 syn.e = 0 //*** Assumed data at physio temp
pre_list.append(syn)
// Total of 12 synapses 0-3 PP; 4-7 GC; 8-11 MC
}
proc connect_pre() { // $o1 target point process, $o2 returned NetCon
soma $o2 = new NetCon (&v(1), $o1)
}
func is_art() { return 0 }
endtemplate HIPPCell
//************************************************************************************************************
objref PPSt[npp]
begintemplate PPstim
public pp, connect_pre, is_art, acell
create acell
objref pp
proc init() {
actemp()
}
proc actemp() {
acell pp = new NetStim(.5)
pp.interval = 20 //100
pp.number = 1 //1
pp.start = 2001
pp.noise = 0
}
func is_art() {return 1}
proc connect_pre() {acell $o2 = new NetCon(pp, $o1)}
endtemplate PPstim
//*************************************************************
//*************************************************************
objref SYSt[sync]
begintemplate SYstim
public pp, connect_pre, is_art
external acell_home_
objref pp
proc init() {
actemp()
}
proc actemp() {
acell_home_ pp = new NetStim(.5)
pp.interval = 400
pp.number = 20
pp.start = 10
pp.noise = 0.7
}
func is_art() {return 1}
proc connect_pre() {$o2 = new NetCon(pp, $o1)}
endtemplate SYstim
//###############################################################################################################
// NETWORK SPECIFICATION INTERFACE
for i=0, ngcell-1 {Gcell[i] = new GranuleCell(i)}
for i=0, nbcell-1 {Bcell[i] = new BasketCell(i)}
for i=0, nmcell-1 {Mcell[i] = new MossyCell(i)}
for i=0, nhcell-1 {Hcell[i] = new HIPPCell(i)}
for i =0, npp-1 {PPSt[i] = new PPstim(i)}
for i =0, sync-1 {SYSt[i] = new SYstim(i)}
objref nclist, netcon, cells, net_c, net_d, net_gr, net_bc, net_mc, net_hc, vbc2gc, vmc2gc, vhc2gc
{ cells = new List()
nclist = new List()
}
func cell_append() {cells.append($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 vbc2gc, vmc2gc, vhc2gc, vgc2bc, vbc2bc, vmc2bc, vhc2bc, vgc2mc, vbc2mc, vmc2mc, vhc2mc, vgc2hc, vmc2hc,vgc2gc
objref killMC, killHC
{
vgc2bc = new Vector(nbcell, 0)
vbc2bc = new Vector(nbcell, 0)
vmc2bc = new Vector(nbcell, 0)
vhc2bc = new Vector(nbcell, 0)
vgc2mc = new Vector(nmcell, 0)
vbc2mc = new Vector(nmcell, 0)
vmc2mc = new Vector(nmcell, 0)
vhc2mc = new Vector(nmcell, 0)
vgc2hc = new Vector(nhcell, 0)
vmc2hc = new Vector(nhcell, 0)
vbc2gc = new Vector(ngcell, 0)
vmc2gc = new Vector(ngcell, 0)
vhc2gc = new Vector(ngcell, 0)
vgc2gc = new Vector(ngcell, 0)
killMC = new Vector(mcKILL, -1)
killHC = new Vector(hcKILL, -1)
}
//initiating randm number generator
objref rdsynb, rdsyna, rdgc2hc, rdgc2bc, rdgc2mc, rdbc2gc, rdbc2bc, rdbc2mc, deadMC, deadHC, rdgap, rddend
objref rdmc2gc1, rdmc2gc2, rdmc2bc, rdmc2mc, rdmc2mc1, rdmc2hc, rdhc2gc, rdhc2bc, rdhc2mc, rdgc2gc
/*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=53641.34
//************************************GC***********************************************
rdgc2bc = new Random(rseed) // use for syn.connections
proc new_rdgc2bc() {rdgc2bc.discunif(-1,1)}
new_rdgc2bc()
rdgc2mc = new Random(rseed) // use for syn.connections
proc new_rdgc2mc() {rdgc2mc.discunif(0,2)}
new_rdgc2mc()
rdgc2hc = new Random(rseed) // use for syn.connections
proc new_rdgc2hc() {rdgc2hc.discunif(-2 , 2)}
new_rdgc2hc()
rdgc2gc = new Random(rseed) // use for syn.connections
proc new_rdgc2gc() {rdgc2gc.discunif(-50, 50)}
new_rdgc2gc()
//************************************BC***********************************************
rdbc2gc = new Random(rseed) // use for syn.connections
proc new_rdbc2gc() {rdbc2gc.discunif(-70, 70)}
new_rdbc2gc()
