/* nontuftRS/nontuftRS_template.hoc
automatically written from f2nrn/neuron_code_writer.f
via subroutines that were inserted into the fortran
code e.g., nontuftRS/integrate_nontuftRS.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 nontuftRS
public type
public name
strdef name
// 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[ 50+1]
objref level[ 14+1], Soma, Dendrites
objref Soma_Dendrites, Axon
objref synlist
func type() {return 8 }
proc init() {
doubler = 1
comp[0] delete_section() // clean up for fortran code
traub_connect( 50+1)
titlePrint()
presyn_comp = 48
// 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()
name = "nontuftRS"
}
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 "nontuftRS 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[ 51] // 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, 45, 0.198549254, 0)
traub_connect(this, 1, 2, 0.0301505266, 1)
traub_connect(this, 1, 3, 0.0301505266, 1)
traub_connect(this, 1, 4, 0.0301505266, 1)
traub_connect(this, 1, 5, 0.0301505266, 1)
traub_connect(this, 1, 6, 0.0301505266, 1)
traub_connect(this, 1, 35, 0.111528865, 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, 0.0140949874, 1.)
traub_connect(this, 7, 18, 0.00805084797, 1.)
traub_connect(this, 12, 35, 0.0140949874, 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, 0.0526533469, 1.)
traub_connect(this, 36, 37, 0.0456162311, 1.)
traub_connect(this, 37, 38, 0.0390817811, 1.)
traub_connect(this, 38, 39, 0.033050001, 1.)
traub_connect(this, 39, 40, 0.027520897, 1.)
traub_connect(this, 40, 41, 0.0224944787, 1.)
traub_connect(this, 41, 42, 0.0179707614, 1.)
traub_connect(this, 42, 43, 0.0139497717, 1.)
traub_connect(this, 43, 44, 0.0104315572, 1.)
traub_connect(this, 45, 46, 0.0472757183, 1.)
traub_connect(this, 46, 47, 0.0208024203, 1)
traub_connect(this, 46, 49, 0.0208024203, 1)
traub_connect(this, 47, 48, 0.01570795, 1.)
traub_connect(this, 47, 49, 0.01570795, 1)
traub_connect(this, 49, 50, 0.01570795, 1.)
traub_connect(this, 36, 8, 0.0138397854, 1.)
traub_connect(this, 37, 9, 0.0135359971, 1.)
traub_connect(this, 37, 10, 0.0135359971, 1.)
traub_connect(this, 36, 11, 0.0138397854, 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 = 14
objref level[top_level+1]
for i=0,top_level { level[i] = new SectionList() }
comp[ 1] { level[ 1].append() L= 20. diam = 2* 8. }
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= 50. diam = 2* 1.5 }
comp[ 36] { level[ 6].append() L= 50. diam = 2* 1.4 }
comp[ 37] { level[ 7].append() L= 50. diam = 2* 1.3 }
comp[ 38] { level[ 8].append() L= 50. diam = 2* 1.2 }
comp[ 39] { level[ 9].append() L= 50. diam = 2* 1.1 }
comp[ 40] { level[ 10].append() L= 50. diam = 2* 1. }
comp[ 41] { level[ 11].append() L= 50. diam = 2* 0.9 }
comp[ 42] { level[ 12].append() L= 50. diam = 2* 0.8 }
comp[ 43] { level[ 13].append() L= 50. diam = 2* 0.7 }
comp[ 44] { level[ 14].append() L= 50. diam = 2* 0.6 }
comp[ 45] { level[ 0].append() L= 25. diam = 2* 0.9 }
