// Trying to open ../diagnostic/tstop.dat // new end time timtot = 150. // Trying to open ../diagnostic/dt_F.dat // new dt = 0.002 // gam( 1, 2)= 0.0301519221 // gam( 1, 3)= 0.0301519221 // gam( 1, 4)= 0.0301519221 // gam( 1, 5)= 0.0301519221 // gam( 1, 6)= 0.0301519221 // gam( 1, 35)= 0.131870466 // gam( 1, 56)= 0.198609787 // gam( 2, 13)= 0.0151319918 // gam( 3, 14)= 0.0151319918 // gam( 4, 15)= 0.0151319918 // gam( 5, 16)= 0.0151319918 // gam( 6, 17)= 0.0151319918 // gam( 7, 18)= 0.00805084797 // gam( 7, 35)= 0.0143749099 // gam( 8, 19)= 0.00805084797 // gam( 8, 36)= 0.0142102732 // gam( 9, 20)= 0.00805084797 // gam( 9, 37)= 0.0140221731 // gam( 10, 21)= 0.00805084797 // gam( 10, 37)= 0.0140221731 // gam( 11, 22)= 0.00805084797 // gam( 11, 36)= 0.0142102732 // gam( 12, 23)= 0.00805084797 // gam( 12, 35)= 0.0143749099 // gam( 13, 24)= 0.0151319918 // gam( 14, 25)= 0.0151319918 // gam( 15, 26)= 0.0151319918 // gam( 16, 27)= 0.0151319918 // gam( 17, 28)= 0.0151319918 // gam( 18, 29)= 0.00805084797 // gam( 19, 30)= 0.00805084797 // gam( 20, 31)= 0.00805084797 // gam( 21, 32)= 0.00805084797 // gam( 22, 33)= 0.00805084797 // gam( 23, 34)= 0.00805084797 // gam( 35, 36)= 0.0635858917 // gam( 36, 37)= 0.0572189482 // gam( 37, 38)= 0.0511871097 // gam( 38, 39)= 0.0454903769 // gam( 39, 40)= 0.0401287504 // gam( 40, 41)= 0.0351022313 // gam( 41, 42)= 0.0304108207 // gam( 42, 43)= 0.0260545207 // gam( 43, 44)= 0.0197765666 // gam( 44, 45)= 0.0130771876 // gam( 45, 46)= 0.00929984778 // gam( 46, 47)= 0.00695437146 // gam( 47, 48)= 0.00617996773 // gam( 47, 49)= 0.00617996773 // gam( 48, 49)= 0.00633553983 // gam( 48, 50)= 0.00633553983 // gam( 49, 51)= 0.00633553983 // gam( 50, 52)= 0.00633553983 // gam( 51, 53)= 0.00633553983 // gam( 52, 54)= 0.00633553983 // gam( 53, 55)= 0.00633553983 // gam( 56, 57)= 0.0472757183 // gam( 57, 58)= 0.0208024203 // gam( 57, 59)= 0.0208024203 // gam( 58, 59)= 0.01570795 // gam( 58, 60)= 0.01570795 // gam( 59, 61)= 0.01570795 // 1/gam( 1, 2)= 33.1653815 // 1/gam( 1, 3)= 33.1653815 // 1/gam( 1, 4)= 33.1653815 // 1/gam( 1, 5)= 33.1653815 // 1/gam( 1, 6)= 33.1653815 // 1/gam( 1, 35)= 7.5831991 // 1/gam( 1, 56)= 5.03499859 // 1/gam( 2, 13)= 66.0851533 // 1/gam( 3, 14)= 66.0851533 // 1/gam( 4, 15)= 66.0851533 // 1/gam( 5, 16)= 66.0851533 // 1/gam( 6, 17)= 66.0851533 // 1/gam( 7, 18)= 124.210518 // 1/gam( 7, 35)= 69.5656534 // 1/gam( 8, 19)= 124.210518 // 1/gam( 8, 36)= 70.371624 // 1/gam( 9, 20)= 124.210518 // 1/gam( 9, 37)= 71.3156225 // 1/gam( 10, 21)= 124.210518 // 1/gam( 10, 37)= 71.3156225 // 1/gam( 11, 22)= 124.210518 // 1/gam( 11, 36)= 70.371624 // 1/gam( 12, 23)= 124.210518 // 1/gam( 12, 35)= 69.5656534 // 1/gam( 13, 24)= 66.0851533 // 1/gam( 14, 25)= 66.0851533 // 1/gam( 15, 26)= 66.0851533 // 1/gam( 16, 27)= 66.0851533 // 1/gam( 17, 28)= 66.0851533 // 1/gam( 18, 29)= 124.210518 // 1/gam( 19, 30)= 124.210518 // 1/gam( 20, 31)= 124.210518 // 1/gam( 21, 32)= 124.210518 // 1/gam( 22, 33)= 124.210518 // 1/gam( 23, 34)= 124.210518 // 1/gam( 35, 36)= 15.7267591 // 1/gam( 36, 37)= 17.4767281 // 1/gam( 37, 38)= 19.5361685 // 1/gam( 38, 39)= 21.9826712 // 1/gam( 39, 40)= 24.9197892 // 1/gam( 40, 41)= 28.4882175 // 1/gam( 41, 42)= 32.8830323 // 1/gam( 42, 43)= 38.3810553 // 1/gam( 43, 44)= 50.5648944 // 1/gam( 44, 45)= 76.4690412 // 1/gam( 45, 46)= 107.528642 // 1/gam( 46, 47)= 143.794447 // 1/gam( 47, 48)= 161.813143 // 1/gam( 47, 49)= 161.813143 // 1/gam( 48, 49)= 157.839746 // 1/gam( 48, 50)= 157.839746 // 1/gam( 49, 51)= 157.839746 // 1/gam( 50, 52)= 157.839746 // 1/gam( 51, 53)= 157.839746 // 1/gam( 52, 54)= 157.839746 // 1/gam( 53, 55)= 157.839746 // 1/gam( 56, 57)= 21.1525078 // 1/gam( 57, 58)= 48.0713295 // 1/gam( 57, 59)= 48.0713295 // 1/gam( 58, 59)= 63.662031 // 1/gam( 58, 60)= 63.662031 // 1/gam( 59, 61)= 63.662031 /* tuftIB/tuftIB_template.hoc automatically written from f2nrn/neuron_code_writer.f via subroutines that were inserted into the fortran code e.g., tuftIB/integrate_tuftIB.hoc The template's form was derived by Tom Morse and Michael Hines from a template, pyr3_template created by Roger Traub and Maciej Lazarewicz when they ported Traub RD, Buhl EH, Gloveli T, Whittington MA. Fast Rhythmic Bursting Can Be Induced in Layer 2/3 Cortical Neurons by Enhancing Persistent Na(+) Conductance or by Blocking BK Channels.J Neurophysiol. 2003 Feb;89(2):909-21. to NEURON */ begintemplate tuftIB public type // parts of the template were lifted from a default // cell writing from Network Builder NetGUI[0] public is_art public init, topol, basic_shape, subsets public geom, biophys public synlist, x, y, z, position public connect2target public set_netcon_src_comp // the above function added to set neton // compartment source in the presyn cell public comp, level, Soma, Dendrites public Soma_Dendrites, Axon, all public presyn_comp, top_level // it is the responsibility of the calling // program to set the above presynaptic // compartment number external traub_connect objref this create comp[ 61+1] objref level[ 18+1], Soma, Dendrites objref Soma_Dendrites, Axon objref synlist func type() {return 6 } proc init() { doubler = 1 comp[0] delete_section() // clean up for fortran code traub_connect( 61+1) titlePrint() presyn_comp = 60 // in Traub model;changed by calling prog. objref Soma, Axon, Dendrites, Soma_Dendrites objref level topol() shape() geom() // the geometry and subsets() // subsets and biophys() // active currents synlist = new List() // list of synapses // NetGUI[0] stores synapses in the cell object, in // Traub model it is easier to store them outside set_doubler() // to double or not if (doubler) {double_dend_cond()} /* for taking spine membrane area correction into account (the method used doubles max cond's when spines present) */ more_adjustments() } proc double_dend_cond() { /* this function gets replaced later with another one if double_dend_cond() is tacked on. */ } proc titlePrint() { /* print " print "-----" print " print "tuftIB Neuron Model based on " print "Traub RD et al (2005, 2003)" print " print "-----" Remove title printing with this comment for now. Printing otherwise repeats (for each cell) -too voluminous for a network creation */ } proc set_doubler() {doubler=1} // this function gets replaced with one that // sets doubler to 0 when there are no spines // in the cell (for no spines the additional // hoc code is written from integrate_cell.f // where cell is nRT, TCR. Woops I just // found that deepaxax, deepbask, deepLTS, // supaxax, supbask, supLTS all use the script // cell/run_fortran.sh to replace the =1's with // =0's. I will change the fortran code to // make it all run_fortran.sh replacements or // not for uniformity. proc topol() { // create comp[ 62] // note one greater than numcomp due to fortran indicies // last argument, parent location for connection // is overwritten to 1 for parents with connected children // in below traub_connect proc calls traub_connect(this, 1, 56, 0.198609787, 0) traub_connect(this, 1, 2, 0.0301519221, 1) traub_connect(this, 1, 3, 0.0301519221, 1) traub_connect(this, 1, 