rdbc2bc = new Random(rseed) // use for syn.connections
proc new_rdbc2bc() {rdbc2bc.discunif(-1, 1)}
new_rdbc2bc()
rdbc2mc = new Random(rseed) // use for syn.connections
proc new_rdbc2mc() {rdbc2mc.discunif(-3, 3)}
new_rdbc2mc()
rdgap = new Random(rseed)
proc new_rdgap() {rdgap.discunif(-1,1)} // use for gap junc
new_rdgap()
rddend = new Random(rseed)
proc new_rddend() {rddend.discunif(0,3)}
new_rddend()
//*************************************MC********************************************
deadMC = new Random(rseed) // use for syn.connections
proc new_deadMC() {deadMC.discunif(ngcell+nbcell, ngcell+nbcell+nmcell-1)}
new_deadMC()
for i= 0, mcKILL-1 {
MC = deadMC.repick()
if (killMC.contains(MC) == 0) {
killMC.x[i] = MC
} else {i -=1}
}
rdmc2gc1 = new Random(rseed) // use for syn.connections
proc new_rdmc2gc1() {rdmc2gc1.discunif(25, 175)}
new_rdmc2gc1()
rdmc2gc2 = new Random(rseed) // use for syn.connections
proc new_rdmc2gc2() {rdmc2gc2.discunif(-175, -25)}
new_rdmc2gc2()
rdmc2bc = new Random(rseed) // use for syn.connections
proc new_rdmc2bc() {rdmc2bc.discunif(-3,3)}
new_rdmc2bc()
rdmc2mc = new Random(rseed) // use for syn.connections
proc new_rdmc2mc() {rdmc2mc.discunif(ngcell+nbcell, ngcell+nbcell+nmcell-1)}
new_rdmc2mc()
rdmc2mc1 = new Random(rseed) // use for syn.connections
proc new_rdmc2mc1() {rdmc2mc1.discunif(-3, 3)}
new_rdmc2mc1()
rdmc2hc = new Random(rseed) // use for syn.connections
proc new_rdmc2hc() {rdmc2hc.discunif(-2, 2)}
new_rdmc2hc()
//*************************************HC********************************************
deadHC = new Random(rseed) // use for syn.connections
proc new_deadHC() {deadHC.discunif(ngcell+nbcell+nmcell, ngcell+nbcell+nmcell+nhcell-1)}
new_deadHC()
for i= 0, hcKILL-1 {
HC = deadHC.repick()
if(killHC.contains(HC) == 0) {
print HC
killHC.x[i] = HC
} else {i -=1}
}
rdhc2gc = new Random(rseed) // use for syn.connections
proc new_rdhc2gc() {rdhc2gc.discunif(-130, 130)}
new_rdhc2gc()
rdhc2bc = new Random(rseed) // use for syn.connections
proc new_rdhc2bc() {rdhc2bc.discunif(-2, 2)}
new_rdhc2bc()
rdhc2mc = new Random(rseed) // use for syn.connections
proc new_rdhc2mc() {rdhc2mc.discunif(-2, 2)}
new_rdhc2mc()
//*********************************************************************************
rdsyna = new Random(rseed) // initialize random distr.
proc new_rdsyna() {rdsyna.discunif(0, 1)}
new_rdsyna()
rdsynb = new Random(rseed) // initialize random distr.
proc new_rdsynb() {rdsynb.discunif(0, 3)}
new_rdsynb()
// NETWORK INITIATION
for i = 0, ngcell-1 {cell_append(Gcell[i])} // cells 0-4 GCs
for i = 0, nbcell-1 {cell_append(Bcell[i])} // cells 5-6 BC
for i = 0, nmcell-1 {cell_append(Mcell[i])} // cell 7 MC
for i = 0, nhcell-1 {cell_append(Hcell[i])} // cell 8 HC
for i = 0, npp-1 {cell_append(PPSt[i])} // cell 9 PP
for i = 0, sync-1 {cell_append(SYSt[i])}
//********************************************Preforant Path synaptic connections ************************************************
objref randomVector, connectionFile
proc initPP() { local i,j
for i=450,550 {
nc_append(ngcell+nbcell+nmcell+nhcell, i, 0, 2e-2, 3, 10) // Gcell[3] to Bcell[1]
nc_append(ngcell+nbcell+nmcell+nhcell, i, 1, 2e-2, 3, 1) // Gcell[3] to Bcell[1]
}
for j= 1005,1006 {
nc_append(ngcell+nbcell+nmcell+nhcell, j, 0, 0.5e-2, 3, 10) // Gcell[3] to Bcell[1]
nc_append(ngcell+nbcell+nmcell+nhcell, j, 1, 0.5e-2, 3, 10) // Gcell[3] to Bcell[1]
}
}
//******************************************************************************************
