// Trying to open ../diagnostic/tstop.dat
// new end time timtot = 150.
// Trying to open ../diagnostic/dt_F.dat
// new dt = 0.002
// comp[ 1] neighs: 54 2 15 28 41
// comp[ 2] neighs: 1 3 4 0 0
// comp[ 3] neighs: 2 4 5 6 0
// comp[ 4] neighs: 2 3 7 0 0
// comp[ 5] neighs: 3 6 8 0 0
// comp[ 6] neighs: 3 5 9 0 0
// comp[ 7] neighs: 4 10 0 0 0
// comp[ 8] neighs: 5 11 0 0 0
// comp[ 9] neighs: 6 0 0 0 0
// comp[ 10] neighs: 7 0 0 0 0
// comp[ 11] neighs: 8 12 0 0 0
// comp[ 12] neighs: 11 13 0 0 0
// comp[ 13] neighs: 12 14 0 0 0
// comp[ 14] neighs: 13 0 0 0 0
// comp[ 15] neighs: 1 16 17 0 0
// comp[ 16] neighs: 15 17 18 19 0
// comp[ 17] neighs: 15 16 20 0 0
// comp[ 18] neighs: 16 19 21 0 0
// comp[ 19] neighs: 16 18 22 0 0
// comp[ 20] neighs: 17 23 0 0 0
// comp[ 21] neighs: 18 24 0 0 0
// comp[ 22] neighs: 19 0 0 0 0
// comp[ 23] neighs: 20 0 0 0 0
// comp[ 24] neighs: 21 25 0 0 0
// comp[ 25] neighs: 24 26 0 0 0
// comp[ 26] neighs: 25 27 0 0 0
// comp[ 27] neighs: 26 0 0 0 0
// comp[ 28] neighs: 1 29 30 0 0
// comp[ 29] neighs: 28 30 31 32 0
// comp[ 30] neighs: 28 29 33 0 0
// comp[ 31] neighs: 29 32 34 0 0
// comp[ 32] neighs: 29 31 35 0 0
// comp[ 33] neighs: 30 36 0 0 0
// comp[ 34] neighs: 31 37 0 0 0
// comp[ 35] neighs: 32 0 0 0 0
// comp[ 36] neighs: 33 0 0 0 0
// comp[ 37] neighs: 34 38 0 0 0
// comp[ 38] neighs: 37 39 0 0 0
// comp[ 39] neighs: 38 40 0 0 0
// comp[ 40] neighs: 39 0 0 0 0
// comp[ 41] neighs: 1 42 43 0 0
// comp[ 42] neighs: 41 43 44 45 0
// comp[ 43] neighs: 41 42 46 0 0
// comp[ 44] neighs: 42 45 47 0 0
// comp[ 45] neighs: 42 44 48 0 0
// comp[ 46] neighs: 43 49 0 0 0
// comp[ 47] neighs: 44 50 0 0 0
// comp[ 48] neighs: 45 0 0 0 0
// comp[ 49] neighs: 46 0 0 0 0
// comp[ 50] neighs: 47 51 0 0 0
// comp[ 51] neighs: 50 52 0 0 0
// comp[ 52] neighs: 51 53 0 0 0
// comp[ 53] neighs: 52 0 0 0 0
// comp[ 54] neighs: 1 55 0 0 0
// comp[ 55] neighs: 54 56 58 0 0
// comp[ 56] neighs: 55 57 58 0 0
// comp[ 57] neighs: 56 0 0 0 0
// comp[ 58] neighs: 55 56 59 0 0
// comp[ 59] neighs: 58 0 0 0 0
// COMPART. LEVEL RADIUS LENGTH(MU)
// 1 1 7.50 20.0
// 2 2 1.06 40.0
// 3 3 0.67 40.0
// 4 3 0.67 40.0
// 5 4 0.42 40.0
// 6 4 0.42 40.0
// 7 4 0.67 40.0
// 8 5 0.42 40.0
// 9 5 0.42 40.0
// 10 5 0.67 40.0
// 11 6 0.42 40.0
// 12 7 0.42 40.0
// 13 8 0.42 40.0
// 14 9 0.42 40.0
// 15 2 1.06 40.0
// 16 3 0.67 40.0
// 17 3 0.67 40.0
// 18 4 0.42 40.0
// 19 4 0.42 40.0
// 20 4 0.67 40.0
// 21 5 0.42 40.0
// 22 5 0.42 40.0
// 23 5 0.67 40.0
// 24 6 0.42 40.0
// 25 7 0.42 40.0
// 26 8 0.42 40.0