4, 0.0301519221, 1) traub_connect(this, 1, 5, 0.0301519221, 1) traub_connect(this, 1, 6, 0.0301519221, 1) traub_connect(this, 1, 35, 0.131870466, 1) traub_connect(this, 2, 13, 0.0151319918, 1.) traub_connect(this, 3, 14, 0.0151319918, 1.) traub_connect(this, 4, 15, 0.0151319918, 1.) traub_connect(this, 5, 16, 0.0151319918, 1.) traub_connect(this, 6, 17, 0.0151319918, 1.) traub_connect(this, 7, 35, 0.0143749099, 1.) traub_connect(this, 7, 18, 0.00805084797, 1.) traub_connect(this, 12, 35, 0.0143749099, 1.) traub_connect(this, 12, 23, 0.00805084797, 1.) traub_connect(this, 13, 24, 0.0151319918, 1.) traub_connect(this, 14, 25, 0.0151319918, 1.) traub_connect(this, 15, 26, 0.0151319918, 1.) traub_connect(this, 16, 27, 0.0151319918, 1.) traub_connect(this, 17, 28, 0.0151319918, 1.) traub_connect(this, 18, 29, 0.00805084797, 1.) traub_connect(this, 23, 34, 0.00805084797, 1.) traub_connect(this, 35, 36, 0.0635858917, 1.) traub_connect(this, 36, 37, 0.0572189482, 1.) traub_connect(this, 37, 38, 0.0511871097, 1.) traub_connect(this, 38, 39, 0.0454903769, 1.) traub_connect(this, 39, 40, 0.0401287504, 1.) traub_connect(this, 40, 41, 0.0351022313, 1.) traub_connect(this, 41, 42, 0.0304108207, 1.) traub_connect(this, 42, 43, 0.0260545207, 1.) traub_connect(this, 43, 44, 0.0197765666, 1.) traub_connect(this, 44, 45, 0.0130771876, 1.) traub_connect(this, 45, 46, 0.00929984778, 1.) traub_connect(this, 46, 47, 0.00695437146, 1.) traub_connect(this, 47, 48, 0.00617996773, 1) traub_connect(this, 47, 49, 0.00617996773, 1) traub_connect(this, 48, 49, 0.00633553983, 1) traub_connect(this, 48, 50, 0.00633553983, 1.) traub_connect(this, 49, 51, 0.00633553983, 1.) traub_connect(this, 50, 52, 0.00633553983, 1.) traub_connect(this, 51, 53, 0.00633553983, 1.) traub_connect(this, 52, 54, 0.00633553983, 1.) traub_connect(this, 53, 55, 0.00633553983, 1.) traub_connect(this, 56, 57, 0.0472757183, 1.) traub_connect(this, 57, 58, 0.0208024203, 1) traub_connect(this, 57, 59, 0.0208024203, 1) traub_connect(this, 58, 59, 0.01570795, 1) traub_connect(this, 58, 60, 0.01570795, 1.) traub_connect(this, 59, 61, 0.01570795, 1.) traub_connect(this, 36, 8, 0.0142102732, 1.) traub_connect(this, 37, 9, 0.0140221731, 1.) traub_connect(this, 37, 10, 0.0140221731, 1.) traub_connect(this, 36, 11, 0.0142102732, 1.) traub_connect(this, 8, 19, 0.00805084797, 1.) traub_connect(this, 10, 21, 0.00805084797, 1.) traub_connect(this, 19, 30, 0.00805084797, 1.) traub_connect(this, 21, 32, 0.00805084797, 1.) traub_connect(this, 9, 20, 0.00805084797, 1.) traub_connect(this, 20, 31, 0.00805084797, 1.) traub_connect(this, 11, 22, 0.00805084797, 1.) traub_connect(this, 22, 33, 0.00805084797, 1.) access comp[1] // handy statement if want to start gui's from nrnmainmenu } proc geom() { // the "traub level" subsets are created and defined below top_level = 18 objref level[top_level+1] for i=0,top_level { level[i] = new SectionList() } comp[ 1] { level[ 1].append() L= 25. diam = 2* 9. } comp[ 2] { level[ 2].append() L= 60. diam = 2* 0.85 } comp[ 3] { level[ 2].append() L= 60. diam = 2* 0.85 } comp[ 4] { level[ 2].append() L= 60. diam = 2* 0.85 } comp[ 5] { level[ 2].append() L= 60. diam = 2* 0.85 } comp[ 6] { level[ 2].append() L= 60. diam = 2* 0.85 } comp[ 7] { level[ 2].append() L= 60. diam = 2* 0.62 } comp[ 8] { level[ 2].append() L= 60. diam = 2* 0.62 } comp[ 9] { level[ 2].append() L= 60. diam = 2* 0.62 } comp[ 10] { level[ 2].append() L= 60. diam = 2* 0.62 } comp[ 11] { level[ 2].append() L= 60. diam = 2* 0.62 } comp[ 12] { level[ 2].append() L= 