//**************Sync Stim connections connections ******************************
objref randomVector, connectionFile
proc initSY() { local i,j
for j=0, ngcell-1 {
nc_append(j+ngcell+nbcell+nmcell+nhcell+npp, j, 0, 2e-2, 3, 10) // Gcell[3] to Bcell[1]
nc_append(j+ngcell+nbcell+nmcell+nhcell+npp, j, 1, 2e-2, 3, 1) // Gcell[3] to Bcell[1]
}
for i= ngcell, ngcell+nbcell-1 {
nc_append(i+ngcell+nbcell+nmcell+nhcell+npp, i, 0, 0.25e-2, 3, 10) // Gcell[3] to Bcell[1]
nc_append(i+ngcell+nbcell+nmcell+nhcell+npp, i, 1, 0.25e-2, 3, 10) // Gcell[3] to Bcell[1]
}
}
//******************************************************************************************
//******************************************************************
randomVector = new Vector(ngcell)
connectionFile = new File()
connectionFile.wopen("./connections.dat")
//**************Granule Cell post synaptic connections ******************************
proc initGcell() { local i,j
for i=0, ngcell-1 {
connectionFile.printf("%d\t",i)
vectorIndex = 0
randomVector.resize(nbcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 2) {
if (i < 84) { a=0}
if ((i > 83) && (i < 166)) { a=1}
if ((i > 165) && (i < 252)) { a=2}
if ((i > 251) && (i < 336)) { a=3}
if ((i > 335) && (i < 420)) { a=4}
if ((i > 419) && (i < 500)) { a=5}
if ((i > 499) && (i < 582)) {a=6}
if ((i > 581) && (i < 663)) {a=7}
if ((i > 662) && (i < 745)) {a=8}
if ((i > 744) && (i < 827)) {a=9}
if ((i > 826) && (i < 909)) {a=10}
if ((i > 908) && (i < 1000)){a=11}
Gauz3 = rdgc2bc.repick()
if (a+Gauz3 > nbcell-1) {npost = a+Gauz3-nbcell }
if (a+Gauz3 < 0) {npost = a+Gauz3+nbcell}
if ((a+Gauz3 > -1) && (a+Gauz3 < nbcell)) {npost = a+Gauz3}
if ((randomVector.x[npost] == 0) && (vgc2bc.x[npost] < 175)) {
randomVector.x[npost] += 1
vgc2bc.x[npost] += 1
}
dbr = rdsynb.repick()
}
for k = 0, randomVector.size-1 {
if (randomVector.x[k] == 1) {
nc_append(i, ngcell+k, dbr+2, 4.7e-3, .8, 10)
connectionFile.printf("%d\t",ngcell+k)
}
}
randomVector.resize(nmcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 1) {
if (i < 100) { a=0}
if ((i > 99) && (i < 200)) { a=1}
if ((i > 199) && (i < 300)) { a=2}
if ((i > 299) && (i < 400)) { a=3}
if ((i > 399) && (i < 500)) { a=4}
if ((i > 499) && (i < 600)) { a=5}
if ((i > 599) && (i < 700)) { a=6}
if ((i > 699) && (i < 800)) { a=7}
if ((i > 799) && (i < 900)) { a=8}
if ((i > 899) && (i < 1000)) { a=9}
b=a*3
npost = rdgc2mc.repick()
if ((randomVector.x[npost+b] == 0) && (vgc2mc.x[npost+b] < 38)) {
randomVector.x[npost+b] += 1
vgc2mc.x[npost+b] += 1
}
dbr = rdsynb.repick()
}
for k = 0, randomVector.size-1 {
if ((randomVector.x[k] == 1)&& (killMC.contains(ngcell+nbcell+k) == 0)) {
nc_append(i, ngcell+nbcell+k, dbr+4, 0.2e-3, 1.5, 10)
connectionFile.printf("%d\t",ngcell+nbcell+k)
}
}
randomVector.resize(nhcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 3) {
if (i < 84) { a=0}
if ((i > 83) && (i < 166)) {a=1}
if ((i > 165) && (i < 252)) {a=2}
if ((i > 251) && (i < 336)) {a=3}
if ((i > 335) && (i < 420)) {a=4}
if ((i > 419) && (i < 500)) {a=5}
if ((i > 499) && (i < 582)) {a=6}
if ((i > 581) && (i < 663)) {a=7}
if ((i > 662) && (i < 745)) {a=8}
if ((i > 744) && (i < 827)) {a=9}
if ((i > 826) && (i < 909)) {a=10}
if ((i > 908) && (i < 1000)){a=11}
Gauz3 = rdgc2hc.repick()
if (a+Gauz3 > nhcell-1) {npost = a+Gauz3-nhcell }
if (a+Gauz3 < 0) {npost = a+Gauz3+nhcell}
if ((a+Gauz3 > -1) && (a+Gauz3 < nhcell)) {npost = a+Gauz3}
if ((randomVector.x[npost] == 0) && (vgc2hc.x[npost] < 275)) {
randomVector.x[npost] += 1
vgc2hc.x[npost] += 1
}
dbr = rdsynb.repick()
}
