// Trying to open ../diagnostic/tstop.dat
// new end time timtot = 150.
// Trying to open ../diagnostic/dt_F.dat
// new dt = 0.002
// COMPART. LEVEL RADIUS LENGTH(MU)
// 1 1 10.00 42.0
// 2 2 0.73 20.0
// 3 3 0.58 57.5
// 4 3 0.58 57.5
// 5 3 0.58 57.5
// 6 4 0.44 57.5
// 7 4 0.44 57.5
// 8 4 0.44 57.5
// 9 4 0.44 57.5
// 10 4 0.44 57.5
// 11 4 0.44 57.5
// 12 4 0.44 57.5
// 13 4 0.44 57.5
// 14 4 0.44 57.5
// 15 2 0.73 20.0
// 16 3 0.58 57.5
// 17 3 0.58 57.5
// 18 3 0.58 57.5
// 19 4 0.44 57.5
// 20 4 0.44 57.5
// 21 4 0.44 57.5
// 22 4 0.44 57.5
// 23 4 0.44 57.5
// 24 4 0.44 57.5
// 25 4 0.44 57.5
// 26 4 0.44 57.5
// 27 4 0.44 57.5
// 28 2 0.73 20.0
// 29 3 0.58 57.5
// 30 3 0.58 57.5
// 31 3 0.58 57.5
// 32 4 0.44 57.5
// 33 4 0.44 57.5
// 34 4 0.44 57.5
// 35 4 0.44 57.5
// 36 4 0.44 57.5
// 37 4 0.44 57.5
// 38 4 0.44 57.5
// 39 4 0.44 57.5
// 40 4 0.44 57.5
// 41 2 0.73 20.0
// 42 3 0.58 57.5
// 43 3 0.58 57.5
// 44 3 0.58 57.5
// 45 4 0.44 57.5
// 46 4 0.44 57.5
// 47 4 0.44 57.5
// 48 4 0.44 57.5
// 49 4 0.44 57.5
// 50 4 0.44 57.5
// 51 4 0.44 57.5
// 52 4 0.44 57.5
// 53 4 0.44 57.5
// 54 2 0.73 20.0
// 55 3 0.58 57.5
// 56 3 0.58 57.5
// 57 3 0.58 57.5
// 58 4 0.44 57.5
// 59 4 0.44 57.5
// 60 4 0.44 57.5
// 61 4 0.44 57.5
// 62 4 0.44 57.5
// 63 4 0.44 57.5
// 64 4 0.44 57.5
// 65 4 0.44 57.5
// 66 4 0.44 57.5
// 67 2 0.73 20.0
// 68 3 0.58 57.5
// 69 3 0.58 57.5
// 70 3 0.58 57.5
// 71 4 0.44 57.5
// 72 4 0.44 57.5
// 73 4 0.44 57.5
// 74 4 0.44 57.5
// 75 4 0.44 57.5
// 76 4 0.44 57.5
// 77 4 0.44 57.5
// 78 4 0.44 57.5
// 79 4 0.44 57.5
// 80 2 0.73 20.0
// 81 3 0.58 57.5
// 82 3 0.58 57.5
// 83 3 0.58 57.5
// 84 4 0.44 57.5
// 85 4 0.44 57.5
// 86 4 0.44 57.5
// 87 4 0.44 57.5
// 88 4 0.44 57.5
// 89 4 0.44 57.5
// 90 4 0.44 57.5
// 91 4 0.44 57.5
// 92 4 0.44 57.5
// 93 2 0.73 20.0
// 94 3 0.58 57.5
// 95 3 0.58 57.5
// 96 3 0.58 57.5
// 97 4 0.44 57.5
// 98 4 0.44 57.5
// 99 4 0.44 57.5
// 100 4 0.44 57.5
// 101 4 0.44 57.5
// 102 4 0.44 57.5
// 103 4 0.44 57.5
// 104 4 0.44 57.5
// 105 4 0.44 57.5
// 106 2 0.73 20.0
// 107 3 0.58 57.5
// 108 3 0.58 57.5
// 109 3 0.58 57.5
// 110 4 0.44 57.5
// 111 4 0.44 57.5
// 112 4 0.44 57.5
// 113 4 0.44 57.5
// 114 4 0.44 57.5
// 115 4 0.44 57.5
// 116 4 0.44 57.5
// 117 4 0.44 57.5
// 118 4 0.44 57.5
// 119 2 0.73 20.0
// 120 3 0.58 57.5
// 121 3 0.58 57.5
// 122 3 0.58 57.5
// 123 4 0.44 57.5
// 124 4 0.44 57.5
// 125 4 0.44 57.5
// 126 4 0.44 57.5
// 127 4 0.44 57.5
// 128 4 0.44 57.5
// 129 4 0.44 57.5
// 130 4 0.44 57.5
// 131 4 0.44 57.5
// 132 0 0.80 50.0
// 133 0 0.70 50.0
// 134 0 0.50 50.0
// 135 0 0.50 50.0
// 136 0 0.50 50.0
// 137 0 0.50 50.0
// Comp1 Comp2 Conductance_between_1_2
// 1 132 0.0796751205
// 1 2 0.0946071642
// 1 15 0.0946071642
// 1 28 0.0946071642
// 1 41 0.0946071642
// 1 54 0.0946071642
// 1 67 0.0946071642
// 1 80 0.0946071642
// 1 93 0.0946071642
// 1 106 0.0946071642
// 1 119 0.0946071642
// 2 3 0.0174185429
// 2 4 0.0174185429
// 2 5 0.0174185429
// 3 6 0.00766658232
// 3 7 0.00766658232
// 3 8 0.00766658232
// 4 9 0.00766658232
// 4 10 0.00766658232