60. diam = 2* 0.62 } comp[ 13] { level[ 3].append() L= 60. diam = 2* 0.85 } comp[ 14] { level[ 3].append() L= 60. diam = 2* 0.85 } comp[ 15] { level[ 3].append() L= 60. diam = 2* 0.85 } comp[ 16] { level[ 3].append() L= 60. diam = 2* 0.85 } comp[ 17] { level[ 3].append() L= 60. diam = 2* 0.85 } comp[ 18] { level[ 3].append() L= 60. diam = 2* 0.62 } comp[ 19] { level[ 3].append() L= 60. diam = 2* 0.62 } comp[ 20] { level[ 3].append() L= 60. diam = 2* 0.62 } comp[ 21] { level[ 3].append() L= 60. diam = 2* 0.62 } comp[ 22] { level[ 3].append() L= 60. diam = 2* 0.62 } comp[ 23] { level[ 3].append() L= 60. diam = 2* 0.62 } comp[ 24] { level[ 4].append() L= 60. diam = 2* 0.85 } comp[ 25] { level[ 4].append() L= 60. diam = 2* 0.85 } comp[ 26] { level[ 4].append() L= 60. diam = 2* 0.85 } comp[ 27] { level[ 4].append() L= 60. diam = 2* 0.85 } comp[ 28] { level[ 4].append() L= 60. diam = 2* 0.85 } comp[ 29] { level[ 4].append() L= 60. diam = 2* 0.62 } comp[ 30] { level[ 4].append() L= 60. diam = 2* 0.62 } comp[ 31] { level[ 4].append() L= 60. diam = 2* 0.62 } comp[ 32] { level[ 4].append() L= 60. diam = 2* 0.62 } comp[ 33] { level[ 4].append() L= 60. diam = 2* 0.62 } comp[ 34] { level[ 4].append() L= 60. diam = 2* 0.62 } comp[ 35] { level[ 5].append() L= 75. diam = 2* 2. } comp[ 36] { level[ 6].append() L= 75. diam = 2* 1.9 } comp[ 37] { level[ 7].append() L= 75. diam = 2* 1.8 } comp[ 38] { level[ 8].append() L= 75. diam = 2* 1.7 } comp[ 39] { level[ 9].append() L= 75. diam = 2* 1.6 } comp[ 40] { level[ 10].append() L= 75. diam = 2* 1.5 } comp[ 41] { level[ 11].append() L= 75. diam = 2* 1.4 } comp[ 42] { level[ 12].append() L= 75. diam = 2* 1.3 } comp[ 43] { level[ 13].append() L= 75. diam = 2* 1.2 } comp[ 44] { level[ 14].append() L= 75. diam = 2* 1. } comp[ 45] { level[ 15].append() L= 75. diam = 2* 0.8 } comp[ 46] { level[ 16].append() L= 75. diam = 2* 0.7 } comp[ 47] { level[ 17].append() L= 75. diam = 2* 0.6 } comp[ 48] { level[ 18].append() L= 60. diam = 2* 0.55 } comp[ 49] { level[ 18].append() L= 60. diam = 2* 0.55 } comp[ 50] { level[ 18].append() L= 60. diam = 2* 0.55 } comp[ 51] { level[ 18].append() L= 60. diam = 2* 0.55 } comp[ 52] { level[ 18].append() L= 60. diam = 2* 0.55 } comp[ 53] { level[ 18].append() L= 60. diam = 2* 0.55 } comp[ 54] { level[ 18].append() L= 60. diam = 2* 0.55 } comp[ 55] { level[ 18].append() L= 60. diam = 2* 0.55 } comp[ 56] { level[ 0].append() L= 25. diam = 2* 0.9 } comp[ 57] { level[ 0].append() L= 50. diam = 2* 0.7 } comp[ 58] { level[ 0].append() L= 50. diam = 2* 0.5 } comp[ 59] { level[ 0].append() L= 50. diam = 2* 0.5 } comp[ 60] { level[ 0].append() L= 50. diam = 2* 0.5 } comp[ 61] { level[ 0].append() L= 50. diam = 2* 0.5 } } // Here are some commonly used subsets of sections objref all proc subsets() { local i objref Soma, Dendrites, Soma_Dendrites, Axon objref all Soma = new SectionList() Dendrites = new SectionList() Soma_Dendrites = new SectionList() Axon = new SectionList() for i=1,top_level { forsec level[i] { // recall level 0 is axon, 1 is soma, higher are dends Soma_Dendrites.append() if (i>1) {Dendrites.append()} } } forsec level[1] { Soma.append() } forsec level[0] { Axon.append() } all = new SectionList() for i=1, 61 comp[i] all.append() } proc shape() { /* This section could contain statements like {pt3dclear() pt3dadd(-1,-1,0,1) pt3dadd(-1,-2,0,1)} These visual settings do not effect the electrical and chemical systems of equations. */ } proc biophys() { // // insert the mechanisms and assign max conductances // forsec all { insert