for k = 0, randomVector.size-1 {
if (randomVector.x[k] == 1) {
nc_append(i, ngcell+nbcell+nmcell+k, dbr, 0.5e-3, 1.5, 10)
connectionFile.printf("%d\t",ngcell+nbcell+nmcell+k)
}
}
// print npost, dbr
randomVector.resize(ngcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < sproutNumber) {
Gauz3 = rdgc2gc.repick()
if (i+Gauz3 > ngcell-1) {npost = i+Gauz3-ngcell }
if (i+Gauz3 < 0) {npost = i+Gauz3+ngcell}
if ((i+Gauz3 > -1) && (i+Gauz3 < ngcell)) {npost = i+Gauz3}
if ((randomVector.x[npost] == 0) && (vgc2gc.x[npost] < sproutNumber + 0.15*sproutNumber + 8)) {
randomVector.x[npost] += 1
vgc2gc.x[npost] += 1
}
dbr = rdsyna.repick()
}
for k = 0, randomVector.size-1 {
if (randomVector.x[k] == 1) {
nc_append(i, k, dbr+7, Spr*2e-3, .8, 10) // (i, k, dbr+7, 2e-6, .8, 10)
connectionFile.printf("%d\t",k)
}
}
print i
connectionFile.printf("-1\n")
}
}
//**************Basket Cell post synaptic connections ******************************
proc initBcell() { local i,j, u, v, w
u=0
v=0
w=0
for i=0, nbcell-1 {
connectionFile.printf("%d\t",i)
randomVector.resize(ngcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 100) {
Gauz3 = rdbc2gc.repick()
if (i*83+41+Gauz3 > ngcell-1) {npost = i*83+41+Gauz3-ngcell }
if (i*83+41+Gauz3 < 0) {npost = i*83+41+Gauz3+ngcell}
if ((i*83+41+Gauz3 > -1) && (i*83+41+Gauz3 < ngcell)) {npost = i*83+41+Gauz3}
if ((randomVector.x[npost] == 0) && (vbc2gc.x[npost] < 2)) {
randomVector.x[npost] += 1
vbc2gc.x[npost] += 1
}
}
for k = 0, randomVector.size-1 {
if (randomVector.x[k] == 1) {
nc_append(i+ngcell, k, 6, 1.6e-3, .85, 0) //(i+ngcell, k, 6, 1.6e-3, .85, 10)
print "Connecting ",i+ngcell," to ",k," ****************** ",randomVector.sum
connectionFile.printf("%d\t",k)
}
}
randomVector.resize(nbcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 2) {
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] < 3)) {
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+ngcell, k+ngcell, dbr+8, 7.6e-3, .8, 0) // (i+ngcell, k+ngcell, dbr+8, 7.6e-3, .8, 10)
print "Connecting ",i+ngcell," to ",k+ngcell
connectionFile.printf("%d\t",k+ngcell)
//print "starting tonic connect" bc to bc
u=k+ngcell
v=u+1
w=u-1
r=0.5*TC
if (v > 1011) {v = v-1}
if (w < 1000) {w = w+1}
nc_append(i+ngcell, v, 12, r*0.2e-3, 2, 10)
nc_append(i+ngcell, v, 13, r*0.2e-3, 2, 10)
nc_append(i+ngcell, v, 14, r*0.1e-3, 4, 10)
nc_append(i+ngcell, v, 15, r*0.1e-3, 4, 10)
nc_append(i+ngcell, v, 16, r*0.1e-3, 4, 10)
nc_append(i+ngcell, v, 17, r*0.1e-3, 4, 10)
nc_append(i+ngcell, v, 18, r*0.05e-3, 8, 10)
nc_append(i+ngcell, v, 19, r*0.05e-3, 8, 10)
nc_append(i+ngcell, u, 12, TC*0.2e-3, 2, 10)
nc_append(i+ngcell, u, 13, TC*0.2e-3, 2, 10)
nc_append(i+ngcell, u, 14, TC*0.1e-3, 4, 10)
nc_append(i+ngcell, u, 15, TC*0.1e-3, 4, 10)
nc_append(i+ngcell, u, 16, TC*0.1e-3, 4, 10)
nc_append(i+ngcell, u, 17, TC*0.1e-3, 4, 10)
nc_append(i+ngcell, u, 18, TC*0.05e-3, 8, 10)
nc_append(i+ngcell, u, 19, TC*0.05e-3, 8, 10)
nc_append(i+ngcell, w, 12, r*0.2e-3, 2, 10)
nc_append(i+ngcell, w, 13, r*0.2e-3, 2, 10)
nc_append(i+ngcell, w, 14, r*0.1e-3, 4, 10)
nc_append(i+ngcell, w, 15, r*0.1e-3, 4, 10)
nc_append(i+ngcell, w, 16, r*0.1e-3, 4, 10)
nc_append(i+ngcell, w, 17, r*0.1e-3, 4, 10)
nc_append(i+ngcell, w, 18, r*0.05e-3, 8, 10)
nc_append(i+ngcell, w, 19, r*0.05e-3, 8, 10)
connectionFile.printf("%d\t",k)
}
}
randomVector.resize(nmcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 5) {
Gauz3 = rdbc2mc.repick()
if (i*2+2+Gauz3 > nmcell-1) {npost = i*2+2+Gauz3-nmcell }
if (i*2+2+Gauz3 < 0) {npost = i*2+2+Gauz3+nmcell}