// 27 9 0.42 40.0
// 28 2 1.06 40.0
// 29 3 0.67 40.0
// 30 3 0.67 40.0
// 31 4 0.42 40.0
// 32 4 0.42 40.0
// 33 4 0.67 40.0
// 34 5 0.42 40.0
// 35 5 0.42 40.0
// 36 5 0.67 40.0
// 37 6 0.42 40.0
// 38 7 0.42 40.0
// 39 8 0.42 40.0
// 40 9 0.42 40.0
// 41 2 1.06 40.0
// 42 3 0.67 40.0
// 43 3 0.67 40.0
// 44 4 0.42 40.0
// 45 4 0.42 40.0
// 46 4 0.67 40.0
// 47 5 0.42 40.0
// 48 5 0.42 40.0
// 49 5 0.67 40.0
// 50 6 0.42 40.0
// 51 7 0.42 40.0
// 52 8 0.42 40.0
// 53 9 0.42 40.0
// 54 0 0.70 50.0
// 55 0 0.60 50.0
// 56 0 0.50 50.0
// 57 0 0.50 50.0
// 58 0 0.50 50.0
// 59 0 0.50 50.0
/* deepaxax/deepaxax_template.hoc
automatically written from f2nrn/neuron_code_writer.f
via subroutines that were inserted into the fortran
code e.g., deepaxax/integrate_deepaxax.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 deepaxax
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[ 59+1]
objref level[ 9+1], Soma, Dendrites
objref Soma_Dendrites, Axon
objref synlist
func type() {return 10 }
proc init() {
doubler = 1
comp[0] delete_section() // clean up for fortran code
traub_connect( 59+1)
titlePrint()
presyn_comp = 59
// 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 "deepaxax 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=0}
// 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[ 60] // 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, 54, 0.0611490233, 0)
traub_connect(this, 1, 2, 0.0873746044, 1)
traub_connect(this, 1, 15, 0.0873746044, 1)
traub_connect(this, 1, 28, 0.0873746044, 1)
traub_connect(this, 1, 41, 0.0873746044, 1)
traub_connect(this, 2, 3, 0.0250126876, 1)
traub_connect(this, 2, 4, 0.0250126876, 1)
traub_connect(this, 3, 4, 0.0174532778, 1)
traub_connect(this, 3, 5, 0.00988321907, 1)
traub_connect(this, 3, 6, 0.00988321907, 1)
traub_connect(this, 4, 7, 0.0174532778, 1.)
traub_connect(this, 5, 6, 0.00689334805, 1)
traub_connect(this, 5, 8, 0.00689334805, 1.)
traub_connect(this, 6, 9, 0.00689334805, 1.)
traub_connect(this, 7, 10, 0.0174532778, 1.)
traub_connect(this, 8, 11, 0.00689334805, 1.)
traub_connect(this, 11, 12, 0.00689334805, 1.)
traub_connect(this, 12, 13, 0.00689334805, 1.)
traub_connect(this, 13, 14, 0.00689334805, 1.)
traub_connect(this, 15, 16, 0.0250126876, 1)
traub_connect(this, 15, 17, 0.0250126876, 1)
traub_connect(this, 16, 17, 0.0174532778, 1)
traub_connect(this, 16, 18, 0.00988321907, 1)
traub_connect(this, 16, 19, 0.00988321907, 1)
traub_connect(this, 17, 20, 0.0174532778, 1.)
traub_connect(this, 18, 19, 0.00689334805, 1)
traub_connect(this, 18, 21, 0.00689334805, 1.)