pas } // g_pas has two values; soma-dend,axon forsec level[ 0] { insert naf gbar_naf = 0.45 insert kdr gbar_kdr = 0.45 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.03 insert k2 gbar_k2 = 0.0005 } forsec level[ 1] { insert naf gbar_naf = 0.2 insert nap gbar_nap = 0.0008 insert kdr gbar_kdr = 0.17 insert kc gbar_kc = 0.008 insert ka_ib gbar_ka_ib = 0.02 insert km gbar_km = 0.0085 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.004 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.01 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 4333.33333 } forsec level[ 2] { insert naf gbar_naf = 0.075 insert nap gbar_nap = 0.0003 insert kdr gbar_kdr = 0.075 insert kc gbar_kc = 0.008 insert ka_ib gbar_ka_ib = 0.008 insert km gbar_km = 0.0136 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.004 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.02 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 3] { insert naf gbar_naf = 0.015 insert nap gbar_nap = 6.E-05 insert kc gbar_kc = 0.00025 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.0136 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.004 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 4] { insert naf gbar_naf = 0.015 insert nap gbar_nap = 6.E-05 insert kc gbar_kc = 0.00025 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.0136 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.004 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 5] { insert naf gbar_naf = 0.15 insert nap gbar_nap = 0.0006 insert kdr gbar_kdr = 0.12 insert kc gbar_kc = 0.008 insert ka_ib gbar_ka_ib = 0.008 insert km gbar_km = 0.0136 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.004 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 6] { insert naf gbar_naf = 0.075 insert nap gbar_nap = 0.0003 insert kdr gbar_kdr = 0.075 insert kc gbar_kc = 0.008 insert ka_ib gbar_ka_ib = 0.008 insert km gbar_km = 0.0136 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.004 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 7] { insert naf gbar_naf = 0.015 insert nap gbar_nap = 6.E-05 insert kc gbar_kc = 0.00025 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.0136 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.004 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 8] { insert naf gbar_naf = 0.015 insert nap gbar_nap = 6.E-05 insert kc gbar_kc = 0.00025 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.0136 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.001 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 9] { insert naf gbar_naf = 0.015 insert nap gbar_nap = 6.E-05 insert kc gbar_kc = 0.00025 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.0136 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.001 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 10] { insert naf gbar_naf = 0.015 insert nap gbar_nap = 6.E-05 insert kc gbar_kc = 0.00025 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.0136 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.001 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 11] { insert naf gbar_naf = 0.015 insert nap gbar_nap = 6.E-05 insert kc gbar_kc = 0.00025 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.0136 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.001 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 12] { insert naf gbar_naf = 0.015 insert nap gbar_nap = 6.E-05 insert kc gbar_kc = 0.00025 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.0136 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.001 