// 4 11 0.00766658232
// 5 12 0.00766658232
// 5 13 0.00766658232
// 5 14 0.00766658232
// 6 7 0.00598951744
// 6 8 0.00598951744
// 7 8 0.00598951744
// 9 10 0.00598951744
// 9 11 0.00598951744
// 10 11 0.00598951744
// 12 13 0.00598951744
// 12 14 0.00598951744
// 13 14 0.00598951744
// 15 16 0.0174185429
// 15 17 0.0174185429
// 15 18 0.0174185429
// 16 19 0.00766658232
// 16 20 0.00766658232
// 16 21 0.00766658232
// 17 22 0.00766658232
// 17 23 0.00766658232
// 17 24 0.00766658232
// 18 25 0.00766658232
// 18 26 0.00766658232
// 18 27 0.00766658232
// 19 20 0.00598951744
// 19 21 0.00598951744
// 20 21 0.00598951744
// 22 23 0.00598951744
// 22 24 0.00598951744
// 23 24 0.00598951744
// 25 26 0.00598951744
// 25 27 0.00598951744
// 26 27 0.00598951744
// 28 29 0.0174185429
// 28 30 0.0174185429
// 28 31 0.0174185429
// 29 32 0.00766658232
// 29 33 0.00766658232
// 29 34 0.00766658232
// 30 35 0.00766658232
// 30 36 0.00766658232
// 30 37 0.00766658232
// 31 38 0.00766658232
// 31 39 0.00766658232
// 31 40 0.00766658232
// 32 33 0.00598951744
// 32 34 0.00598951744
// 33 34 0.00598951744
// 35 36 0.00598951744
// 35 37 0.00598951744
// 36 37 0.00598951744
// 38 39 0.00598951744
// 38 40 0.00598951744
// 39 40 0.00598951744
// 41 42 0.0174185429
// 41 43 0.0174185429
// 41 44 0.0174185429
// 42 45 0.00766658232
// 42 46 0.00766658232
// 42 47 0.00766658232
// 43 48 0.00766658232
// 43 49 0.00766658232
// 43 50 0.00766658232
// 44 51 0.00766658232
// 44 52 0.00766658232
// 44 53 0.00766658232
// 45 46 0.00598951744
// 45 47 0.00598951744
// 46 47 0.00598951744
// 48 49 0.00598951744
// 48 50 0.00598951744
// 49 50 0.00598951744
// 51 52 0.00598951744
// 51 53 0.00598951744
// 52 53 0.00598951744
// 54 55 0.0174185429
// 54 56 0.0174185429
// 54 57 0.0174185429
// 55 58 0.00766658232
// 55 59 0.00766658232
// 55 60 0.00766658232
// 56 61 0.00766658232
// 56 62 0.00766658232
// 56 63 0.00766658232
// 57 64 0.00766658232
// 57 65 0.00766658232
// 57 66 0.00766658232
// 58 59 0.00598951744
// 58 60 0.00598951744
// 59 60 0.00598951744
// 61 62 0.00598951744
// 61 63 0.00598951744
// 62 63 0.00598951744
// 64 65 0.00598951744
// 64 66 0.00598951744
// 65 66 0.00598951744
// 67 68 0.0174185429
// 67 69 0.0174185429
// 67 70 0.0174185429
// 68 71 0.00766658232
// 68 72 0.00766658232
// 68 73 0.00766658232
// 69 74 0.00766658232
// 69 75 0.00766658232
// 69 76 0.00766658232
// 70 77 0.00766658232
// 70 78 0.00766658232
// 70 79 0.00766658232
// 71 72 0.00598951744
// 71 73 0.00598951744
// 72 73 0.00598951744
// 74 75 0.00598951744
// 74 76 0.00598951744
// 75 76 0.00598951744
// 77 78 0.00598951744
// 77 79 0.00598951744
// 78 79 0.00598951744
// 80 81 0.0174185429
// 80 82 0.0174185429
// 80 83 0.0174185429
// 81 84 0.00766658232
// 81 85 0.00766658232
// 81 86 0.00766658232
// 82 87 0.00766658232
// 82 88 0.00766658232
// 82 89 0.00766658232
// 83 90 0.00766658232
// 83 91 0.00766658232
// 83 92 0.00766658232
// 84 85 0.00598951744
// 84 86 0.00598951744
// 85 86 0.00598951744
// 87 88 0.00598951744
// 87 89 0.00598951744
// 88 89 0.00598951744
// 90 91 0.00598951744
