// 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=300 //1500 // define network size ngcell = 500 nbcell = 6 nmcell = 15 nhcell = 6 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 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() { 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 { 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) } //initiating randm number generator objref rdsynb, rdsyna, rdgc2hc, rdgc2bc, rdgc2mc, rdbc2gc, rdbc2bc, rdbc2mc 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 = 0 hindx = 1 hindx_inc = 1e6 //************************************GC*********************************************** rdgc2bc = new Random(rseed) // use for syn.connections rdgc2bc.MCellRan4(hindx += hindx_inc) proc new_rdgc2bc() {rdgc2bc.discunif(-1,1)} new_rdgc2bc() rdgc2mc = new Random(rseed) // use for syn.connections rdgc2mc.MCellRan4(hindx += hindx_inc) proc new_rdgc2mc() {rdgc2mc.discunif(0,2)} new_rdgc2mc() rdgc2hc = new Random(rseed) // use for syn.connections rdgc2hc.MCellRan4(hindx += hindx_inc) proc new_rdgc2hc() {rdgc2hc.discunif(-2 , 2)} new_rdgc2hc() rdgc2gc = new Random(rseed) // use for syn.connections rdgc2gc.MCellRan4(hindx += hindx_inc) proc new_rdgc2gc() {rdgc2gc.discunif(-50, 50)} new_rdgc2gc() //************************************BC*********************************************** rdbc2gc = new Random(rseed) // use for syn.connections rdbc2gc.MCellRan4(hindx += hindx_inc) proc new_rdbc2gc() {rdbc2gc.discunif(0, ngcell-1)} new_rdbc2gc() rdbc2bc = new Random(rseed) // use for syn.connections rdbc2bc.MCellRan4(hindx += hindx_inc) proc new_rdbc2bc() {rdbc2bc.discunif(ngcell, ngcell+nbcell-1)} new_rdbc2bc() rdbc2mc = new Random(rseed) // use for syn.connections rdbc2mc.MCellRan4(hindx += hindx_inc) proc new_rdbc2mc() {rdbc2mc.discunif(ngcell+nbcell, ngcell+nbcell+nmcell-1)} new_rdbc2mc() //*************************************MC******************************************** rdmc2gc1 = new Random(rseed) // use for syn.connections rdmc2gc1.MCellRan4(hindx += hindx_inc) proc new_rdmc2gc1() {rdmc2gc1.discunif(25, 175)} new_rdmc2gc1() rdmc2gc2 = new Random(rseed) // use for syn.connections rdmc2gc2.MCellRan4(hindx += hindx_inc) proc new_rdmc2gc2() {rdmc2gc2.discunif(-175, -25)} new_rdmc2gc2() rdmc2bc = new Random(rseed) // use for syn.connections rdmc2bc.MCellRan4(hindx += hindx_inc) proc new_rdmc2bc() {rdmc2bc.discunif(-3,3)} new_rdmc2bc() rdmc2mc = new Random(rseed) // use for syn.connections rdmc2mc.MCellRan4(hindx += hindx_inc) proc new_rdmc2mc() {rdmc2mc.discunif(ngcell+nbcell, ngcell+nbcell+nmcell-1)} new_rdmc2mc() rdmc2mc1 = new Random(rseed) // use for syn.connections rdmc2mc1.MCellRan4(hindx += hindx_inc) proc new_rdmc2mc1() {rdmc2mc1.discunif(-3, 3)} new_rdmc2mc1() rdmc2hc = new Random(rseed) // use for syn.connections rdmc2hc.MCellRan4(hindx += hindx_inc) proc new_rdmc2hc() {rdmc2hc.discunif(-2, 2)} new_rdmc2hc() //*************************************HC******************************************** rdhc2gc = new Random(rseed) // use for syn.connections rdhc2gc.MCellRan4(hindx += hindx_inc) proc new_rdhc2gc() {rdhc2gc.discunif(0, ngcell-1)} new_rdhc2gc() rdhc2bc = new Random(rseed) // use for syn.connections rdhc2bc.MCellRan4(hindx += hindx_inc) proc new_rdhc2bc() {rdhc2bc.discunif(ngcell, ngcell+nbcell-1)} new_rdhc2bc() rdhc2mc = new Random(rseed) // use for syn.connections rdhc2mc.MCellRan4(hindx += hindx_inc) proc new_rdhc2mc() {rdhc2mc.discunif(ngcell+nbcell, ngcell+nbcell+nmcell-1)} new_rdhc2mc() //********************************************************************************* rdsyna = new Random(rseed) // initialize random distr. rdsyna.MCellRan4(hindx += hindx_inc) proc new_rdsyna() {rdsyna.discunif(0, 1)} new_rdsyna() rdsynb = new Random(rseed) // initialize random distr. rdsynb.MCellRan4(hindx += hindx_inc) 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 //**************Preforant Path synaptic connections ****************************** proc initNet() { local i,j for i=0, npp-1 { for j=0, 99 { //ngcell-1{ nc_append(i+ngcell+nbcell+nmcell+nhcell, j, 0, 2e-2, 3, 10) // Gcell[3] to Bcell[1] nc_append(i+ngcell+nbcell+nmcell+nhcell, j, 1, 2e-2, 3, 1) // Gcell[3] to Bcell[1] } for j= ngcell, ngcell { //ngcell+nbcell-1{ 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, 0 { // 15% of MCs have OML dendrites npost = rdmc2mc.repick() dbr = rdsynb.repick() if ((is_connected(MossyCell[npost-ngcell-nbcell], PPstim[0]) == 0) && (npost < ngcell+nbcell+3)) { 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"} } } //****************************************************************************************** //**************Granule Cell post synaptic connections ****************************** for i=0, ngcell-1 { for j=0, 1 { 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() 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() print npost, a if ((is_connected(BasketCell[npost], GranuleCell[i]) == 