// This is a fully wired network that functions with 500 Granule Cells, 15 Mossy cells, 6 Basket cells and 6 HIPP Cells
//Model is based on Santhakumar et al., 2005 Fig7. The output data replicates panels A2 and B2
//Network activity is initiated by a single artificial stimulation of the Perforant Path (PP) input to 100GCs and some MC and BCs
//NOTE: Simulations include only AMPA and GABA synapses
//NOTE: single cell templates are based on physiological data obtained in synaptic blockers
//Cells are arranged in a RING and connections are made with TOPOGRAPHIC constraints
//NOTE: This simulation includes SPROUTED connections between GC axons on to GC dendrites - not present in the normal dentate
secondorder=2
tstep=0
period=2
dt=0.1
tstop=300 //1500
// define network size
ngcell = 500
nbcell = 6
nmcell = 15
nhcell = 6
npp = 1
//********************** GRANULE CELL ****************************************
//Defining granule cell modified from Aradi and Holmes 1999
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
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 //modified from Aradi and Soltesz 2002
gnatbar_ichan2=0.12
gkfbar_ichan2=0.016
gksbar_ichan2=0.006
insert borgka //KA from Aradi and Soltesz 2002
gkabar_borgka=0.012
insert nca // HAV-N- Ca channel modified from Aradi and Soltesz 2002
gncabar_nca=0.002
insert lca // L type Ca from Migliore et al., 1995
glcabar_lca=0.005
insert cat //T-type Ca adapted from Aradi and Holmes 1999
gcatbar_cat=0.000037
insert gskch //SK channel from Aradi and Soltesz 2002
gskbar_gskch=0.001
insert cagk //from Migliore et al., 1995
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
gncabar_nca=0.001
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
gncabar_nca=0.001
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 }
}
proc connect_pre() {
soma $o2 = new NetCon (&v(1), $o1)
}
// Define synapses on to GCs 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]
objref syn
proc synapse() {
gcdend1[3] syn = new Exp2Syn(0.5) // PP syn based on data from Greg Hollrigel and Kevin 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) // NOTE: SPROUTED SYNAPSE based on Molnar and Nadler
syn.tau1 = 1.5 syn.tau2 = 5.5 syn.e = 0
pre_list.append(syn)
gcdend2[1] syn = new Exp2Syn(0.5) // NOTE: SPROUTED SYNAPSE
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
// ********* BASKET CELL **************************************
// Define Basket Cell template
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
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
gncabar_nca=0.0008
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 }
}
//Defining Synapses on to Basket Cells
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
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
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() {
soma $o2 = new NetCon (&v(1), $o1)
}
func is_art() { return 0 }
endtemplate BasketCell
//**************** MOSSY CELL ***********************************************************
//Define Mossy Cell template
//NOTE that fluctuating conductance fl can be included to simulate low input resistance in the absence of synaptic blockers Ratzliff et al., 2004
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
//to include steady state current injection
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}
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
gncabar_nca=0.00008
insert lca
glcabar_lca=0.0006
insert gskch
gskbar_gskch=0.016
insert cagk
gkbar_cagk=0.0165
insert hyperde3 //Ih mechanism from contro Ih in Chen et al., 2001
ghyfbar_hyperde3=0.000005
ghysbar_hyperde3=0.000005
}
soma {insert ichan2
gnatbar_ichan2=0.12
gkfbar_ichan2=0.0005
gl_ichan2 = 0.000011
cm=0.6}
forsec pdend {insert ichan2
gnatbar_ichan2=0.12
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 }
// CURRENT INJECTION
//for i=0,0 {
//stimdel[i]=1
//stimdur[i]=300
//stimamp[i]=0.65 // to reproduce 2-4Hz firing in vitro in the presence of baseline fluctuations
//soma stim[i] = new IClamp(0.5)
//stim.del[i]=stimdel[i]
//stim.dur[i]=stimdur[i]
//stim.amp[i]=stimamp[i]
//}
// FLUCTUATING CONDUCTANCE DESTEXHE ET AL., 2001
//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