// 90 92 0.00598951744
// 91 92 0.00598951744
// 93 94 0.0174185429
// 93 95 0.0174185429
// 93 96 0.0174185429
// 94 97 0.00766658232
// 94 98 0.00766658232
// 94 99 0.00766658232
// 95 100 0.00766658232
// 95 101 0.00766658232
// 95 102 0.00766658232
// 96 103 0.00766658232
// 96 104 0.00766658232
// 96 105 0.00766658232
// 97 98 0.00598951744
// 97 99 0.00598951744
// 98 99 0.00598951744
// 100 101 0.00598951744
// 100 102 0.00598951744
// 101 102 0.00598951744
// 103 104 0.00598951744
// 103 105 0.00598951744
// 104 105 0.00598951744
// 106 107 0.0174185429
// 106 108 0.0174185429
// 106 109 0.0174185429
// 107 110 0.00766658232
// 107 111 0.00766658232
// 107 112 0.00766658232
// 108 113 0.00766658232
// 108 114 0.00766658232
// 108 115 0.00766658232
// 109 116 0.00766658232
// 109 117 0.00766658232
// 109 118 0.00766658232
// 110 111 0.00598951744
// 110 112 0.00598951744
// 111 112 0.00598951744
// 113 114 0.00598951744
// 113 115 0.00598951744
// 114 115 0.00598951744
// 116 117 0.00598951744
// 116 118 0.00598951744
// 117 118 0.00598951744
// 119 120 0.0174185429
// 119 121 0.0174185429
// 119 122 0.0174185429
// 120 123 0.00766658232
// 120 124 0.00766658232
// 120 125 0.00766658232
// 121 126 0.00766658232
// 121 127 0.00766658232
// 121 128 0.00766658232
// 122 129 0.00766658232
// 122 130 0.00766658232
// 122 131 0.00766658232
// 123 124 0.00598951744
// 123 125 0.00598951744
// 124 125 0.00598951744
// 126 127 0.00598951744
// 126 128 0.00598951744
// 127 128 0.00598951744
// 129 130 0.00598951744
// 129 131 0.00598951744
// 130 131 0.00598951744
// 132 133 0.0348744292
// 133 134 0.0208024203
// 133 136 0.0208024203
// 134 135 0.01570795
// 134 136 0.01570795
// 136 137 0.01570795
/* TCR/TCR_template.hoc
automatically written from f2nrn/neuron_code_writer.f
via subroutines that were inserted into the fortran
code e.g., TCR/integrate_TCR.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 TCR
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 presynapf_tcrtic
// compartment number
external traub_connect
objref this
create comp[ 137+1]
objref level[ 4+1], Soma, Dendrites
objref Soma_Dendrites, Axon
objref synlist
func type() {return 12 }
proc init() {
doubler = 1
comp[0] delete_section() // clean up for fortran code
traub_connect( 137+1)
titlePrint()
presyn_comp = 135
// 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 "TCR 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[ 138] // 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, 132, 0.0796751205, 0)
traub_connect(this, 1, 2, 0.0946071642, 1)
traub_connect(this, 1, 15, 0.0946071642, 1)
traub_connect(this, 1, 28, 0.0946071642, 1)
traub_connect(this, 1, 41, 0.0946071642, 1)
traub_connect(this, 1, 54, 0.0946071642, 1)
traub_connect(this, 1, 67, 0.0946071642, 1)
traub_connect(this, 1, 80, 0.0946071642, 1)
traub_connect(this, 1, 93, 0.0946071642, 1)
traub_connect(this, 1, 106, 0.0946071642, 1)
traub_connect(this, 1, 119, 0.0946071642, 1)
traub_connect(this, 2, 3, 0.0174185429, 1.)
traub_connect(this, 2, 4, 0.0174185429, 1.)
traub_connect(this, 2, 5, 0.0174185429, 1.)