0) && (vgc2bc.x[npost] < 180)) { nc_append(i, ngcell+npost, dbr+2, 4.7e-3, .8, 10) // Gcell[3] to Bcell[1] print i, npost, dbr+2 vgc2bc.x[npost] +=1 } else {j -= 1 print "sdtf"} } 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 ((is_connected(MossyCell[npost+b], GranuleCell[i]) == 0) && (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 "mdtf"} } 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] < 270)) { 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"} } 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 { // npost = rdbc2gc.repick() // 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 { // npost = rdbc2bc.repick() // dbr = rdsyna.repick() // if ((is_connected(BasketCell[npost-ngcell], BasketCell[i]) == 0) && (vbc2bc.x[npost-ngcell] < 3)) { // nc_append(i+ngcell, npost, dbr+8, 7.6e-3, .8, 10) // Gcell[3] to Bcell[1] // print npost, dbr+8 // vbc2bc.x[npost-ngcell] +=1 // } else {j -= 1 print "bc2bc"} // } // for j=0, 4 { // npost = rdbc2mc.repick() // if ((is_connected(MossyCell[npost-ngcell-nbcell], BasketCell[i]) == 0) && (vbc2mc.x[npost-ngcell-nbcell] < 3)) { // nc_append(i+ngcell, npost, 12, 1.5e-3, 1.5, 10) // Gcell[3] to Bcell[1] // print npost, 12 // vbc2mc.x[npost-ngcell-nbcell] +=1 // } else { j -= 1 print "bc2mc"} // } //} //****************************************************************************************** //**************Mossy Cell post synaptic connections ****************************** for i=0, nmcell-1 { 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 ((is_connected(BasketCell[npost], MossyCell[i]) == 0) && (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)) { 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"} } 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] < 6) && (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 { // npost = rdhc2gc.repick() // 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 { // npost = rdhc2bc.repick() // dbr = rdsyna.repick() // if ((is_connected(BasketCell[npost-ngcell], HIPPCell[i]) == 0) && (vhc2bc.x[npost-ngcell] < 5)) { // nc_append(i+ngcell+nbcell+nmcell, npost, dbr+10, 0.5e-3, 1.6, 10) // Gcell[3] to Bcell[1] // print npost, dbr+10 // vhc2bc.x[npost-ngcell] += 1 // } else {j -= 1 print "hc2bc"} // } // for j=0, 3 { // npost = rdhc2mc.repick() // dbr = rdsynb.repick() // if ((is_connected(MossyCell[npost-ngcell-nbcell], HIPPCell[i]) == 0) && (vhc2mc.x[npost-ngcell-nbcell] < 2)) { // nc_append(i+ngcell+nbcell+nmcell, npost, dbr+13, 1.5e-3, 1, 10) // Gcell[3] to Bcell[1] // print npost, dbr+13 // vhc2mc.x[npost-ngcell-nbcell] += 1 // } else { j -= 1 print "hc2mc"} // } //} } //*********************************Print out Net cons********************************************************* strdef strvar objref dfile dfile = new File() proc saveNet(){ local i dfile.wopen("N2I10sp") 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() } //****************************************************************************************** strdef strmat objref efile efile = new File() efile.wopen("M2I10sp.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("M2I10sp.txt") proc sMatrix(){ local j efile.aopen("M2I10sp.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("M2I10sp.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)) } } 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("S2I10sp.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("S2I10sp.txt") } objref r_plt proc initrPlt() { r_plt = new Graph(0) r_plt.size(0, tstop,0, cells.count) r_plt.label(0.95, 0.02, "ms") r_plt.label(0.01, 0.82, "neu") r_plt.view(0,0, tstop, cells.count,320,20,300,230) } initrPlt() proc plotAP() { local i, a a=1 r_plt.erase() while(j < cells.count-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 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) } { 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) //save_window_.addexpr("NetStim[0].interval",6,1) //save_window_.addexpr("NetStim[0].y",7,1) } //{ //save_window_ = new Graph(0) //save_window_.size(0,1500,0,0.029) //scene_vector_[3] = save_window_ //{save_window_.view(0, 0, 1500, 0.029, 76, 213, 947.52, 385.6)} //graphList[0].append(save_window_) //save_window_.save_name("graphList[0].") //save_window_.addexpr("Gcell[0].soma.cai_ccanl*1e2",1,1) //save_window_.addexpr("Gcell[0].soma.isk_gskch*1e2",5,1) //save_window_.addexpr("Gcell[0].soma.ik_borgka*1e2",2,1) //save_window_.addexpr("Gcell[0].soma.ikf_ichan2",4,1) //save_window_.addexpr("Gcell[0].soma.ik_cagk*1e2",3,1) //save_window_.addexpr("Gcell[0].soma.inca_nca*1e2",4,1) //save_window_.addexpr("Gcell[0].soma.ilca_lca*1e2",3,1) //} proc rrun(){ setuptime = startsw() initNet() setuptime = startsw() - setuptime saveNet() runtime = startsw() run() runtime = startsw() - runtime SpkMx() } rrun() plotAP() objectvar scene_vector_[1] {doNotify()} //quit() // the below allows modelview to run access GranuleCell[0].soma print "setuptime=", setuptime print "runtime=", runtime