if ((i*2+2+Gauz3 >-1) && (i*2+2+Gauz3 < nmcell)) {npost = i*2+2+Gauz3}
//print npost
if ((randomVector.x[npost] == 0) && (vbc2mc.x[npost] < 3)) {
randomVector.x[npost] += 1
vbc2mc.x[npost] += 1
}
}
for k = 0, randomVector.size-1 {
if ((randomVector.x[k] == 1)&& (killMC.contains(ngcell+nbcell+k) == 0)) {
nc_append(i+ngcell, k+ngcell+nbcell, 12, 1.5e-3, 1.5, 0) //(i+ngcell, k+ngcell+nbcell, 12, 1.5e-3, 1.5, 10)
print "Connecting ",i+ngcell," to ",k+ngcell+nbcell
connectionFile.printf("%d\t",ngcell+nbcell+k)
}
}
print i
connectionFile.printf("-1\n")
}
}
//**************Mossy Cell post synaptic connections ******************************
proc initMcell() {local i,j
for i=0, nmcell-1 {
if (killMC.contains(ngcell+nbcell+i) == 0) {
connectionFile.printf("%d\t",i)
if (i < 3) { y=0}
if ((i > 2) && (i < 6)) { y=1}
if ((i > 5) && (i < 9)) { y=2}
if ((i > 8) && (i < 12)) { y=3}
if ((i > 11) && (i < 15)) { y=4}
if ((i > 14) && (i < 18)) { y=5}
if ((i > 17) && (i < 21)) { y=6}
if ((i > 20) && (i < 24)) { y=7}
if ((i > 23) && (i < 27)) { y=8}
if ((i > 26) && (i < 30)) { y=9}
print "I got here 2"
randomVector.resize(ngcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 100) {
Gauz1 = rdmc2gc1.repick()
if (i*33+17+Gauz1 > ngcell-1) {
npost1 = i*33+17+Gauz1-ngcell
} else {npost1 =i*33+17+Gauz1}
print "I got here 3 ******************** ", randomVector.sum
if ((randomVector.x[npost1] == 0) && (vmc2gc.x[npost1] < 7)) {
randomVector.x[npost1] += 1
vmc2gc.x[npost1] += 1
}
dbr = rdsyna.repick()
}
print "I got here 4"
for k = 0, randomVector.size-1 {
if (randomVector.x[k] == 1) {
nc_append(i+ngcell+nbcell, k, dbr+2, 0.3e-3, 3, 10)
print "Connecting ",i+ngcell+nbcell," to ",k
connectionFile.printf("%d\t",k)
}
}
randomVector.resize(ngcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 100) {
Gauz2 = rdmc2gc2.repick()
if (i*33+17+Gauz2 < 0) {
npost2 =i*33+17+Gauz2+ngcell
} else {npost2 =i*33+17+Gauz2}
if ((randomVector.x[npost2] == 0) && (vmc2gc.x[npost2] < 7)) {
randomVector.x[npost2] += 1
vmc2gc.x[npost2] += 1
}
dbr = rdsyna.repick()
}
for k = 0, randomVector.size-1 {
if (randomVector.x[k] == 1) {
nc_append(i+ngcell+nbcell, k, dbr+2, 0.3e-3, 3, 10)
connectionFile.printf("%d\t",k)
}
}
randomVector.resize(nbcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 1) {
Gauz3 = rdmc2bc.repick()
if (y+Gauz3 > nbcell-1) {npost = y+Gauz3-nbcell}
if (y+Gauz3 < 0) {npost = y+Gauz3+nbcell}
if ((y+Gauz3 > -1) && (y+Gauz3 < nbcell)) {npost = y+Gauz3}
if ((randomVector.x[npost] == 0) && (vmc2bc.x[npost] < 4) && (Gauz3 != 0)) {
randomVector.x[npost] += 1
vmc2bc.x[npost] += 1
}
dbr = rdsyna.repick()
}
for k = 0, randomVector.size-1 {
if (randomVector.x[k] == 1) {
nc_append(i+ngcell+nbcell, ngcell+k, dbr+6, 0.3e-3, 3, 10)
connectionFile.printf("%d\t",k+ngcell)
}
}
randomVector.resize(nmcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 3) {
Gauz3 = rdmc2mc1.repick()
//print Gauz3
if (i+Gauz3 > nmcell-1) {npost = i+Gauz3-nmcell }
if (i+Gauz3 < 0) {npost = i+Gauz3+nmcell}
if ((i+Gauz3 >-1) && (i+Gauz3 < nmcell)) {npost = i+Gauz3}
//print npost
if ((randomVector.x[npost] == 0) && (vmc2mc.x[npost] < 4) && (Gauz3 != 0)) {
randomVector.x[npost] += 1
vmc2mc.x[npost] += 1
}
dbr = rdsynb.repick()
}
for k = 0, randomVector.size-1 {
if ((randomVector.x[k] == 1)&& (killMC.contains(ngcell+nbcell+k) == 0)) {
nc_append(i+ngcell+nbcell, k+ngcell+nbcell, dbr+8, 0.5e-3, 2, 10)
connectionFile.printf("%d\t",k+ngcell+nbcell)
}
}
randomVector.resize(nhcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 2) {