comp[ 46] { level[ 0].append() L= 50. diam = 2* 0.7 }
comp[ 47] { level[ 0].append() L= 50. diam = 2* 0.5 }
comp[ 48] { level[ 0].append() L= 50. diam = 2* 0.5 }
comp[ 49] { level[ 0].append() L= 50. diam = 2* 0.5 }
comp[ 50] { 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, 50 comp[i] all.append()
}
proc shape() {
comp[1] {pt3dclear() pt3dadd(0.0, 0.0, 0.0, 16.0) pt3dadd(0.0, 10.0, 0.0, 16.0)}
comp[1] {pt3dadd(-4.371139E-7, 20.0, 0.0, 16.0)}
comp[45] {pt3dclear() pt3dadd(0.0, 0.0, 0.0, 1.8) pt3dadd(12.5, 0.0, 0.0, 1.8)}
comp[45] {pt3dadd(25.0, 9.2276395E-7, -6.94707E-14, 1.8)}
comp[35] {pt3dclear() pt3dadd(0.0, 20.0, 0.0, 3.0) pt3dadd(0.0, 45.0, 0.0, 3.0)}
comp[35] {pt3dadd(-1.6583364E-5, 69.99997, 0.0, 3.0)}
comp[6] {pt3dclear() pt3dadd(0.0, 20.0, 0.0, 1.7) pt3dadd(0.0, -1.2132034, 21.213203, 1.7)}
comp[6] {pt3dadd(1.1551366E-5, -22.426464, 42.426445, 1.7)}
comp[5] {pt3dclear() pt3dadd(0.0, 20.0, 0.0, 1.7) pt3dadd(0.0, -1.2132034, -21.213203, 1.7)}
comp[5] {pt3dadd(7.984267E-6, -22.426373, -42.42637, 1.7)}
comp[4] {pt3dclear() pt3dadd(0.0, 20.0, 0.0, 1.7) pt3dadd(-21.213203, -1.2132034, 0.0, 1.7)}
comp[4] {pt3dadd(-42.42636, -22.42638, 0.0, 1.7)}
comp[3] {pt3dclear() pt3dadd(0.0, 20.0, 0.0, 1.7) pt3dadd(21.213203, -1.2132034, 0.0, 1.7)}
comp[3] {pt3dadd(42.42646, -22.426445, 0.0, 1.7)}
comp[2] {pt3dclear() pt3dadd(0.0, 20.0, 0.0, 1.7) pt3dadd(0.0, -9.999994, 0.0, 1.7)}
comp[2] {pt3dadd(-1.3068187E-4, -40.00004, 0.0, 1.7)}
comp[46] {pt3dclear() pt3dadd(25.0, 9.2276395E-7, -6.94707E-14, 1.4) pt3dadd(50.0, 1.2789027E-6, 6.947164E-14, 1.4)}
comp[46] {pt3dadd(75.0, 1.4565248E-7, 2.0841583E-13, 1.4)}
comp[36] {pt3dclear() pt3dadd(0.0, 70.0, 0.0, 2.8) pt3dadd(0.0, 100.0, 0.0, 2.8)}
comp[36] {pt3dadd(3.04693E-4, 124.99974, 0.0, 2.8)}
comp[12] {pt3dclear() pt3dadd(0.0, 70.0, 0.0, 1.24) pt3dadd(-30.0, 70.0, 0.0, 1.24)}
comp[12] {pt3dadd(-60.00023, 69.99986, 0.0, 1.24)}
comp[7] {pt3dclear() pt3dadd(0.0, 70.0, 0.0, 1.24) pt3dadd(30.0, 70.0, 0.0, 1.24)}
comp[7] {pt3dadd(60.00001, 70.00002, 0.0, 1.24)}
comp[17] {pt3dclear() pt3dadd(1.1551366E-5, -22.426464, 42.426445, 1.7) pt3dadd(2.33004E-5, -43.639362, 63.639324, 1.7)}
comp[17] {pt3dadd(-1.4493322E-4, -64.853096, 84.853195, 1.7)}
comp[16] {pt3dclear() pt3dadd(7.984267E-6, -22.426373, -42.42637, 1.7) pt3dadd(2.3281485E-5, -43.639473, -63.63946, 1.7)}
comp[16] {pt3dadd(3.1499014E-5, -64.852646, -84.85263, 1.7)}
comp[15] {pt3dclear() pt3dadd(-42.42636, -22.42638, 0.0, 1.7) pt3dadd(-63.63944, -43.639492, 0.0, 1.7)}
comp[15] {pt3dadd(-84.8526, -64.85267, 0.0, 1.7)}
comp[14] {pt3dclear() pt3dadd(42.42646, -22.426445, 0.0, 1.7) pt3dadd(63.639362, -43.639328, 0.0, 1.7)}
comp[14] {pt3dadd(84.85303, -64.85327, 0.0, 1.7)}
comp[13] {pt3dclear() pt3dadd(-1.3068187E-4, -40.00004, 0.0, 1.7) pt3dadd(6.618662E-5, -69.999565, 0.0, 1.7)}
comp[13] {pt3dadd(-9.839095E-5, -99.999695, 0.0, 1.7)}
comp[49] {pt3dclear() pt3dadd(75.0, 1.4565248E-7, 2.0841583E-13, 1.0) pt3dadd(98.02649, -9.735456, 1.7022016E-6, 1.0)}
