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testnet.hoc
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testnet.hoc
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// this file is a modified version of RI10sp.hoc that was created for
// tests: if run without errors it implies the longer original version
// of this file would run without errors. Also once this shorter file is
// run a modeler can explore the cells and mechanisms with modelview
// if desired.
// The network connectivity generated in this file is not intended to
// represent anything and therefore should be disregarded as a triviality
// or rather a matter of convenience for testing...
// From modified RI10sp.hoc file:
// 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
// The synaptic parameters need to be checked
secondorder=2
tstep=0
period=2
dt=0.1
tstop=5 //300 or 1500
// define network size
ngcell = 5
nbcell = 2
nmcell = 2
nhcell = 2
npp = 1
// 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]
//***********************************************************************************************
//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
nst=10
objectvar stim[nst]
double stimdur[nst], stimdel[nst], stimamp[nst]
public stim, stimdur, stimamp, stimdel
create soma, gcdend1[ndend1], gcdend2[ndend2]
objref syn, pre_list
proc init() {
pre_list = new List()
subsets()
gctemp()
synapse()
}
objref all, gcldend, pdend, mdend, ddend
proc subsets(){ local i
objref all, gcldend, pdend, mdend, ddend
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()
}
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
// current injection
//for i=0,0 {
//stimdel[i]=500
//stimdur[i]=200
//stimamp[i]=0.2
//soma stim[i] = new IClamp(0.5)
//stim.del[i]=stimdel[i]
//stim.dur[i]=stimdur[i]
//stim.amp[i]=stimamp[i]
//}
}
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
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
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
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
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
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
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
syn.tau1 = 0.26 syn.tau2 = 5.5 syn.e = -70
pre_list.append(syn)
gcdend1[1] syn = new Exp2Syn(0.5) // Sprouted Syn*************
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend2[1] syn = new Exp2Syn(0.5) // Sprouted Syn*********
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
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, adend, bdend, cdend, ddend
proc subsets() { local i
objref all, adend, bdend, cdend, ddend
all = new SectionList()
soma all.append()
for i=0, 3 bcdend1 [i] all.append()
for i=0, 3 bcdend2 [i] all.append()
for i=0, 3 bcdend3 [i] all.append()
for i=0, 3 bcdend4 [i] all.append()
adend = new SectionList()
bcdend1 [0] adend.append()
bcdend2 [0] adend.append()
bcdend3 [0] adend.append()
bcdend4 [0] adend.append()
bdend = new SectionList()
bcdend1 [1] bdend.append()
bcdend2 [1] bdend.append()
bcdend3 [1] bdend.append()
bcdend4 [1] bdend.append()
cdend = new SectionList()
bcdend1 [2] cdend.append()
bcdend2 [2] cdend.append()
bcdend3 [2] cdend.append()
bcdend4 [2] cdend.append()
ddend = new SectionList()
bcdend1 [3] ddend.append()
bcdend2 [3] ddend.append()
bcdend3 [3] ddend.append()
bcdend4 [3] ddend.append()
}
proc temp() {
soma {nseg=1 L=20 diam=15} // changed L & diam
bcdend1 [0] {nseg=1 L=75 diam=4} // bcdend 1 and 2 are apical
bcdend1 [1] {nseg=1 L=75 diam=3}
bcdend1 [2] {nseg=1 L=75 diam=2}
bcdend1 [3] {nseg=1 L=75 diam=1}
bcdend2 [0] {nseg=1 L=75 diam=4}
bcdend2 [1] {nseg=1 L=75 diam=3}
bcdend2 [2] {nseg=1 L=75 diam=2}
bcdend2 [3] {nseg=1 L=75 diam=1}
bcdend3 [0] {nseg=1 L=50 diam=4} // bcdend 3 and 4 are basal
bcdend3 [1] {nseg=1 L=50 diam=3}
bcdend3 [2] {nseg=1 L=50 diam=2}
bcdend3 [3] {nseg=1 L=50 diam=1}
bcdend4 [0] {nseg=1 L=50 diam=4}
bcdend4 [1] {nseg=1 L=50 diam=3}
bcdend4 [2] {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
}
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 bcdend2[0](0), soma(1)
connect bcdend3[0](0), soma(0)
connect bcdend4[0](0), soma(0)
for i=1,3 {
connect bcdend1[i](0), bcdend1[i-1](1)
}
for i=1,3 {
connect bcdend2[i](0), bcdend2[i-1](1)
}
for i=1,3 {
connect bcdend3[i](0), bcdend3[i-1](1)
}
for i=1,3 {
connect bcdend4[i](0), bcdend4[i-1](1)
}
forsec all {Ra=100}
forsec all {enat = 55 ekf = -90 ek=-90 elca=130 esk=-90