}
//Defining synapses on to Mossy Cells
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() {
soma $o2 = new NetCon (&v(1), $o1)
}
func is_art() { return 0 }
endtemplate MossyCell
//*************** HIPP CELL ****************************
// Define HIPP CELL template
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
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}
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
gncabar_nca=0.0
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
gnatbar_ichan2=0.2
gkfbar_ichan2=0.006
gl_ichan2 = 0.000036
cm=1.1}
forsec pdend {insert ichan2
gnatbar_ichan2=0.2
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 }
}
// Defining synapses on to HIPP cells
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() {
soma $o2 = new NetCon (&v(1), $o1)
}
func is_art() { return 0 }
endtemplate HIPPCell
//********** Perforant Path Stimulus ***********************************************
//Define artificial stimulus to activate PP
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 = 100
pp.number = 1
pp.start = 5
}
func is_art() {return 1}
proc connect_pre() {acell $o2 = new NetCon(pp, $o1)}
endtemplate PPstim
//###############################################################################################################
//############## CONNECTING THE CELLS #############################
// NETWORK SPECIFICATION INTERFACE
for i=0, ngcell-1 {Gcell[i] = new GranuleCell(i)}
for i=0, nbcell-1 {Bcell[i] = new BasketCell(i)}
for i=0, nmcell-1 {Mcell[i] = new MossyCell(i)}
for i=0, nhcell-1 {Hcell[i] = new HIPPCell(i)}
for i =0, npp-1 {PPSt[i] = new PPstim(i)}
objref nclist, netcon, cells, net_c, net_d, net_gr, net_bc, net_mc, net_hc, vbc2gc, vmc2gc, vhc2gc
{ cells = new List()
nclist = new List()
}
// Include all cells in cells
func cell_append() {cells.append($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 = $6
}
nclist.append(netcon)
return nclist.count-1
}
// To check for preexisting connections between randomly selected cells
//to avoid multiple contacts between same 2 cells
func is_connected() {local i, c
c=0
for i=0, nclist.count-1 {
net_c= nclist.object(i)
if (($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
//To delete certain randomly selected cells from net - in this case 8 of 15 MCs
objref killMC
{
vgc2bc = new Vector(nbcell, 0) //defines vectors for each "pre2post" pair, vector length is same as number of post cells fills with 0
vbc2bc = new Vector(nbcell, 0)
vmc2bc = new Vector(nbcell, 0)
vhc2bc = new Vector(nbcell, 0)
//To delete certain randomly selected cells from net - in this case 8 of 15 MCs
killMC = new Vector(8, 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)
}
//initiating randm number generator for each pre2post pair
//also randomly select MC to kill "deadMC"
objref rdsynb, rdsyna, rdgc2hc, rdgc2bc, rdgc2mc, rdbc2gc, rdbc2bc, rdbc2mc, deadMC
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()
}
//************************************ GC ***********************************************
rdgc2bc = new Random(rseed) // use for syn.connections
proc new_rdgc2bc() {rdgc2bc.discunif(-1,1)} // range is based on spread of connections on either side of RING- precell loc =0
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)} // range is based on spread of connections on either side of RING- precell loc =0
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()
//************************************* MC ********************************************
//deadMC = new Random(rseed) //randomly select MC to kill "deadMC"
//proc new_deadMC() {deadMC.discunif(ngcell+nbcell, ngcell+nbcell+nmcell-1)}
//new_deadMC()
// Check to see if 8 different cells are killed
//for i= 0, 7 {
//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)} // range is based on spread of connections on either side of RING- precell loc =0
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 ********************************************
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()
//**************** randomizer for the dendritic location of synapse **************************************
rdsyna = new Random(rseed) // initialize random distr.