comp[49] {pt3dadd(121.05301, -19.470882, 3.404398E-6, 1.0)}
comp[47] {pt3dclear() pt3dadd(75.0, 1.4565248E-7, 2.0841583E-13, 1.0) pt3dadd(98.0265, 9.735463, -1.7022022E-6, 1.0)}
comp[47] {pt3dadd(121.05301, 19.470919, -3.4044026E-6, 1.0)}
comp[11] {pt3dclear() pt3dadd(0.0, 125.0, 0.0, 1.24) pt3dadd(0.0, 125.0, -30.0, 1.24)}
comp[11] {pt3dadd(-3.9912673E-4, 125.0, -60.000046, 1.24)}
comp[8] {pt3dclear() pt3dadd(0.0, 125.0, 0.0, 1.24) pt3dadd(0.0, 125.0, 30.0, 1.24)}
comp[8] {pt3dadd(4.4153922E-4, 125.00026, 59.999832, 1.24)}
comp[37] {pt3dclear() pt3dadd(0.0, 125.0, 0.0, 2.6) pt3dadd(0.0, 150.0, 0.0, 2.6)}
comp[37] {pt3dadd(-6.4953038E-6, 174.99948, 0.0, 2.6)}
comp[23] {pt3dclear() pt3dadd(-60.00023, 69.99986, 0.0, 1.24) pt3dadd(-90.00041, 69.999855, 0.0, 1.24)}
comp[23] {pt3dadd(-119.99962, 70.000145, 0.0, 1.24)}
comp[18] {pt3dclear() pt3dadd(60.00001, 70.00002, 0.0, 1.24) pt3dadd(90.0, 70.00005, 0.0, 1.24)}
comp[18] {pt3dadd(120.0, 70.000084, 0.0, 1.24)}
comp[28] {pt3dclear() pt3dadd(-1.4493322E-4, -64.853096, 84.853195, 1.7) pt3dadd(-1.1118335E-4, -86.06622, 106.06629, 1.7)}
comp[28] {pt3dadd(-7.2776886E-5, -107.27936, 127.27937, 1.7)}
comp[27] {pt3dclear() pt3dadd(3.1499014E-5, -64.852646, -84.85263, 1.7) pt3dadd(3.911812E-5, -86.06582, -106.065796, 1.7)}
comp[27] {pt3dadd(7.813368E-6, -107.27897, -127.27896, 1.7)}
comp[26] {pt3dclear() pt3dadd(-84.8526, -64.85267, 0.0, 1.7) pt3dadd(-106.06576, -86.06585, 0.0, 1.7)}
comp[26] {pt3dadd(-127.27894, -107.27899, 0.0, 1.7)}
comp[25] {pt3dclear() pt3dadd(84.85303, -64.85327, 0.0, 1.7) pt3dadd(106.06616, -86.06635, 0.0, 1.7)}
comp[25] {pt3dadd(127.2793, -107.27943, 0.0, 1.7)}
comp[24] {pt3dclear() pt3dadd(-9.839095E-5, -99.999695, 0.0, 1.7) pt3dadd(-1.7607235E-4, -129.99988, 0.0, 1.7)}
comp[24] {pt3dadd(-3.4862006E-4, -160.00003, 0.0, 1.7)}
comp[50] {pt3dclear() pt3dadd(121.05301, -19.470882, 3.404398E-6, 1.0) pt3dadd(144.08, -29.206375, 5.1066063E-6, 1.0)}
comp[50] {pt3dadd(167.106, -38.94187, 6.8088148E-6, 1.0)}
comp[48] {pt3dclear() pt3dadd(121.05301, 19.470919, -3.4044026E-6, 1.0) pt3dadd(144.08, 29.206419, -5.106612E-6, 1.0)}
comp[48] {pt3dadd(167.106, 38.941826, -6.808804E-6, 1.0)}
comp[22] {pt3dclear() pt3dadd(-3.9912673E-4, 125.0, -60.000046, 1.24) pt3dadd(-8.4935466E-4, 125.0, -89.999985, 1.24)}
comp[22] {pt3dadd(-3.4218514E-4, 124.99999, -119.99954, 1.24)}
comp[19] {pt3dclear() pt3dadd(4.4153922E-4, 125.00026, 59.999832, 1.24) pt3dadd(0.0010041951, 125.00052, 89.99986, 1.24)}
comp[19] {pt3dadd(9.4755244E-4, 125.00078, 119.99925, 1.24)}
comp[10] {pt3dclear() pt3dadd(0.0, 175.0, 0.0, 1.24) pt3dadd(21.213203, 175.0, 21.213203, 1.24)}
comp[10] {pt3dadd(42.426598, 174.99991, 42.42608, 1.24)}
comp[9] {pt3dclear() pt3dadd(0.0, 175.0, 0.0, 1.24) pt3dadd(-21.213203, 175.0, -21.213203, 1.24)}
comp[9] {pt3dadd(-42.426537, 175.00044, -42.426445, 1.24)}
comp[38] {pt3dclear() pt3dadd(0.0, 175.0, 0.0, 2.4) pt3dadd(0.0, 200.0, 0.0, 2.4)}