traub_connect(this, 3, 6, 0.00766658232, 1)
traub_connect(this, 3, 7, 0.00766658232, 1)
traub_connect(this, 3, 8, 0.00766658232, 1)
traub_connect(this, 4, 9, 0.00766658232, 1)
traub_connect(this, 4, 10, 0.00766658232, 1)
traub_connect(this, 4, 11, 0.00766658232, 1)
traub_connect(this, 5, 12, 0.00766658232, 1)
traub_connect(this, 5, 13, 0.00766658232, 1)
traub_connect(this, 5, 14, 0.00766658232, 1)
traub_connect(this, 6, 7, 0.00598951744, 1)
traub_connect(this, 6, 8, 0.00598951744, 1)
traub_connect(this, 7, 8, 0.00598951744, 1)
traub_connect(this, 9, 10, 0.00598951744, 1)
traub_connect(this, 9, 11, 0.00598951744, 1)
traub_connect(this, 10, 11, 0.00598951744, 1)
traub_connect(this, 12, 13, 0.00598951744, 1)
traub_connect(this, 12, 14, 0.00598951744, 1)
traub_connect(this, 13, 14, 0.00598951744, 1)
traub_connect(this, 15, 16, 0.0174185429, 1.)
traub_connect(this, 15, 17, 0.0174185429, 1.)
traub_connect(this, 15, 18, 0.0174185429, 1.)
traub_connect(this, 16, 19, 0.00766658232, 1)
traub_connect(this, 16, 20, 0.00766658232, 1)
traub_connect(this, 16, 21, 0.00766658232, 1)
traub_connect(this, 17, 22, 0.00766658232, 1)
traub_connect(this, 17, 23, 0.00766658232, 1)
traub_connect(this, 17, 24, 0.00766658232, 1)
traub_connect(this, 18, 25, 0.00766658232, 1)
traub_connect(this, 18, 26, 0.00766658232, 1)
traub_connect(this, 18, 27, 0.00766658232, 1)
traub_connect(this, 19, 20, 0.00598951744, 1)
traub_connect(this, 19, 21, 0.00598951744, 1)
traub_connect(this, 20, 21, 0.00598951744, 1)
traub_connect(this, 22, 23, 0.00598951744, 1)
traub_connect(this, 22, 24, 0.00598951744, 1)
traub_connect(this, 23, 24, 0.00598951744, 1)
traub_connect(this, 25, 26, 0.00598951744, 1)
traub_connect(this, 25, 27, 0.00598951744, 1)
traub_connect(this, 26, 27, 0.00598951744, 1)
traub_connect(this, 28, 29, 0.0174185429, 1.)
traub_connect(this, 28, 30, 0.0174185429, 1.)
traub_connect(this, 28, 31, 0.0174185429, 1.)
traub_connect(this, 29, 32, 0.00766658232, 1)
traub_connect(this, 29, 33, 0.00766658232, 1)
traub_connect(this, 29, 34, 0.00766658232, 1)
traub_connect(this, 30, 35, 0.00766658232, 1)
traub_connect(this, 30, 36, 0.00766658232, 1)
traub_connect(this, 30, 37, 0.00766658232, 1)
traub_connect(this, 31, 38, 0.00766658232, 1)
traub_connect(this, 31, 39, 0.00766658232, 1)
traub_connect(this, 31, 40, 0.00766658232, 1)
traub_connect(this, 32, 33, 0.00598951744, 1)
traub_connect(this, 32, 34, 0.00598951744, 1)
traub_connect(this, 33, 34, 0.00598951744, 1)
traub_connect(this, 35, 36, 0.00598951744, 1)
traub_connect(this, 35, 37, 0.00598951744, 1)
traub_connect(this, 36, 37, 0.00598951744, 1)
traub_connect(this, 38, 39, 0.00598951744, 1)
traub_connect(this, 38, 40, 0.00598951744, 1)
traub_connect(this, 39, 40, 0.00598951744, 1)
traub_connect(this, 41, 42, 0.0174185429, 1.)
traub_connect(this, 41, 43, 0.0174185429, 1.)
traub_connect(this, 41, 44, 0.0174185429, 1.)
traub_connect(this, 42, 45, 0.00766658232, 1)
traub_connect(this, 42, 46, 0.00766658232, 1)
traub_connect(this, 42, 47, 0.00766658232, 1)
traub_connect(this, 43, 48, 0.00766658232, 1)
traub_connect(this, 43, 49, 0.00766658232, 1)
traub_connect(this, 43, 50, 0.00766658232, 1)
traub_connect(this, 44, 51, 0.00766658232, 1)
traub_connect(this, 44, 52, 0.00766658232, 1)
traub_connect(this, 44, 53, 0.00766658232, 1)
traub_connect(this, 45, 46, 0.00598951744, 1)
traub_connect(this, 45, 47, 0.00598951744, 1)
traub_connect(this, 46, 47, 0.00598951744, 1)
traub_connect(this, 48, 49, 0.00598951744, 1)
traub_connect(this, 48, 50, 0.00598951744, 1)
traub_connect(this, 49, 50, 0.00598951744, 1)
traub_connect(this, 51, 52, 0.00598951744, 1)
traub_connect(this, 51, 53, 0.00598951744, 1)
traub_connect(this, 52, 53, 0.00598951744, 1)
traub_connect(this, 54, 55, 0.0174185429, 1.)
traub_connect(this, 54, 56, 0.0174185429, 1.)