traub_connect(this, 19, 22, 0.00689334805, 1.)
traub_connect(this, 20, 23, 0.0174532778, 1.)
traub_connect(this, 21, 24, 0.00689334805, 1.)
traub_connect(this, 24, 25, 0.00689334805, 1.)
traub_connect(this, 25, 26, 0.00689334805, 1.)
traub_connect(this, 26, 27, 0.00689334805, 1.)
traub_connect(this, 28, 29, 0.0250126876, 1)
traub_connect(this, 28, 30, 0.0250126876, 1)
traub_connect(this, 29, 30, 0.0174532778, 1)
traub_connect(this, 29, 31, 0.00988321907, 1)
traub_connect(this, 29, 32, 0.00988321907, 1)
traub_connect(this, 30, 33, 0.0174532778, 1.)
traub_connect(this, 31, 32, 0.00689334805, 1)
traub_connect(this, 31, 34, 0.00689334805, 1.)
traub_connect(this, 32, 35, 0.00689334805, 1.)
traub_connect(this, 33, 36, 0.0174532778, 1.)
traub_connect(this, 34, 37, 0.00689334805, 1.)
traub_connect(this, 37, 38, 0.00689334805, 1.)
traub_connect(this, 38, 39, 0.00689334805, 1.)
traub_connect(this, 39, 40, 0.00689334805, 1.)
traub_connect(this, 41, 42, 0.0250126876, 1)
traub_connect(this, 41, 43, 0.0250126876, 1)
traub_connect(this, 42, 43, 0.0174532778, 1)
traub_connect(this, 42, 44, 0.00988321907, 1)
traub_connect(this, 42, 45, 0.00988321907, 1)
traub_connect(this, 43, 46, 0.0174532778, 1.)
traub_connect(this, 44, 45, 0.00689334805, 1)
traub_connect(this, 44, 47, 0.00689334805, 1.)
traub_connect(this, 45, 48, 0.00689334805, 1.)
traub_connect(this, 46, 49, 0.0174532778, 1.)
traub_connect(this, 47, 50, 0.00689334805, 1.)
traub_connect(this, 50, 51, 0.00689334805, 1.)
traub_connect(this, 51, 52, 0.00689334805, 1.)
traub_connect(this, 52, 53, 0.00689334805, 1.)
traub_connect(this, 54, 55, 0.026078893, 1.)
traub_connect(this, 55, 56, 0.0185405311, 1)
traub_connect(this, 55, 58, 0.0185405311, 1)
traub_connect(this, 56, 57, 0.01570795, 1.)
traub_connect(this, 56, 58, 0.01570795, 1)
traub_connect(this, 58, 59, 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 = 9
objref level[top_level+1]
for i=0,top_level { level[i] = new SectionList() }
comp[ 1] { level[ 1].append() L= 20. diam = 2* 7.5 }
comp[ 2] { level[ 2].append() L= 40. diam = 2* 1.06 }
comp[ 3] { level[ 3].append() L= 40. diam = 2* 0.666666667 }
comp[ 4] { level[ 3].append() L= 40. diam = 2* 0.666666667 }
comp[ 5] { level[ 4].append() L= 40. diam = 2* 0.418972332 }
comp[ 6] { level[ 4].append() L= 40. diam = 2* 0.418972332 }
comp[ 7] { level[ 4].append() L= 40. diam = 2* 0.666666667 }
comp[ 8] { level[ 5].append() L= 40. diam = 2* 0.418972332 }
comp[ 9] { level[ 5].append() L= 40. diam = 2* 0.418972332 }
comp[ 10] { level[ 5].append() L= 40. diam = 2* 0.666666667 }
comp[ 11] { level[ 6].append() L= 40. diam = 2* 0.418972332 }
comp[ 12] { level[ 7].append() L= 40. diam = 2* 0.418972332 }
comp[ 13] { level[ 8].append() L= 40. diam = 2* 0.418972332 }
comp[ 14] { level[ 9].append() L= 40. diam = 2* 0.418972332 }
comp[ 15] { level[ 2].append() L= 40. diam = 2* 1.06 }
comp[ 16] { level[ 3].append() L= 40. diam = 2* 0.666666667 }
comp[ 17] { level[ 3].append() L= 40. diam = 2* 0.666666667 }
comp[ 18] { level[ 4].append() L= 40. diam = 2* 0.418972332 }
comp[ 19] { level[ 4].append() L= 40. diam = 2* 0.418972332 }