Gauz3 = rdmc2hc.repick()
if (y+Gauz3 > nhcell-1) {npost = y+Gauz3-nhcell}
if (y+Gauz3 < 0) {npost = y+Gauz3+nhcell}
if ((y+Gauz3 > -1) && (y+Gauz3 < nhcell)) {npost = y+Gauz3}
if ((randomVector.x[npost] == 0) && (vmc2hc.x[npost] < 7) && (Gauz3 != 0)) {
randomVector.x[npost] += 1
vmc2hc.x[npost] += 1
}
dbr = rdsynb.repick()
}
for k = 0, randomVector.size-1 {
if ((randomVector.x[k] == 1)&& (killHC.contains(ngcell+nbcell+nmcell+k) == 0)) {
nc_append(i+ngcell+nbcell, ngcell+nbcell+nmcell+k, dbr+4, 0.2e-3, 3, 10)
connectionFile.printf("%d\t",k+ngcell+nbcell+nmcell)
}
}
print i
connectionFile.printf("-1\n")
}
}
}
//******************************************************************************************
//**************HIPP Cell post synaptic connections ******************************
proc initHcell() { local i,j
for i=0, nhcell-1 {
if (killHC.contains(ngcell+nbcell+nmcell+i) == 0) {
connectionFile.printf("%d\t",i)
randomVector.resize(ngcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 160) {
Gauz3 = rdhc2gc.repick()
if (i*83+41+Gauz3 > ngcell-1) {npost = i*83+41+Gauz3-ngcell }
if (i*83+41+Gauz3 < 0) {npost = i*83+41+Gauz3+ngcell}
if ((i*83+41+Gauz3 > -1) && (i*83+41+Gauz3 < ngcell)) {npost = i*83+41+Gauz3}
if ((randomVector.x[npost] == 0) && (vhc2gc.x[npost] < 3)) {
randomVector.x[npost] += 1
vhc2gc.x[npost] += 1
}
dbr = rdsyna.repick()
}
for k = 0, randomVector.size-1 {
if (randomVector.x[k] == 1) {
for z= 0, InhNet-1 {
Drand=rdmc2hc.repick()
Drand=Drand*0.05
dbr = rdsyna.repick()
nc_append(i+ngcell+nbcell+nmcell, k, dbr+4, IPSCmod*0.5e-3, 1.6, 10)
}
connectionFile.printf("%d\t",k)
}
}
randomVector.resize(nbcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 4) {
Gauz3 = rdhc2bc.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) && (vhc2bc.x[npost] < nbcell-1)) {
randomVector.x[npost] += 1
vhc2bc.x[npost] += 1
}
dbr = rdsyna.repick()
}
for k = 0, randomVector.size-1 {
if (randomVector.x[k] == 1) {
nc_append(i+ngcell+nbcell+nmcell, k+ngcell, dbr+10, 0.5e-3, 1.6, 10)
connectionFile.printf("%d\t",k+ngcell)
//print "starting tonic connect" hipp to bc
u=k+ngcell
v=u+1
w=u-1
r=0.5*TC
if (v > 1011) {v = v-1}
if (w < 1000) {w = w+1}
nc_append(i+ngcell+nbcell+nmcell, v, 12, r*0.05e-3, 2, 10)
nc_append(i+ngcell+nbcell+nmcell, v, 13, r*0.05e-3, 2, 10)
nc_append(i+ngcell+nbcell+nmcell, v, 14, r*0.005e-3, 4, 10)
nc_append(i+ngcell+nbcell+nmcell, v, 15, r*0.005e-3, 4, 10)
nc_append(i+ngcell+nbcell+nmcell, v, 16, r*0.005e-3, 4, 10)
nc_append(i+ngcell+nbcell+nmcell, v, 17, r*0.005e-3, 4, 10)
nc_append(i+ngcell+nbcell+nmcell, v, 18, r*0.001e-3, 8, 10)
nc_append(i+ngcell+nbcell+nmcell, v, 19, r*0.001e-3, 8, 10)
nc_append(i+ngcell+nbcell+nmcell, u, 12, TC*0.05e-3, 2, 10)
nc_append(i+ngcell+nbcell+nmcell, u, 13, TC*0.05e-3, 2, 10)
nc_append(i+ngcell+nbcell+nmcell, u, 14, TC*0.005e-3, 4, 10)
nc_append(i+ngcell+nbcell+nmcell, u, 15, TC*0.005e-3, 4, 10)
nc_append(i+ngcell+nbcell+nmcell, u, 16, TC*0.005e-3, 4, 10)
nc_append(i+ngcell+nbcell+nmcell, u, 17, TC*0.005e-3, 4, 10)
nc_append(i+ngcell+nbcell+nmcell, u, 18, TC*0.001e-3, 8, 10)
nc_append(i+ngcell+nbcell+nmcell, u, 19, TC*0.001e-3, 8, 10)
nc_append(i+ngcell+nbcell+nmcell, w, 12, r*0.05e-3, 2, 10)
nc_append(i+ngcell+nbcell+nmcell, w, 13, r*0.05e-3, 2, 10)
nc_append(i+ngcell+nbcell+nmcell, w, 14, r*0.005e-3, 4, 10)
nc_append(i+ngcell+nbcell+nmcell, w, 15, r*0.005e-3, 4, 10)
nc_append(i+ngcell+nbcell+nmcell, w, 16, r*0.005e-3, 4, 10)
nc_append(i+ngcell+nbcell+nmcell, w, 17, r*0.005e-3, 4, 10)
nc_append(i+ngcell+nbcell+nmcell, w, 18, r*0.001e-3, 8, 10)