el_ichan2 =-60.06
cao_ccanl=2 } // make catau slower70e-3 cao=2 cai=50.e-6
//for i=0,0 {
//stimdel[i]=1000
//stimdur[i]=200
//stimamp[i]=0.5
/* 0.4 stim when we want the cell to fire with regular spikes */
//soma stim[i] = new IClamp(0.5)
//stim.del[i]=stimdel[i]
//stim.dur[i]=stimdur[i]
//stim.amp[i]=stimamp[i]
//}
}
objref syn
proc synapse() {
bcdend1 [3] syn = new Exp2Syn(0.5) //PP(AMPA) syn to apical dist dend Dingledine '95
syn.tau1 = 2 syn.tau2 = 6.3 syn.e = 0 // *** check Tau rise 2ms is the rise time
pre_list.append(syn)
bcdend2 [3] syn = new Exp2Syn(0.5) //PP(AMPA) syn to apical dist dend Dingledine '95
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
syn.tau1 = .3 syn.tau2 = .6 syn.e = 0
pre_list.append(syn)
bcdend2 [0] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend Geiger '97
syn.tau1 = .3 syn.tau2 = .6 syn.e = 0
pre_list.append(syn)
bcdend3 [0] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend Geiger '97
syn.tau1 = .3 syn.tau2 = .6 syn.e = 0
pre_list.append(syn)
bcdend4 [0] syn = new Exp2Syn(0.5) //GC(AMPA) syn to prox dend Geiger '97
syn.tau1 = .3 syn.tau2 = .6 syn.e = 0
pre_list.append(syn)
bcdend1 [1] syn = new Exp2Syn(0.5) //MC(AMPA) syn to apical IML dend
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
syn.tau1 = 0.9 syn.tau2 = 3.6 syn.e = 0 // *** Estimated based on CA3>BC min stim Dingledine '95
pre_list.append(syn)
bcdend1 [1] syn = new Exp2Syn(0.5) //BC(GABA) syn to apical IML dend Bartos
syn.tau1 = 0.16 syn.tau2 = 1.8 syn.e = -70
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 = -70
pre_list.append(syn)
bcdend1 [3] syn = new Exp2Syn(0.5) //HIPP(GABA) syn to apical distal dend
syn.tau1 = 0.4 syn.tau2 = 5.8 syn.e = -70 // *** Estimated as HIPP>GC
pre_list.append(syn)
bcdend2 [3] syn = new Exp2Syn(0.5) //HIPP(GABA) syn to apical distal dend
syn.tau1 = 0.4 syn.tau2 = 5.8 syn.e = -70 // *** Estimated as HIPP>GC
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)
//alternative statement $o1.soma pre_list.append(new NetCon(soma.v(1),syn,0,Delsyn,0))
}
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}
forall {
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)}
forall {Ra=100}
forall {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
//for i=0,0 {
//stimdel[i]=500
//stimdur[i]=500
//stimamp[i]=0.2
/* 0.4 stim when we want the cell to fire with regular spikes */
//soma stim[i] = new IClamp(0.5)
//stim.del[i]=stimdel[i]
//stim.dur[i]=stimdur[i]
//stim.amp[i]=stimamp[i]
//}
//objref fl
//soma fl = new Gfluct2(0.5)
//fl.g_e0 = 0.0242
//fl.g_i0 = 0.1146
//fl.std_e = 0.0375
//fl.std_i = 0.01875
}
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}
forall {
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)}
forall {Ra=100}
forall {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
//for i=0,0 {
//stimdel[i]=500
//stimdur[i]=500
//stimamp[i]=0.1
/* 0.4 stim when we want the cell to fire with regular spikes */
//soma stim[i] = new IClamp(0.5)
//stim.del[i]=stimdel[i]
//stim.dur[i]=stimdur[i]
//stim.amp[i]=stimamp[i]
//}
}
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 pre_list,pp, connect_pre, is_art, acell
create acell
objref pp
proc init() {
actemp()
}
proc actemp() {
acell pp = new NetStim(.5)
pp.interval = 100
pp.number = 1
pp.start = 5
}
func is_art() {return 1}
proc connect_pre() {acell $o2 = new NetCon(pp, $o1)}
endtemplate PPstim
//###############################################################################################################
// NETWORK SPECIFICATION INTERFACE
for i=0, ngcell-1 {Gcell[i] = new GranuleCell(i)}
for i=0, nbcell-1 {Bcell[i] = new BasketCell(i)}
for i=0, nmcell-1 {Mcell[i] = new MossyCell(i)}
for i=0, nhcell-1 {Hcell[i] = new HIPPCell(i)}
for i =0, npp-1 {PPSt[i] = new PPstim(i)}
objref nclist, netcon, cells, net_c, net_d, net_gr, net_bc, net_mc, net_hc, vbc2gc, vmc2gc, vhc2gc
{ cells = new List()
nclist = new List()
}
func cell_append() {cells.append($o1)
return cells.count -1}
func nc_append() {
print "in nc_append",$1,$2, $3, $4, $5, $6
if ( $2>=11 || $1 >=11) { return 0 } // test statement
if ($3 >= 0 ) {
cells.object($1).connect_pre(cells.object($2).pre_list.object($3),netcon)
netcon.weight = $4 netcon.delay = $5 netcon.threshold = $6
}
nclist.append(netcon)
print "leaving nc_append"
return nclist.count-1
}
func is_connected() {local i, c
c=0
for i=0, nclist.count-1 {
net_c= nclist.object(i)
if (($o1 == net_c.postcell()) && ($o2 == net_c.precell())) {c=1}
}