traub_connect(this, 54, 57, 0.0174185429, 1.)
traub_connect(this, 55, 58, 0.00766658232, 1)
traub_connect(this, 55, 59, 0.00766658232, 1)
traub_connect(this, 55, 60, 0.00766658232, 1)
traub_connect(this, 56, 61, 0.00766658232, 1)
traub_connect(this, 56, 62, 0.00766658232, 1)
traub_connect(this, 56, 63, 0.00766658232, 1)
traub_connect(this, 57, 64, 0.00766658232, 1)
traub_connect(this, 57, 65, 0.00766658232, 1)
traub_connect(this, 57, 66, 0.00766658232, 1)
traub_connect(this, 58, 59, 0.00598951744, 1)
traub_connect(this, 58, 60, 0.00598951744, 1)
traub_connect(this, 59, 60, 0.00598951744, 1)
traub_connect(this, 61, 62, 0.00598951744, 1)
traub_connect(this, 61, 63, 0.00598951744, 1)
traub_connect(this, 62, 63, 0.00598951744, 1)
traub_connect(this, 64, 65, 0.00598951744, 1)
traub_connect(this, 64, 66, 0.00598951744, 1)
traub_connect(this, 65, 66, 0.00598951744, 1)
traub_connect(this, 67, 68, 0.0174185429, 1.)
traub_connect(this, 67, 69, 0.0174185429, 1.)
traub_connect(this, 67, 70, 0.0174185429, 1.)
traub_connect(this, 68, 71, 0.00766658232, 1)
traub_connect(this, 68, 72, 0.00766658232, 1)
traub_connect(this, 68, 73, 0.00766658232, 1)
traub_connect(this, 69, 74, 0.00766658232, 1)
traub_connect(this, 69, 75, 0.00766658232, 1)
traub_connect(this, 69, 76, 0.00766658232, 1)
traub_connect(this, 70, 77, 0.00766658232, 1)
traub_connect(this, 70, 78, 0.00766658232, 1)
traub_connect(this, 70, 79, 0.00766658232, 1)
traub_connect(this, 71, 72, 0.00598951744, 1)
traub_connect(this, 71, 73, 0.00598951744, 1)
traub_connect(this, 72, 73, 0.00598951744, 1)
traub_connect(this, 74, 75, 0.00598951744, 1)
traub_connect(this, 74, 76, 0.00598951744, 1)
traub_connect(this, 75, 76, 0.00598951744, 1)
traub_connect(this, 77, 78, 0.00598951744, 1)
traub_connect(this, 77, 79, 0.00598951744, 1)
traub_connect(this, 78, 79, 0.00598951744, 1)
traub_connect(this, 80, 81, 0.0174185429, 1.)
traub_connect(this, 80, 82, 0.0174185429, 1.)
traub_connect(this, 80, 83, 0.0174185429, 1.)
traub_connect(this, 81, 84, 0.00766658232, 1)
traub_connect(this, 81, 85, 0.00766658232, 1)
traub_connect(this, 81, 86, 0.00766658232, 1)
traub_connect(this, 82, 87, 0.00766658232, 1)
traub_connect(this, 82, 88, 0.00766658232, 1)
traub_connect(this, 82, 89, 0.00766658232, 1)
traub_connect(this, 83, 90, 0.00766658232, 1)
traub_connect(this, 83, 91, 0.00766658232, 1)
traub_connect(this, 83, 92, 0.00766658232, 1)
traub_connect(this, 84, 85, 0.00598951744, 1)
traub_connect(this, 84, 86, 0.00598951744, 1)
traub_connect(this, 85, 86, 0.00598951744, 1)
traub_connect(this, 87, 88, 0.00598951744, 1)
traub_connect(this, 87, 89, 0.00598951744, 1)
traub_connect(this, 88, 89, 0.00598951744, 1)
traub_connect(this, 90, 91, 0.00598951744, 1)
traub_connect(this, 90, 92, 0.00598951744, 1)
traub_connect(this, 91, 92, 0.00598951744, 1)
traub_connect(this, 93, 94, 0.0174185429, 1.)
traub_connect(this, 93, 95, 0.0174185429, 1.)
traub_connect(this, 93, 96, 0.0174185429, 1.)
traub_connect(this, 94, 97, 0.00766658232, 1)
traub_connect(this, 94, 98, 0.00766658232, 1)
traub_connect(this, 94, 99, 0.00766658232, 1)
traub_connect(this, 95, 100, 0.00766658232, 1)
traub_connect(this, 95, 101, 0.00766658232, 1)
traub_connect(this, 95, 102, 0.00766658232, 1)
traub_connect(this, 96, 103, 0.00766658232, 1)
traub_connect(this, 96, 104, 0.00766658232, 1)
traub_connect(this, 96, 105, 0.00766658232, 1)
traub_connect(this, 97, 98, 0.00598951744, 1)
traub_connect(this, 97, 99, 0.00598951744, 1)
traub_connect(this, 98, 99, 0.00598951744, 1)
traub_connect(this, 100, 101, 0.00598951744, 1)
traub_connect(this, 100, 102, 0.00598951744, 1)
traub_connect(this, 101, 102, 0.00598951744, 1)
traub_connect(this, 103, 104, 0.00598951744, 1)
traub_connect(this, 103, 105, 0.00598951744, 1)
traub_connect(this, 104, 105, 0.00598951744, 1)
traub_connect(this, 106, 107, 0.0174185429, 1.)