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 13] { insert naf gbar_naf = 0.015 insert nap gbar_nap = 6.E-05 insert kc gbar_kc = 0.00025 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.0136 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.001 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 14] { insert naf gbar_naf = 0.015 insert nap gbar_nap = 6.E-05 insert kc gbar_kc = 0.00025 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.0136 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.001 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 15] { insert naf gbar_naf = 0.003 insert nap gbar_nap = 1.2E-05 insert kc gbar_kc = 0.0006 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.004 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.001 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 16] { insert naf gbar_naf = 0.003 insert nap gbar_nap = 1.2E-05 insert kc gbar_kc = 0.0006 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.004 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.001 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 17] { insert naf gbar_naf = 0.003 insert nap gbar_nap = 1.2E-05 insert kc gbar_kc = 0.0006 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.004 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.001 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0001 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } forsec level[ 18] { insert naf gbar_naf = 0.003 insert nap gbar_nap = 1.2E-05 insert kc gbar_kc = 0.0006 insert ka_ib gbar_ka_ib = 0.0006 insert km gbar_km = 0.004 insert k2 gbar_k2 = 0.0005 insert kahp_deeppyr gbar_kahp_deeppyr = 0.0002 insert cal gbar_cal = 0.0006 insert cat gbar_cat = 0.0001 insert ar gbar_ar = 0.0002 insert cad // *** ca diffusion: beta=1/tau beta_cad = 0.075 // cafor(I) (FORTRAN) converted to phi (NEURON) phi_cad = 86666.6667 } // Special case: individually specified beta_cad's in level 2 comp[ 2] beta_cad = 0.02 comp[ 3] beta_cad = 0.075 comp[ 4] beta_cad = 0.075 comp[ 5] beta_cad = 0.02 comp[ 6] beta_cad = 0.02 comp[ 7] beta_cad = 0.075 comp[ 8] beta_cad = 0.075 comp[ 9] beta_cad = 0.075 comp[ 10] beta_cad = 0.075 comp[ 11] beta_cad = 0.075 comp[ 12] beta_cad = 0.075 forsec all { cm = 0.9 // assign global specific capac. } // // passive membrane resistance (leak) and axial resistance // forsec Soma_Dendrites { g_pas = 2.E-05 Ra = 250. } forsec Axon { g_pas = 0.001 Ra = 100. } ceiling_cad = 1e6 // nearly unlimited Ca concentration // print "made it to end of initialization from SCORTMAJ_FRB()" } // end of biophys // Compartment Area: Dendritic.spines double area of // dend. membrane, which in Traubs method is equivalent to // only multiplying all dend. max conductances by two // (the area is doubled but the volume is const.) proc double_dend_cond() { spine_area_multiplier = 2 forsec Dendrites { if (ismembrane("nap")) { gbar_nap *= spine_area_multiplier } if (ismembrane("napf")) { gbar_napf *= spine_area_multiplier } if (ismembrane("napf_tcr")) { gbar_napf_tcr *= spine_area_multiplier } if (ismembrane("naf")) { gbar_naf *= spine_area_multiplier } if (ismembrane("naf_tcr")) { gbar_naf_tcr *= spine_area_multiplier } if (ismembrane("naf2")) { gbar_naf2 *= spine_area_multiplier } if (ismembrane("kc")) { gbar_kc *= spine_area_multiplier } if (ismembrane("kc_fast")) { gbar_kc_fast *= spine_area_multiplier } if (ismembrane("kahp_deeppyr")) { gbar_kahp_deeppyr *= spine_area_multiplier } if (ismembrane("km")) { gbar_km *= spine_area_multiplier } if (ismembrane("kdr")) { gbar_kdr *= spine_area_multiplier } if (ismembrane("kdr_fs")) { gbar_kdr_fs *= spine_area_multiplier } if (ismembrane("ka_ib")) { gbar_ka_ib *= spine_area_multiplier } if (ismembrane("ka_ib_ib")) { gbar_ka_ib_ib *= spine_area_multiplier } if (ismembrane("k2")) { gbar_k2 *= spine_area_multiplier } if (ismembrane("cal")) { gbar_cal *= spine_area_multiplier } if (ismembrane("cat")) { gbar_cat *= spine_area_multiplier } if (ismembrane("cat_a")) { gbar_cat_a *= spine_area_multiplier } if (ismembrane("ar")) { gbar_ar *= spine_area_multiplier } if (ismembrane("pas")) { g_pas *= spine_area_multiplier } cm = cm * spine_area_multiplier } } // double_dend_cond() // run for cells w/ spines // The below is after doubling of dendritic area to // take into account the effect of spines // These areas were used in the FORTRAN code to // compute the conductances from specific conductances. // I AREA(I) (compartments and their areas) // 1 1413.7155 // 2 640.88436 // 3 640.88436 // 4 640.88436 // 5 640.88436 // 6 640.88436 // 7 467.468592 // 8 467.468592 // 9 467.468592 // 10 467.468592 // 11 467.468592 // 12 467.468592 // 13 640.88436 // 14 640.88436 // 15 640.88436 // 16 640.88436 // 17 640.88436 // 18 467.468592 // 19 467.468592 // 20 467.468592 // 21 467.468592 // 22 467.468592 // 23 467.468592 // 24 640.88436 // 25 640.88436 // 26 640.88436 // 27 640.88436 // 28 640.88436 // 29 467.468592 // 30 467.468592 // 31 467.468592 // 32 467.468592 // 33 467.468592 // 34 467.468592 // 35 1884.954 // 36 1790.7063 // 37 1696.4586 // 38 1602.2109 // 39 1507.9632 // 40 1413.7155 // 41 1319.4678 // 42 1225.2201 // 43 1130.9724 // 44 942.477 // 45 753.9816 // 46 659.7339 // 47 565.4862 // 48 414.68988 // 49 414.68988 // 50 414.68988 // 51 414.68988 // 52 414.68988 // 53 414.68988 // 54 414.68988 // 55 414.68988 // 56 141.37155 // 57 219.9113 // 58 157.0795 // 59 157.0795 // 60 157.0795 // 61 157.0795 proc position() { local i // comp switched to comp[1] since 0 deleted comp[1] for i = 0, n3d()-1 { pt3dchange(i, $1-x+x3d(i), \ $2-y+y3d(i), $3-z+z3d(i),diam3d(i)) } x=$1 y=$2 z=$3 } proc connect2target() { // $o1 targ point process, $o2 returned NetCon comp[presyn_comp] $o2 = new NetCon(&v(1),$o1) $o2.threshold = 0 } objref syn_ proc synapses() { // place for each compartment that has input // statements like //comp[3] syn_=new AlphaSynKinT(1) synlist.append(syn_) //comp[4] syn_=new NMDA(1) synlist.append(syn_) } // is not an artificial cell: func is_art() { return 0 } proc more_adjustments() { forsec all { // global reversal potentials ek = -95. e_pas = -70. ena = 50. vca = 125. forsec all if (ismembrane("ar")) erev_ar = -35. e_gaba_a = -75. } // v(1,1)= -70. forsec all if (ismembrane("naf")) {fastNa_shift_naf=-3.5} // extended initializations from integrate_tuftIB() forsec Soma_Dendrites { if (ismembrane("nap")) {gbar_nap *= 0.2}} forsec Soma_Dendrites { if (ismembrane("kc")) {gbar_kc *= 2.}} forsec Soma_Dendrites { if (ismembrane("cal")) {gbar_cal *= 1.}} forsec Soma_Dendrites { if (ismembrane("km")) {gbar_km *= 1.4}} comp[48] { if (ismembrane("cal")) {gbar_cal *= 4.5 }} comp[49] { if (ismembrane("cal")) {gbar_cal *= 4.5 }} comp[ 38] { if (ismembrane("cal")) {gbar_cal *= 2.0 }} comp[ 39] { if (ismembrane("cal")) {gbar_cal *= 2.0 }} comp[ 40] { if (ismembrane("cal")) {gbar_cal *= 2.0 }} comp[ 41] { if (ismembrane("cal")) {gbar_cal *= 2.0 }} comp[ 42] { if (ismembrane("cal")) {gbar_cal *= 2.0 }} comp[ 43] { if (ismembrane("cal")) {gbar_cal *= 2.0 }} comp[ 44] { if (ismembrane("cal")) {gbar_cal *= 2.0 }} } endtemplate tuftIB