comp[38] {pt3dadd(1.1079743E-5, 225.0, 0.0, 2.4)}
comp[34] {pt3dclear() pt3dadd(-119.99962, 70.000145, 0.0, 1.24) pt3dadd(-149.9998, 70.00013, 0.0, 1.24)}
comp[34] {pt3dadd(-179.99992, 70.00004, 0.0, 1.24)}
comp[29] {pt3dclear() pt3dadd(120.0, 70.000084, 0.0, 1.24) pt3dadd(150.0, 70.00011, 0.0, 1.24)}
comp[29] {pt3dadd(179.99998, 70.00014, 0.0, 1.24)}
comp[33] {pt3dclear() pt3dadd(-3.4218514E-4, 124.99999, -119.99954, 1.24) pt3dadd(-4.34654E-4, 124.99999, -150.00043, 1.24)}
comp[33] {pt3dadd(-8.648856E-4, 124.99999, -180.00037, 1.24)}
comp[30] {pt3dclear() pt3dadd(9.4755244E-4, 125.00078, 119.99925, 1.24) pt3dadd(0.0015615688, 125.00104, 149.99931, 1.24)}
comp[30] {pt3dadd(0.0014558281, 125.0013, 180.00014, 1.24)}
comp[21] {pt3dclear() pt3dadd(42.426598, 174.99991, 42.42608, 1.24) pt3dadd(63.64018, 174.99962, 63.638973, 1.24)}
comp[21] {pt3dadd(84.853035, 174.99994, 84.851654, 1.24)}
comp[20] {pt3dclear() pt3dadd(-42.426537, 175.00044, -42.426445, 1.24) pt3dadd(-63.63994, 175.00078, -63.63958, 1.24)}
comp[20] {pt3dadd(-84.853165, 175.00156, -84.853195, 1.24)}
comp[39] {pt3dclear() pt3dadd(1.1079743E-5, 225.0, 0.0, 2.2) pt3dadd(2.3916264E-5, 250.0, 0.0, 2.2)}
comp[39] {pt3dadd(4.9515475E-5, 275.0, 0.0, 2.2)}
comp[32] {pt3dclear() pt3dadd(84.853035, 174.99994, 84.851654, 1.24) pt3dadd(106.06665, 174.99965, 106.064606, 1.24)}
comp[32] {pt3dadd(127.28051, 174.99997, 127.27829, 1.24)}
comp[31] {pt3dclear() pt3dadd(-84.853165, 175.00156, -84.853195, 1.24) pt3dadd(-106.06663, 175.00168, -106.06609, 1.24)}
comp[31] {pt3dadd(-127.27904, 175.00273, -127.27927, 1.24)}
comp[40] {pt3dclear() pt3dadd(4.9515475E-5, 275.0, 0.0, 2.0) pt3dadd(5.4033335E-5, 300.00006, 0.0, 2.0)}
comp[40] {pt3dadd(5.5863948E-5, 325.0, 0.0, 2.0)}
comp[41] {pt3dclear() pt3dadd(5.5863948E-5, 325.0, 0.0, 1.8) pt3dadd(7.79496E-5, 350.00006, 0.0, 1.8)}
comp[41] {pt3dadd(8.949458E-5, 375.00006, 0.0, 1.8)}
comp[42] {pt3dclear() pt3dadd(8.949458E-5, 375.00006, 0.0, 1.6) pt3dadd(9.1325186E-5, 400.00003, 0.0, 1.6)}
comp[42] {pt3dadd(1.169244E-4, 425.00006, 0.0, 1.6)}
comp[43] {pt3dclear() pt3dadd(1.169244E-4, 425.00006, 0.0, 1.4) pt3dadd(1.3063931E-4, 450.00006, 0.0, 1.4)}
comp[43] {pt3dadd(1.3029999E-4, 475.00006, 0.0, 1.4)}
comp[44] {pt3dclear() pt3dadd(1.3029999E-4, 475.00006, 0.0, 1.2) pt3dadd(1.4401489E-4, 500.00006, 0.0, 1.2)}
comp[44] {pt3dadd(1.5989975E-4, 525.0, 0.0, 1.2)}
}
proc biophys() {
//
// insert the mechanisms and assign max conductances
//
forsec all { insert pas
insert extracellular
xraxial=1e+09
xg=1e+09
xc=0
e_extracellular } // 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
gbar_ka = 0.004
insert k2
gbar_k2 = 0.0001
}
forsec level[ 1] {
insert naf
gbar_naf = 0.2
insert nap
gbar_nap = 0.00008
insert kdr
gbar_kdr = 0.17
insert kc
gbar_kc = 0.015
insert ka
gbar_ka = 0.1225
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.01
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 13000.