proc new_rdsyna() {rdsyna.discunif(0, 1)} // randomize among 2 dendrites
new_rdsyna()
rdsynb = new Random(rseed) // initialize random distr.
proc new_rdsynb() {rdsynb.discunif(0, 3)} // randomize among 4 dendrites
new_rdsynb()
// NETWORK INITIATION
for i = 0, ngcell-1 {cell_append(Gcell[i])} // cells 0-499 GCs
for i = 0, nbcell-1 {cell_append(Bcell[i])} // cells 500-505 BC
for i = 0, nmcell-1 {cell_append(Mcell[i])} // cells 506-520 MC
for i = 0, nhcell-1 {cell_append(Hcell[i])} // cells 521-526 HC
for i = 0, npp-1 {cell_append(PPSt[i])} // 527 PP artificial cell
//**************Preforant Path synaptic connections ******************************
proc initNet() { local i,j
for i=0, npp-1 {
for j=0, 100 { // to 101 granule cells
nc_append(i+ngcell+nbcell+nmcell+nhcell, j, 0, 2e-2, 3, 10) // connect PP to GC[j],syn[0],wt,del,threshold
nc_append(i+ngcell+nbcell+nmcell+nhcell, j, 1, 2e-2, 3, 1) // connect PP to GC[j],syn[1],wt,del,threshold
}
for j= ngcell, ngcell+1 { //to 2 BCs
nc_append(ngcell+nbcell+nmcell+nhcell, j, 0, 1e-2, 3, 10) // Gcell[3] to Bcell[1]
nc_append(ngcell+nbcell+nmcell+nhcell, j, 1, 1e-2, 3, 10) // Gcell[3] to Bcell[1]
}
// for j=0, 1 { // 15% of MCs have OML dendrites so 2 of 15 MCs could get PP input
// npost = rdmc2mc.repick() //pick MC at random
// dbr = rdsynb.repick()
// if the MC is not already connected to PP and the randomly picked MC is proximal to the stimulated GCs
// if ((is_connected(MossyCell[npost-ngcell-nbcell], PPstim[0]) == 0) && (npost < ngcell+nbcell+3) && (killMC.contains(npost) == 0)) {
//connect PP syn to the selected mossy
// nc_append(ngcell+nbcell+nmcell+nhcell, npost, dbr, 0.5e-2, 3, 10) // Gcell[3] to Bcell[1]
// print npost, dbr
// } else { j -= 1 print "pp2mc"}
// if (killMC.contains(npost) == 1) {j +=1}
// }
}
//******************************************************************************************
//**************Granule Cell post synaptic connections ******************************
for i=0, ngcell-1 {
for j=0, 0 {
// Based on the lamellar distribution of the GCs to BCs - 500 GCs were divided into 6 groups proximal to each of the 6 BCs
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}
Gauz3 = rdgc2bc.repick() // randomly pick location of post synaptic Bcell
if (a+Gauz3 > 5) {npost = a+Gauz3-6 } //determine appropriate post syn BC
if (a+Gauz3 < 0) {npost = a+Gauz3+6}
if ((a+Gauz3 > -1) && (a+Gauz3 < 6)) {npost = a+Gauz3}
dbr = rdsynb.repick() // randomly pick the dendrite to connect to
print npost, a
if (vgc2bc.x[npost] < 90) { //check to make sure that post syn BC does not get more than 90 GC synapses
nc_append(i, ngcell+npost, dbr+2, 4.7e-3, .8, 10) // connect GC[i] to BC[j],syn[2]+dendritic_var,wt,del,threshold
print i, npost, dbr+2