comp[ 20] { level[ 4].append() L= 40. diam = 2* 0.666666667 }
comp[ 21] { level[ 5].append() L= 40. diam = 2* 0.418972332 }
comp[ 22] { level[ 5].append() L= 40. diam = 2* 0.418972332 }
comp[ 23] { level[ 5].append() L= 40. diam = 2* 0.666666667 }
comp[ 24] { level[ 6].append() L= 40. diam = 2* 0.418972332 }
comp[ 25] { level[ 7].append() L= 40. diam = 2* 0.418972332 }
comp[ 26] { level[ 8].append() L= 40. diam = 2* 0.418972332 }
comp[ 27] { level[ 9].append() L= 40. diam = 2* 0.418972332 }
comp[ 28] { level[ 2].append() L= 40. diam = 2* 1.06 }
comp[ 29] { level[ 3].append() L= 40. diam = 2* 0.666666667 }
comp[ 30] { level[ 3].append() L= 40. diam = 2* 0.666666667 }
comp[ 31] { level[ 4].append() L= 40. diam = 2* 0.418972332 }
comp[ 32] { level[ 4].append() L= 40. diam = 2* 0.418972332 }
comp[ 33] { level[ 4].append() L= 40. diam = 2* 0.666666667 }
comp[ 34] { level[ 5].append() L= 40. diam = 2* 0.418972332 }
comp[ 35] { level[ 5].append() L= 40. diam = 2* 0.418972332 }
comp[ 36] { level[ 5].append() L= 40. diam = 2* 0.666666667 }
comp[ 37] { level[ 6].append() L= 40. diam = 2* 0.418972332 }
comp[ 38] { level[ 7].append() L= 40. diam = 2* 0.418972332 }
comp[ 39] { level[ 8].append() L= 40. diam = 2* 0.418972332 }
comp[ 40] { level[ 9].append() L= 40. diam = 2* 0.418972332 }
comp[ 41] { level[ 2].append() L= 40. diam = 2* 1.06 }
comp[ 42] { level[ 3].append() L= 40. diam = 2* 0.666666667 }
comp[ 43] { level[ 3].append() L= 40. diam = 2* 0.666666667 }
comp[ 44] { level[ 4].append() L= 40. diam = 2* 0.418972332 }
comp[ 45] { level[ 4].append() L= 40. diam = 2* 0.418972332 }
comp[ 46] { level[ 4].append() L= 40. diam = 2* 0.666666667 }
comp[ 47] { level[ 5].append() L= 40. diam = 2* 0.418972332 }
comp[ 48] { level[ 5].append() L= 40. diam = 2* 0.418972332 }
comp[ 49] { level[ 5].append() L= 40. diam = 2* 0.666666667 }
comp[ 50] { level[ 6].append() L= 40. diam = 2* 0.418972332 }
comp[ 51] { level[ 7].append() L= 40. diam = 2* 0.418972332 }
comp[ 52] { level[ 8].append() L= 40. diam = 2* 0.418972332 }
comp[ 53] { level[ 9].append() L= 40. diam = 2* 0.418972332 }
comp[ 54] { level[ 0].append() L= 50. diam = 2* 0.7 }
comp[ 55] { level[ 0].append() L= 50. diam = 2* 0.6 }
comp[ 56] { level[ 0].append() L= 50. diam = 2* 0.5 }
comp[ 57] { level[ 0].append() L= 50. diam = 2* 0.5 }
comp[ 58] { level[ 0].append() L= 50. diam = 2* 0.5 }
comp[ 59] { 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, 59 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 naf2
gbar_naf2 = 0.4
insert kdr_fs
gbar_kdr_fs = 0.4
insert ka
gbar_ka = 0.001
insert k2
gbar_k2 = 0.0005
}
forsec level[ 1] {
insert naf2
gbar_naf2 = 0.06
insert nap
gbar_nap = 0.0006
insert kdr_fs
gbar_kdr_fs = 0.1
insert kc_fast
gbar_kc_fast = 0.025
insert ka
gbar_ka = 0.001
insert km
gbar_km = 0.0005
insert k2
gbar_k2 = 0.0005
insert kahp_slower
gbar_kahp_slower = 0.0001
insert cal
gbar_cal = 0.0001
insert cat
gbar_cat = 5.E-05
insert ar
gbar_ar = 2.5E-05
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.02
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 260000.