nc_append(i+ngcell+nbcell+nmcell, w, 19, r*0.001e-3, 8, 10)
connectionFile.printf("%d\t",k)
}
}
randomVector.resize(nmcell)
for k = 0, randomVector.size-1 {randomVector.x[k]=0}
while (randomVector.sum < 4) {
Gauz3 = rdhc2mc.repick()
//print Gauz3
if (i*2+2+Gauz3 > nmcell-1) {npost = i*2+2+Gauz3-nmcell }
if (i*2+2+Gauz3 < 0) {npost = i*2+2+Gauz3+nmcell}
if ((i*2+2+Gauz3 >-1) && (i*2+2+Gauz3 < nmcell)) {npost = i*2+2+Gauz3}
//print npost
if ((randomVector.x[npost] == 0) && (vhc2mc.x[npost] < 2)) {
randomVector.x[npost] += 1
vhc2mc.x[npost] += 1
}
dbr = rdsynb.repick()
}
for k = 0, randomVector.size-1 {
if ((randomVector.x[k] == 1)&& (killMC.contains(ngcell+nbcell+k) == 0)) {
nc_append(i+ngcell+nbcell+nmcell, k+ngcell+nbcell, dbr+13, 1.5e-3, 1, 10)
connectionFile.printf("%d\t",k+ngcell+nbcell)
}
}
print i
connectionFile.printf("-1\n")
}
}
}
//*******************************************************************************************************
//*********************GAPS************************************
objref gaps[12]
for i=0,11{
gaps[i] = new Gap(0.5)
gaps[i].r = 100000
}
n=2
for i=0,5{
npost = rdgap.repick()
d = rddend.repick()
m=n*i //for bcells
x=n*i //for gaps
post = npost+m
if (m == post){post +=1} //makes the gap junctions connected in between neighbouring cells
if (post <= 0){post = nbcell-1}
Bcell[m].bcdend1[d] gaps[x].loc(0.5)
Bcell[post].bcdend1[d] gaps[x+1].loc(0.5)
setpointer gaps[x].vgap, Bcell[post].bcdend1[d].v(0.5)
setpointer gaps[x+1].vgap, Bcell[m].bcdend1[d].v(0.5)
}
//*********************************Print out Net cons***************************************************
strdef strvar
objref dfile
dfile = new File()
proc saveNet(){ local i
//dfile.wopen("/home/rob/testneuron/vijireview/NAI75s1")
dfile.wopen("N_25% -74 spill n tonic 10uS.txt")
dfile.printf("Precell \tps.tcell \t Synapse \n")
for i=0, nclist.count-1 {
dfile.printf("%s\t%s\t%s\n", nclist.object[i].precell, nclist.object[i].postcell, nclist.object[i].syn)}
dfile.printf("TO BC\n GC \tBC \tMC \tHC \n")
for i= 0, nbcell-1 {dfile.printf("%d\t%d\t%d\t%d \n", vgc2bc.x[i], vbc2bc.x[i], vmc2bc.x[i], vhc2bc.x[i])}
print "BCout"
dfile.printf("TO MC\n GC \tBC \tMC \tHC \n")
for i= 0, nmcell-1 {dfile.printf("%d\t%d\t%d\t%d\n", vgc2mc.x[i], vbc2mc.x[i], vmc2mc.x[i], vhc2mc.x[i])}
print "MCout"
dfile.printf("TO HC \n GC\t MC\n")
for i= 0, nhcell-1 {dfile.printf("%d\t%d\n", vgc2hc.x[i], vmc2hc.x[i])}
print "HCout"
dfile.printf("TO GC\n BC\t MC\t HC\t GC\t \n")
for i= 0, ngcell-1 {dfile.printf("%d\t%d\t%d\t%d\n", vbc2gc.x[i], vmc2gc.x[i], vhc2gc.x[i], vgc2gc.x[i])}
print "GCout"
dfile.close("N_25% -74 spill n tonic 10uS.txt")
}
proc Chk(){
dfile.aopen("N_25% -74 spill n tonic 10uS.txt")
dfile.printf("tTC\tSpr\tsproutNumber\trseed\t")
dfile.printf("Sprouting\t")
dfile.printf("\n")
//dfile.printf("%f\t", cells.object[Vcell].fl_list.object[0].g_i0)
dfile.printf("%f\t", TC)
dfile.printf("%f\t", Spr)
dfile.printf("%f\t", sproutNumber)
dfile.printf("%f\t", rseed)
//dfile.printf("%f\t", cells.object[ngcell+nbcell+nmcell+1].fl_list.object[0].g_i0)
//dfile.printf("%f\t", InhNet)
dfile.printf("\n")
dfile.close("N_25% -74 spill n tonic 10uS.txt")
print TC, Spr, sproutNumber, rseed
}
//******************************************************************************************
strdef strmat
objref efile
efile = new File()
efile.wopen("M_25% -74 spill n tonic 10uS.txt")
efile.printf("t\t")
for i = 0, 49 {
b = i*10
efile.printf("%s\t", cells.object[b])}
for i = 998, cells.count-npp-sync-1{