traub_connect(this, 106, 108, 0.0174185429, 1.)
traub_connect(this, 106, 109, 0.0174185429, 1.)
traub_connect(this, 107, 110, 0.00766658232, 1)
traub_connect(this, 107, 111, 0.00766658232, 1)
traub_connect(this, 107, 112, 0.00766658232, 1)
traub_connect(this, 108, 113, 0.00766658232, 1)
traub_connect(this, 108, 114, 0.00766658232, 1)
traub_connect(this, 108, 115, 0.00766658232, 1)
traub_connect(this, 109, 116, 0.00766658232, 1)
traub_connect(this, 109, 117, 0.00766658232, 1)
traub_connect(this, 109, 118, 0.00766658232, 1)
traub_connect(this, 110, 111, 0.00598951744, 1)
traub_connect(this, 110, 112, 0.00598951744, 1)
traub_connect(this, 111, 112, 0.00598951744, 1)
traub_connect(this, 113, 114, 0.00598951744, 1)
traub_connect(this, 113, 115, 0.00598951744, 1)
traub_connect(this, 114, 115, 0.00598951744, 1)
traub_connect(this, 116, 117, 0.00598951744, 1)
traub_connect(this, 116, 118, 0.00598951744, 1)
traub_connect(this, 117, 118, 0.00598951744, 1)
traub_connect(this, 119, 120, 0.0174185429, 1.)
traub_connect(this, 119, 121, 0.0174185429, 1.)
traub_connect(this, 119, 122, 0.0174185429, 1.)
traub_connect(this, 120, 123, 0.00766658232, 1)
traub_connect(this, 120, 124, 0.00766658232, 1)
traub_connect(this, 120, 125, 0.00766658232, 1)
traub_connect(this, 121, 126, 0.00766658232, 1)
traub_connect(this, 121, 127, 0.00766658232, 1)
traub_connect(this, 121, 128, 0.00766658232, 1)
traub_connect(this, 122, 129, 0.00766658232, 1)
traub_connect(this, 122, 130, 0.00766658232, 1)
traub_connect(this, 122, 131, 0.00766658232, 1)
traub_connect(this, 123, 124, 0.00598951744, 1)
traub_connect(this, 123, 125, 0.00598951744, 1)
traub_connect(this, 124, 125, 0.00598951744, 1)
traub_connect(this, 126, 127, 0.00598951744, 1)
traub_connect(this, 126, 128, 0.00598951744, 1)
traub_connect(this, 127, 128, 0.00598951744, 1)
traub_connect(this, 129, 130, 0.00598951744, 1)
traub_connect(this, 129, 131, 0.00598951744, 1)
traub_connect(this, 130, 131, 0.00598951744, 1)
traub_connect(this, 132, 133, 0.0348744292, 1.)
traub_connect(this, 133, 134, 0.0208024203, 1)
traub_connect(this, 133, 136, 0.0208024203, 1)
traub_connect(this, 134, 135, 0.01570795, 1.)