}
forsec level[ 2] {
insert naf2
gbar_naf2 = 0.06
insert nap
gbar_nap = 0.0006
insert kdr_fs
gbar_kdr_fs = 0.1
insert kc_fast
gbar_kc_fast = 0.025
insert ka
gbar_ka = 0.001
insert km
gbar_km = 0.0005
insert k2
gbar_k2 = 0.0005
insert kahp_slower
gbar_kahp_slower = 0.0001
insert cal
gbar_cal = 0.0001
insert cat
gbar_cat = 5.E-05
insert ar
gbar_ar = 2.5E-05
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 520000.
}
forsec level[ 3] {
insert naf2
gbar_naf2 = 0.06
insert nap
gbar_nap = 0.0006
insert kdr_fs
gbar_kdr_fs = 0.1
insert kc_fast
gbar_kc_fast = 0.025
insert ka
gbar_ka = 0.001
insert km
gbar_km = 0.0005
insert k2
gbar_k2 = 0.0005
insert kahp_slower
gbar_kahp_slower = 0.0001
insert cal
gbar_cal = 0.0001
insert cat
gbar_cat = 5.E-05
insert ar
gbar_ar = 2.5E-05
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 520000.
}
forsec level[ 4] {
insert naf2
gbar_naf2 = 0.01
insert nap
gbar_nap = 0.0001
insert kdr_fs
gbar_kdr_fs = 0.01
insert kc_fast
gbar_kc_fast = 0.025
insert ka
gbar_ka = 0.001
insert km
gbar_km = 0.0005
insert k2
gbar_k2 = 0.0005
insert kahp_slower
gbar_kahp_slower = 0.0001
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.002
insert ar
gbar_ar = 2.5E-05
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 520000.
}
forsec level[ 5] {
insert naf2
gbar_naf2 = 0.01
insert nap
gbar_nap = 0.0001
insert kdr_fs
gbar_kdr_fs = 0.01
insert kc_fast
gbar_kc_fast = 0.025
insert ka
gbar_ka = 0.001
insert km
gbar_km = 0.0005
insert k2
gbar_k2 = 0.0005
insert kahp_slower
gbar_kahp_slower = 0.0001
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.002
insert ar
gbar_ar = 2.5E-05
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 520000.
}
forsec level[ 6] {
insert naf2
gbar_naf2 = 0.01
insert nap
gbar_nap = 0.0001
insert kdr_fs
gbar_kdr_fs = 0.01
insert kc_fast
gbar_kc_fast = 0.025
insert ka
gbar_ka = 0.001
insert km
gbar_km = 0.0005
insert k2
gbar_k2 = 0.0005
insert kahp_slower
gbar_kahp_slower = 0.0001
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.002
insert ar
gbar_ar = 2.5E-05
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 520000.
}
forsec level[ 7] {
insert naf2
gbar_naf2 = 0.01
insert nap
gbar_nap = 0.0001
insert kdr_fs
gbar_kdr_fs = 0.01
insert kc_fast
gbar_kc_fast = 0.025
insert ka
gbar_ka = 0.001
insert km
gbar_km = 0.0005
insert k2
gbar_k2 = 0.0005
insert kahp_slower
gbar_kahp_slower = 0.0001
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.002
insert ar
gbar_ar = 2.5E-05
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 520000.