vgc2bc.x[npost] +=1 //increment the no of synapses to the post cell
} else {j -= 1 print "nogc2bc"} // for connection that is not made reconnect axon to another cell
}
// Based on the lamellar distribution of the GCs to MCs - 500 GCs were divided into 5 groups, 3 MCs were distributed in each lamella
for j=0, 0 {
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}
b=a*3
npost = rdgc2mc.repick()
dbr = rdsynb.repick()
// print npost, b
// if ((vgc2mc.x[npost+b] < 38) && (killMC.contains(ngcell+nbcell+npost+b) == 0)){ // use if killing MC
if (vgc2mc.x[npost+b] < 38){
nc_append(i, ngcell+nbcell+npost+b, dbr+4, 0.2e-3, 1.5, 10) // Gcell[3] to Bcell[1]
// print npost+b, dbr+4
vgc2mc.x[npost+b] +=1
} else { j -= 1 print "nogc2mc"}
// if (killMC.contains(ngcell+nbcell+npost+b) == 1) {j +=1 print "dead MC"} // use if killing MC
}
for j=0, 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}
Gauz3 = rdgc2hc.repick()
if (a+Gauz3 > 5) {npost = a+Gauz3-6 }
if (a+Gauz3 < 0) {npost = a+Gauz3+6}
if ((a+Gauz3 > -1) && (a+Gauz3 < 6)) {npost = a+Gauz3}
dbr = rdsynb.repick()
if ((is_connected(HIPPCell[npost], GranuleCell[i]) == 0) && (vgc2hc.x[npost] < 275)) {
nc_append(i, ngcell+nbcell+nmcell+npost, dbr, 0.5e-3, 1.5, 10) // Gcell[3] to Bcell[1]
// print npost, dbr
vgc2hc.x[npost] +=1
} else {j -= 1 print "hhhh"}
}
// NOTE: THIS IS FOR SPROUTED SYNAPSES
for j=0, 9 {
Gauz3 = rdgc2gc.repick()
//print Gauz3
if (i+Gauz3 > 499) {npost = i+Gauz3-500 }
if (i+Gauz3 < 0) {npost = i+Gauz3+500}
if ((i+Gauz3 > -1) && (i+Gauz3 < 500)) {npost = i+Gauz3}
//print npost
dbr = rdsyna.repick()
if ((is_connected(GranuleCell[npost], GranuleCell[i]) == 0) && (vgc2gc.x[npost] < 15)) {
nc_append(i, npost, dbr+7, 2e-3, .8, 10) // Gcell[3] to Bcell[1]
// print npost, dbr+8
vgc2gc.x[npost] +=1
} else {j -= 1 print "gc2gc"}
}
}
//******************************************************************************************
//**************Basket Cell post synaptic connections ******************************
for i=0, nbcell-1 {
for j=0, 99 {
Gauz3 = rdbc2gc.repick()
print Gauz3
if (i*83+41+Gauz3 > 499) {npost = i*83+41+Gauz3-500 }
if (i*83+41+Gauz3 < 0) {npost = i*83+41+Gauz3+500}
if ((i*83+41+Gauz3 > -1) && (i*83+41+Gauz3 < 500)) {npost = i*83+41+Gauz3}
print i, npost
if ((is_connected(GranuleCell[npost], BasketCell[i]) == 0) && (vbc2gc.x[npost] < 2)) {
nc_append(i+ngcell, npost, 6, 1.6e-3, .85, -10) // Gcell[3] to Bcell[1]
vbc2gc.x[npost] +=1
print i, npost, 6
} else {j -= 1 print "BC2GC"}
}
for j=0, 1 {
Gauz3 = rdbc2bc.repick()
//print Gauz3
if (i+Gauz3 > 5) {npost = i+Gauz3-6 }
if (i+Gauz3 < 0) {npost = i+Gauz3+6}
if ((i+Gauz3 >-1) && (i+Gauz3 < 6)) {npost = i+Gauz3}
dbr = rdsyna.repick()
if ((is_connected(BasketCell[npost], BasketCell[i]) == 0) && (vbc2bc.x[npost] < 3)) {