traub_connect(this, 134, 136, 0.01570795, 1)
traub_connect(this, 136, 137, 0.01570795, 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 = 4
objref level[top_level+1]
for i=0,top_level { level[i] = new SectionList() }
comp[ 1] { level[ 1].append() L= 42. diam = 2* 10. }
comp[ 2] { level[ 2].append() L= 20. diam = 2* 0.73 }
comp[ 3] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 4] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 5] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 6] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 7] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 8] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 9] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 10] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 11] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 12] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 13] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 14] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 15] { level[ 2].append() L= 20. diam = 2* 0.73 }
comp[ 16] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 17] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 18] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 19] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 20] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 21] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 22] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 23] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 24] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 25] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 26] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 27] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 28] { level[ 2].append() L= 20. diam = 2* 0.73 }
comp[ 29] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 30] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 31] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 32] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 33] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 34] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 35] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 36] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 37] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 38] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 39] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 40] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 41] { level[ 2].append() L= 20. diam = 2* 0.73 }
comp[ 42] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 43] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 44] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 45] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 46] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 47] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 48] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 49] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 50] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 51] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 52] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 53] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 54] { level[ 2].append() L= 20. diam = 2* 0.73 }
comp[ 55] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 56] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 57] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 58] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 59] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 60] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 61] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 62] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 63] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 64] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 65] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 66] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 67] { level[ 2].append() L= 20. diam = 2* 0.73 }
comp[ 68] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 69] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 70] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 71] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 72] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 73] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 74] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 75] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 76] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
geom1() /* arbitrary subdivision of geom helps
to large a function problem in tcr_template */
}
proc geom1() {
comp[ 77] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 78] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 79] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 80] { level[ 2].append() L= 20. diam = 2* 0.73 }
comp[ 81] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 82] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 83] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 84] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 85] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 86] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 87] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 88] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 89] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 90] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 91] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 92] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 93] { level[ 2].append() L= 20. diam = 2* 0.73 }
comp[ 94] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 95] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 96] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 97] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 98] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 99] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 100] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 101] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 102] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 103] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 104] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 105] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 106] { level[ 2].append() L= 20. diam = 2* 0.73 }
comp[ 107] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 108] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 109] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 110] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 111] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 112] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 113] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 114] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 115] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 116] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 117] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 118] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 119] { level[ 2].append() L= 20. diam = 2* 0.73 }
comp[ 120] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 121] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 122] { level[ 3].append() L= 57.5 diam = 2* 0.584 }
comp[ 123] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 124] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 125] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 126] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 127] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 128] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 129] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 130] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 131] { level[ 4].append() L= 57.5 diam = 2* 0.438 }
comp[ 132] { level[ 0].append() L= 50. diam = 2* 0.8 }
comp[ 133] { level[ 0].append() L= 50. diam = 2* 0.7 }
comp[ 134] { level[ 0].append() L= 50. diam = 2* 0.5 }
comp[ 135] { level[ 0].append() L= 50. diam = 2* 0.5 }
comp[ 136] { level[ 0].append() L= 50. diam = 2* 0.5 }
comp[ 137] { 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, 137 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_tcr
gbar_naf_tcr = 0.4
insert kdr
gbar_kdr = 0.4
insert ka
gbar_ka = 0.001
insert k2
gbar_k2 = 0.0005
}
forsec level[ 1] {
insert naf_tcr
gbar_naf_tcr = 0.1
insert napf_tcr
gbar_napf_tcr = 0.0002
insert kdr
gbar_kdr = 0.075
insert kc
gbar_kc = 0.012
insert ka
gbar_ka = 0.03
insert km
gbar_km = 0 // 0.0005
insert k2
gbar_k2 = 0.002
insert kahp_slower
gbar_kahp_slower = 0 // 5.E-05
insert cal
gbar_cal = 0.0005
insert cat
gbar_cat = 0.0005
insert ar
gbar_ar = 0.00025
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.02
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 52000.
}
forsec level[ 2] {
insert naf_tcr
gbar_naf_tcr = 0.1
insert napf_tcr
gbar_napf_tcr = 0.0002
insert kdr
gbar_kdr = 0.05
insert kc
gbar_kc = 0.012
insert ka
gbar_ka = 0.03
insert km
gbar_km = 0 // 0.0005
insert k2
gbar_k2 = 0.002
insert kahp_slower
gbar_kahp_slower = 0 // 5.E-05
insert cal
gbar_cal = 0.0005
insert cat
gbar_cat = 0.005
insert ar
gbar_ar = 0.0005
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 104000.
}
forsec level[ 3] {
insert naf_tcr
gbar_naf_tcr = 0.005
insert napf_tcr
gbar_napf_tcr = 1.E-05
insert kc
gbar_kc = 0.02
insert ka
gbar_ka = 0.001
insert km
gbar_km = 0 // 0.0005
insert k2
gbar_k2 = 0.002
insert kahp_slower
gbar_kahp_slower = 0 // 5.E-05
insert cal
gbar_cal = 0.00025
insert cat
gbar_cat = 0.003
insert ar
gbar_ar = 0.0003
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 104000.
}
forsec level[ 4] {
insert naf_tcr
gbar_naf_tcr = 0.005
insert napf_tcr
gbar_napf_tcr = 1.E-05
insert kc
gbar_kc = 0.02
insert ka
gbar_ka = 0.001
insert km
gbar_km = 0 // 0.0005
insert k2
gbar_k2 = 0.002
insert kahp_slower
gbar_kahp_slower = 0 // 5.E-05
insert cal
gbar_cal = 0.00025
insert cat
gbar_cat = 0.0005
insert ar
gbar_ar = 0.0003
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 104000.
}
forsec all {
cm = 0.9 // assign global specific capac.
}
//
// passive membrane resistance (leak) and axial resistance
//
forsec Soma_Dendrites {
g_pas = 3.78787879E-05
Ra = 175.