efile.printf("%s\t", cells.object[i])}
efile.printf("\n")
efile.close("M_25% -74 spill n tonic 10uS.txt")
proc sMatrix(){ local j
efile.aopen("M_25% -74 spill n tonic 10uS.txt")
efile.printf("%f\t", t)
for i = 0, 49 {
b = i*10
efile.printf("%f\t", cells.object[b].soma.v(0.5))}
for j =1000, cells.count-npp-sync-1 {
efile.printf("%f\t", cells.object[j].soma.v(0.5))}
efile.printf("\n")
efile.close("M_25% -74 spill n tonic 10uS.txt")}
strdef strvcell
objref gfile
gfile = new File()
gfile.wopen("IGABA soma 25% -74 spill n tonic 10uS.txt")
gfile.printf("t\t")
for i=0,1{
gfile.printf("%s\t", Bcell[i])}
gfile.printf("\n")
gfile.close("IGABA soma 25% -74 spill n tonic 10uS.txt")
proc gMatrix(){ local i
gfile.aopen("IGABA soma 25% -74 spill n tonic 10uS.txt")
gfile.printf("%f\t", t)
for i = 0, 0 {
gfile.printf("%f\t", Bcell[i].soma.igaba_tonic(0.5))}
gfile.printf("\n")
gfile.close("IGABA soma 25% -74 spill n tonic 10uS.txt")
}
strdef strmat
objref jfile
jfile = new File()
jfile.wopen("gapcurrents_10uS_74.txt")
jfile.printf("t\t")
for i = 0, 11 {
jfile.printf("%s\t", Gap[i])}
jfile.printf("\n")
jfile.close("gapcurrents_10uS_74.txt")
proc jMatrix(){ local i
jfile.aopen("gapcurrents_10uS_74.txt")
jfile.printf("%f\t", t)
for i = 0, 11 {
jfile.printf("%f\t", Gap[i].i_gap)}
jfile.printf("\n")
jfile.close("gapcurrents_10uS_74.txt")
}
objref VmT
objref VmMat[cells.count-npp-sync]
VmT = new Vector()
for i=0, cells.count-npp-sync-1 {
VmMat[i] = new Vector()
}
proc VecMx() { local i
VmT.append(t)
for i=0, cells.count-npp-sync-1 {
VmMat[i].append( cells.object[i].soma.v(0.5))
}
}
objref Spike[cells.count-1]
for i=0, cells.count-npp-sync-1 {
Spike[i] = new Vector()
}
strdef Spkstr
objref dfile
dfile = new File()
proc SpkMx() { local i, j
k = 0
for i=0, cells.count-npp-sync-1 {
Spike[i].spikebin(VmMat[i], 0)
}
dfile.wopen("S_25% -74 spill n tonic 10uS.txt")
while(k < VmT.size) {
for j = 0, cells.count-npp-sync-1 {
if(Spike[j].x[k] != 0) {
dfile.printf("%f\t%d\n", VmT.x[k], j)}
}
k +=1 }
dfile.close("S_25% -74 spill n tonic 10uS.txt")
}
objref r_plt
proc initrPlt() {
r_plt = new Graph(0)
r_plt.size(0, tstop,0, cells.count-npp-sync)
r_plt.label(0.95, 0.02, "ms")
r_plt.label(0.01, 0.82, "neu")
r_plt.view(0,0, tstop, cells.count-npp-sync,320,20,300,230)
}
initrPlt()
proc plotAP() { local i, a
a=1
r_plt.erase()
while(j < cells.count-npp-sync-1) {
for i = 0, VmT.size-1 {
if ((j > ngcell-1)&&(j < ngcell+nbcell-1)) { a=2}
if ((j > ngcell+nbcell-1)&&(j < ngcell+nbcell+nmcell-1)) { a=3 }
if ((j > ngcell+nbcell+nmcell-1)&&(j < ngcell+nbcell+nmcell+nhcell-1)) { a=4}
if (j > ngcell+nbcell+nmcell+nhcell-1) { a=5}
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()
jMatrix()
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 = 3500 //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("Gcell[450].soma.v(0.5)",1,1)
save_window_.addexpr("Gcell[0].soma.v(0.5)",1,1)
save_window_.addexpr("Bcell[1].soma.v(0.5)",2,1)
save_window_.addexpr("Mcell[0].soma.v(0.5)",3,1)
save_window_.addexpr("Hcell[0].soma.v(0.5)",4,1)
}
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[0].bcdend4[0].igaba_tonic",2,1)
save_window_.addexpr("Bcell[0].soma.igaba_tonic",3,1)
save_window_.addexpr("Gap[0].i_gap",4)
proc rrun(){
run()
SpkMx()
Chk()
}
proc custom_init() {
initPP()
initSY()
initGcell()
initBcell()
initMcell()
initHcell()
saveNet()
}
xpanel("Yu et al 2013")
xbutton("Custom initialization", "{custom_init()}")
xbutton("Custom run", "{rrun() plotAP()}")
xpanel()
objectvar scene_vector_[1]
{doNotify()}
//quit()