nc_append(i+ngcell, npost+ngcell, dbr+8, 7.6e-3, .8, -10) // Gcell[3] to Bcell[1]
print npost, dbr+8
vbc2bc.x[npost] +=1
} else {j -= 1 print "bc2bc"}
}
for j=0, 2 {
Gauz3 = rdbc2mc.repick()
//print Gauz3
if (i*2+2+Gauz3 > 14) {npost = i*2+2+Gauz3-15 }
if (i*2+2+Gauz3 < 0) {npost = i*2+2+Gauz3+15}
if ((i*2+2+Gauz3 >-1) && (i*2+2+Gauz3 < 15)) {npost = i*2+2+Gauz3}
//print npost
// if ((is_connected(MossyCell[npost], BasketCell[i]) == 0) && (vbc2mc.x[npost] < 3) && (killMC.contains(ngcell+nbcell+npost) == 0)) { // use if killing MC
if ((is_connected(MossyCell[npost], BasketCell[i]) == 0) && (vbc2mc.x[npost] < 3)) {
nc_append(i+ngcell, npost+ngcell+nbcell, 12, 1.5e-3, 1.5, -10) // Gcell[3] to Bcell[1]
print npost, 12
vbc2mc.x[npost] +=1
} else { j -= 1 print "bc2mc"}
// if (killMC.contains(ngcell+nbcell+npost) == 1) {j +=1 print "dead MC"} // use if killing MC
}
}
//******************************************************************************************
//**************Mossy Cell post synaptic connections ******************************
for i=0, nmcell-1 {
//if (killMC.contains(ngcell+nbcell+i) == 0){ // use if killing MC
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}
for j=0, 99 {
Gauz1 = rdmc2gc1.repick()
print Gauz1
if (i*33+17+Gauz1 > 499) {
npost1 = i*33+17+Gauz1-500
} else {npost1 =i*33+17+Gauz1}
print npost1
dbr = rdsyna.repick()
if ((is_connected(GranuleCell[npost1], MossyCell[i]) == 0) && (vmc2gc.x[npost1] < 7)) {
nc_append(i+ngcell+nbcell, npost1, dbr+2, 0.3e-3, 3, 10) // Gcell[3] to Bcell[1]
vmc2gc.x[npost1] +=1
print i, npost1, dbr+2
} else {j -= 1 print "MC2GC1"}
}
for j=0, 99 {
Gauz2 = rdmc2gc2.repick()
//print Gauz2
if (i*33+17+Gauz2 < 0) {
npost2 =i*33+17+Gauz2+500
} else {npost2 =i*33+17+Gauz2}
//print npost2
dbr = rdsyna.repick()
if ((is_connected(GranuleCell[npost2], MossyCell[i]) == 0) && (vmc2gc.x[npost2] < 7)) {
nc_append(i+ngcell+nbcell, npost2, dbr+2, 0.3e-3, 3, 10) // Gcell[3] to Bcell[1]
vmc2gc.x[npost2] +=1
// print i, npost2, dbr+2
} else {j -= 1 print "MC2GC2"}
}
for j=0, 0 {
Gauz3 = rdmc2bc.repick()
if (y+Gauz3 > 5) {npost = y+Gauz3-6}
if (y+Gauz3 < 0) {npost = y+Gauz3+6}
if ((y+Gauz3 > -1) && (y+Gauz3 < 6)) {npost = y+Gauz3}
dbr = rdsyna.repick()
if ((vmc2bc.x[npost] < 4) && (Gauz3 !=0)) {
nc_append(i+ngcell+nbcell, ngcell+npost, dbr+6, 0.3e-3, 3, 10) // Gcell[3] to Bcell[1]
// print npost, dbr+6
vmc2bc.x[npost] += 1
} else {j -= 1 print "mc2bc"}
}
for j=0, 2 {
Gauz3 = rdmc2mc1.repick()
//print Gauz3
if (i+Gauz3 > 14) {npost = i+Gauz3-15 }
if (i+Gauz3 < 0) {npost = i+Gauz3+15}
if ((i+Gauz3 >-1) && (i+Gauz3 < 15)) {npost = i+Gauz3}
//print npost
dbr = rdsynb.repick()
// if ((is_connected(MossyCell[npost], MossyCell[i]) == 0) && (vmc2mc.x[npost] < 4) && (Gauz3 != 0) && (killMC.contains(ngcell+nbcell+npost) == 0)) { // use if killing MC