}
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("napf_tcr")) { gbar_napf_tcr *= spine_area_multiplier }
if (ismembrane("napf_tcrf")) { gbar_napf_tcrf *= spine_area_multiplier }
if (ismembrane("napf_tcrf_tcr")) { gbar_napf_tcrf_tcr *= spine_area_multiplier }
if (ismembrane("naf_tcr")) { gbar_naf_tcr *= spine_area_multiplier }
if (ismembrane("naf_tcr_tcr")) { gbar_naf_tcr_tcr *= spine_area_multiplier }
if (ismembrane("naf_tcr2")) { gbar_naf_tcr2 *= spine_area_multiplier }
if (ismembrane("kc")) { gbar_kc *= spine_area_multiplier }
if (ismembrane("kc_fast")) { gbar_kc_fast *= spine_area_multiplier }
if (ismembrane("kahp")) { gbar_kahp *= spine_area_multiplier }
if (ismembrane("kahp_slower")) { gbar_kahp_slower *= 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 2638.9356
// 2 91.734428
// 3 210.989184
// 4 210.989184
// 5 210.989184
// 6 158.241888
// 7 158.241888
// 8 158.241888
// 9 158.241888
// 10 158.241888
// 11 158.241888
// 12 158.241888
// 13 158.241888
// 14 158.241888
// 15 91.734428
// 16 210.989184
// 17 210.989184
// 18 210.989184
// 19 158.241888
// 20 158.241888
// 21 158.241888
// 22 158.241888
// 23 158.241888
// 24 158.241888
// 25 158.241888
// 26 158.241888
// 27 158.241888
// 28 91.734428
// 29 210.989184
// 30 210.989184
// 31 210.989184
// 32 158.241888
// 33 158.241888
// 34 158.241888
// 35 158.241888
// 36 158.241888
// 37 158.241888
// 38 158.241888
// 39 158.241888
// 40 158.241888
// 41 91.734428
// 42 210.989184
// 43 210.989184
// 44 210.989184
// 45 158.241888
// 46 158.241888
// 47 158.241888
// 48 158.241888
// 49 158.241888
// 50 158.241888
// 51 158.241888
// 52 158.241888
// 53 158.241888
// 54 91.734428
// 55 210.989184
// 56 210.989184
// 57 210.989184
// 58 158.241888
// 59 158.241888
// 60 158.241888
// 61 158.241888
// 62 158.241888
// 63 158.241888
// 64 158.241888
// 65 158.241888
// 66 158.241888
// 67 91.734428
// 68 210.989184
// 69 210.989184
// 70 210.989184
// 71 158.241888
// 72 158.241888
// 73 158.241888
// 74 158.241888
// 75 158.241888
// 76 158.241888
// 77 158.241888
// 78 158.241888
// 79 158.241888
// 80 91.734428
// 81 210.989184
// 82 210.989184
// 83 210.989184
// 84 158.241888
// 85 158.241888
// 86 158.241888
// 87 158.241888
// 88 158.241888
// 89 158.241888
// 90 158.241888
// 91 158.241888
// 92 158.241888
// 93 91.734428
// 94 210.989184
// 95 210.989184
// 96 210.989184
// 97 158.241888
// 98 158.241888
// 99 158.241888
// 100 158.241888
// 101 158.241888
// 102 158.241888
// 103 158.241888
// 104 158.241888
// 105 158.241888
// 106 91.734428
// 107 210.989184
// 108 210.989184
// 109 210.989184
// 110 158.241888
// 111 158.241888
// 112 158.241888
// 113 158.241888
// 114 158.241888
// 115 158.241888
// 116 158.241888
// 117 158.241888
// 118 158.241888
// 119 91.734428
// 120 210.989184
// 121 210.989184
// 122 210.989184
// 123 158.241888
// 124 158.241888
// 125 158.241888
// 126 158.241888
// 127 158.241888
// 128 158.241888
// 129 158.241888
// 130 158.241888
// 131 158.241888
// 132 251.3272
// 133 219.9113
// 134 157.0795
// 135 157.0795
// 136 157.0795
// 137 157.0795
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 = -81.
}
// in FORTRAN do find values
// i= 2
// i= 15
// i= 28
// i= 41
// i= 54
// i= 67
// i= 80
// i= 93
// i= 106
// i= 119
//extended initializations
for i=1,137 {
comp[i] if (ismembrane("ka")) {gbar_ka*=0.2}
}
for i = 132, 137 { // axon
comp[i] gbar_kdr *= 0.45
}
comp[1] gbar_kdr *= 0.45
for (i = 2; i<=119; i += 13) { // level 2
comp[i] gbar_kdr *= 0.45
}
persistentNa_shift = 7
// in the fortran code the napf_tcrf has a 10 mV shift
// but uses the naf_tcr rates (apham_...) which were
// created with a -3 mV shift for total 7 mV
forsec all { if (ismembrane("napf_tcr")){
fastNa_shift_napf_tcr = persistentNa_shift}
}
}
proc set_doubler() {doubler=0}
// this function sets doubler to 0
// because there are no spines
// in the cell, replacing earlier fnc.
endtemplate TCR