}
forsec level[ 2] {
insert naf
gbar_naf = 0.075
insert nap
gbar_nap = 0.00003
insert kdr
gbar_kdr = 0.075
insert kc
gbar_kc = 0.015
insert ka
gbar_ka = 0.0136
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 65000.
}
forsec level[ 3] {
insert naf
gbar_naf = 0.005
insert nap
gbar_nap = 0.000002
insert ka
gbar_ka = 0.0136
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 65000.
}
forsec level[ 4] {
insert naf
gbar_naf = 0.005
insert nap
gbar_nap = 0.000002
insert ka
gbar_ka = 0.0136
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 65000.
}
forsec level[ 5] {
insert naf
gbar_naf = 0.15
insert nap
gbar_nap = 0.00006
insert kdr
gbar_kdr = 0.12
insert kc
gbar_kc = 0.015
insert ka
gbar_ka = 0.1225
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 65000.
}
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 = 0.015
insert ka
gbar_ka = 0.0136
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 65000.
}
forsec level[ 7] {
insert naf
gbar_naf = 0.005
insert nap
gbar_nap = 0.000002
insert ka
gbar_ka = 0.0136
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 65000.
}
forsec level[ 8] {
insert naf
gbar_naf = 0.005
insert nap
gbar_nap = 0.000002
insert ka
gbar_ka = 0.0136
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 65000.
}
forsec level[ 9] {
insert naf
gbar_naf = 0.005
insert nap
gbar_nap = 0.000002
insert ka
gbar_ka = 0.0136
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 65000.
}
forsec level[ 10] {
insert naf
gbar_naf = 0.005
insert nap
gbar_nap = 0.000002
insert ka
gbar_ka = 0.0136
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 65000.
}
forsec level[ 11] {
insert naf
gbar_naf = 0.005
insert nap
gbar_nap = 0.000002
insert ka
gbar_ka = 0.0136
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 65000.
}
forsec level[ 12] {
insert naf
gbar_naf = 0.005
insert nap
gbar_nap = 0.000002
insert ka
gbar_ka = 0.0136
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 65000.
}
forsec level[ 13] {
insert naf
gbar_naf = 0.005
insert nap
gbar_nap = 0.000002
insert ka
gbar_ka = 0.0136
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 65000.
}
forsec level[ 14] {
insert naf
gbar_naf = 0.005
insert nap
gbar_nap = 0.000002
insert ka
gbar_ka = 0.0136
insert km
gbar_km = 0.0042
insert k2
gbar_k2 = 0.0001
insert kahp_deeppyr
gbar_kahp_deeppyr = 0.0002
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.0001
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 65000.
}
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")) { gbar_ka *= spine_area_multiplier }
if (ismembrane("ka_ib")) { gbar_ka_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 1005.3088
// 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
// 35 942.477
// 36 879.6452
// 37 816.8134
// 38 753.9816
// 39 691.1498
// 40 628.318
// 41 565.4862
// 42 502.6544
// 43 439.8226
// 44 376.9908
// 45 141.37155
// 46 219.9113
// 47 157.0795
// 48 157.0795
// 49 157.0795
// 50 157.0795
proc position() { local i
// comp switched to comp[1] since 0 deleted
forsec all { 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.
}
forsec all if (ismembrane("naf")) {fastNa_shift_naf=-3.5}
// extended initializations from integrate_tuftIB()
// forsec all { if (ismembrane("nap")) {gbar_nap *= 0.1}}
// forsec all { if (ismembrane("kc")) {gbar_kc *= 2.}}
}
endtemplate nontuftRS