if ((is_connected(MossyCell[npost], MossyCell[i]) == 0) && (vmc2mc.x[npost] < 4) && (Gauz3 != 0)) {
nc_append(i+ngcell+nbcell, npost+ngcell+nbcell, dbr+8, 0.5e-3, 2, 10) // Gcell[3] to Bcell[1]
// print npost, dbr+8
vmc2mc.x[npost] +=1
} else { j -= 1 print "mc2mc"}
// if (killMC.contains(ngcell+nbcell+npost) == 1){ j += 1 print "dead MC"} // use if killing MC
}
for j=0, 1 {
Gauz3 = rdmc2hc.repick()
if (y+Gauz3 > 5) {npost = y+Gauz3-6}
if (y+Gauz3 < 0) {npost = y+Gauz3+6}
if ((y+Gauz3 > -1) && (y+Gauz3 < 6)) {npost = y+Gauz3}
dbr = rdsynb.repick()
if ((is_connected(HIPPCell[npost], MossyCell[i]) == 0) && (vmc2hc.x[npost] < 7) && (Gauz3 != 0)) {
nc_append(i+ngcell+nbcell, ngcell+nbcell+nmcell+npost, dbr+4, 0.2e-3, 3, 10) // Gcell[3] to Bcell[1]
// print npost, dbr+4
vmc2hc.x[npost] +=1
} else { j -= 1 print y, Gauz3, "mc2hc"}
}
//}
}
//******************************************************************************************
//**************HIPP Cell post synaptic connections ******************************
for i=0, nhcell-1 {
for j=0, 159 {
Gauz3 = rdhc2gc.repick()
//print Gauz3
if (i*83+41+Gauz3 > 499) {npost = i*83+41+Gauz3-500 }
if (i*83+41+Gauz3 < 0) {npost = i*83+41+Gauz3+500}
if ((i*83+41+Gauz3 > -1) && (i*83+41+Gauz3 < 500)) {npost = i*83+41+Gauz3}
//print npost
dbr = rdsyna.repick()
if ((is_connected(GranuleCell[npost], HIPPCell[i]) == 0) && (vhc2gc.x[npost] < 3)) {
nc_append(i+ngcell+nbcell+nmcell, npost, dbr+4, 0.5e-3, 1.6, 10) // Gcell[3] to Bcell[1]
vhc2gc.x[npost] +=1
print i, npost, dbr+4
} else {j -= 1 print "HC2GC"}
}
for j=0, 3 {
Gauz3 = rdhc2bc.repick()
if (i+Gauz3 > 5) {npost = i+Gauz3-6}
if (i+Gauz3 < 0) {npost = i+Gauz3+6}
if ((i+Gauz3 > -1) && (i+Gauz3 < 6)) {npost = i+Gauz3}
dbr = rdsyna.repick()
if ((is_connected(BasketCell[npost], HIPPCell[i]) == 0) && (vhc2bc.x[npost] < 5)) {
nc_append(i+ngcell+nbcell+nmcell, npost+ngcell, dbr+10, 0.5e-3, 1.6, 10) // Gcell[3] to Bcell[1]
print npost, dbr+10
vhc2bc.x[npost] += 1
} else {j -= 1 print "hc2bc"}
}
for j=0, 3 {
Gauz3 = rdhc2mc.repick()
//print Gauz3
if (i*2+2+Gauz3 > 14) {npost = i*2+2+Gauz3-15 }
if (i*2+2+Gauz3 < 0) {npost = i*2+2+Gauz3+15}
if ((i*2+2+Gauz3 >-1) && (i*2+2+Gauz3 < 15)) {npost = i*2+2+Gauz3}
//print npost
dbr = rdsynb.repick()
// if ((is_connected(MossyCell[npost], HIPPCell[i]) == 0) && (vhc2mc.x[npost] < 2) && (killMC.contains(ngcell+nbcell+npost) == 0)) { //use if killing MC
if ((is_connected(MossyCell[npost], HIPPCell[i]) == 0) && (vhc2mc.x[npost] < 2)) {
nc_append(i+ngcell+nbcell+nmcell, npost+ngcell+nbcell, dbr+13, 1.5e-3, 1, 10) // Gcell[3] to Bcell[1]
print npost, dbr+13
vhc2mc.x[npost] += 1
} else { j -= 1 print "hc2mc"}
// if (killMC.contains(ngcell+nbcell+npost) == 1){ j += 1 print "dead MC"} //use if killing MC
}
}
}
//*********************************Print out Net cons*********************************************************
strdef strvar
objref dfile
dfile = new File()
proc saveNet(){ local i
dfile.wopen("DGNC.txt")
dfile.printf("Precell \tpstcell \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])}
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])}
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])}
dfile.printf("TO GC\n BC\t MC\t HC\t GC\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])}
dfile.close()
}
//******* output memb voltage traces of every 10th GC and all other cells to file **********************************************
strdef strmat
objref efile
efile = new File()
efile.wopen("DGVt.txt")
efile.printf("t\t")
for i = 0, 49 {
b = i*10
efile.printf("%s\t", cells.object[b])}
for i = 498, cells.count-2{
efile.printf("%s\t", cells.object[i])}
efile.printf("\n")
efile.close("DGVt.txt")
proc sMatrix(){ local j
efile.aopen("DGVt.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 =498, cells.count-2 {
efile.printf("%f\t", cells.object[j].soma.v(0.5))}
efile.printf("\n")
efile.close("DGVt.txt")
}
objref VmT
objref VmMat[cells.count-1]
VmT = new Vector()
for i=0, cells.count-2 {
VmMat[i] = new Vector()
}
proc VecMx() { local i
VmT.append(t)
for i=0, cells.count-2 {
VmMat[i].append( cells.object[i].soma.v(0.5))
}
}
//Generate spike matrix and save to file
objref Spike[cells.count-1]
for i=0, cells.count-2 {
Spike[i] = new Vector()
}
strdef Spkstr
objref dfile
dfile = new File()
proc SpkMx() { local i, j
for i=0, cells.count-2 {
Spike[i].spikebin(VmMat[i], 0)
}
dfile.wopen("DGSp.txt")
while(k < VmT.size) {
for j = 0, cells.count-2 {
if(Spike[j].x[k] != 0) {
dfile.printf("%f\t%d\n", VmT.x[k], j)}
}
k +=1 }
dfile.close("DGSp.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()
//Plot spike raster
proc plotAP() { local i, a
a=1
r_plt.erase()
while(j < cells.count-2) {
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) { a=4}
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 // negative t step to initialize to steady state
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()
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 = 300 //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)
}
//plot membrane voltage traces
{
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[0].soma.v(0.5)",1,1)
save_window_.addexpr("Bcell[0].soma.v(0.5)",2,1)
save_window_.addexpr("Bcell[1].soma.v(0.5)",5,1)
save_window_.addexpr("Mcell[0].soma.v(0.5)",3,1)
save_window_.addexpr("Hcell[0].soma.v(0.5)",4,1)
}
proc rrun(){
initNet()
saveNet()
run()
SpkMx()
}
rrun()
plotAP()
objectvar scene_vector_[1]
{doNotify()}
//quit()