}
forsec level[ 8] {
insert naf2
gbar_naf2 = 0.01
insert nap
gbar_nap = 0.0001
insert kdr_fs
gbar_kdr_fs = 0.01
insert kc_fast
gbar_kc_fast = 0.025
insert ka
gbar_ka = 0.001
insert km
gbar_km = 0.0005
insert k2
gbar_k2 = 0.0005
insert kahp_slower
gbar_kahp_slower = 0.0001
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.002
insert ar
gbar_ar = 2.5E-05
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 520000.
}
forsec level[ 9] {
insert naf2
gbar_naf2 = 0.01
insert nap
gbar_nap = 0.0001
insert kdr_fs
gbar_kdr_fs = 0.01
insert kc_fast
gbar_kc_fast = 0.025
insert ka
gbar_ka = 0.001
insert km
gbar_km = 0.0005
insert k2
gbar_k2 = 0.0005
insert kahp_slower
gbar_kahp_slower = 0.0001
insert cal
gbar_cal = 0.0002
insert cat
gbar_cat = 0.002
insert ar
gbar_ar = 2.5E-05
insert cad
// *** ca diffusion: beta=1/tau
beta_cad = 0.05
// cafor(I) (FORTRAN) converted to phi (NEURON)
phi_cad = 520000.
}
forsec all {
cm = 1. // assign global specific capac.
}
//
// passive membrane resistance (leak) and axial resistance
//
forsec Soma_Dendrites {
g_pas = 4.E-05
Ra = 200.
}
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("naf2")) { gbar_naf2 *= spine_area_multiplier }
if (ismembrane("naf2_tcr")) { gbar_naf2_tcr *= spine_area_multiplier }
if (ismembrane("naf22")) { gbar_naf22 *= spine_area_multiplier }
if (ismembrane("kc_fast")) { gbar_kc_fast *= spine_area_multiplier }
if (ismembrane("kc_fast_fast")) { gbar_kc_fast_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_fs")) { gbar_kdr_fs *= spine_area_multiplier }
if (ismembrane("kdr_fs_fs")) { gbar_kdr_fs_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)
// 1 942.477
// 2 266.406832
// 3 167.551467
// 4 167.551467
// 5 105.299143
// 6 105.299143
// 7 167.551467
// 8 105.299143
// 9 105.299143
// 10 167.551467
// 11 105.299143
// 12 105.299143
// 13 105.299143
// 14 105.299143
// 15 266.406832
// 16 167.551467
// 17 167.551467
// 18 105.299143
// 19 105.299143
// 20 167.551467
// 21 105.299143
// 22 105.299143
// 23 167.551467
// 24 105.299143
// 25 105.299143
// 26 105.299143
// 27 105.299143
// 28 266.406832
// 29 167.551467
// 30 167.551467
// 31 105.299143
// 32 105.299143
// 33 167.551467
// 34 105.299143
// 35 105.299143
// 36 167.551467
// 37 105.299143
// 38 105.299143
// 39 105.299143
// 40 105.299143
// 41 266.406832
// 42 167.551467
// 43 167.551467
// 44 105.299143
// 45 105.299143
// 46 167.551467
// 47 105.299143
// 48 105.299143
// 49 167.551467
// 50 105.299143
// 51 105.299143
// 52 105.299143
// 53 105.299143
// 54 219.9113
// 55 188.4954
// 56 157.0795
// 57 157.0795
// 58 157.0795
// 59 157.0795
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 {
if (ismembrane("naf2")) {fastNa_shift_naf2=-2.5}
// global reversal potentials
ek = -100.
e_pas = -65.
ena = 50.
vca = 125.
forsec all if (ismembrane("ar")) erev_ar = -40.
e_gaba_a = -75.
}
// more extended initializations
// Note: the following currents are not
// present in fast spiking and LTS interneurons
// Would be slightly more efficient to not include them
forsec all {
if (ismembrane("nap")) {gbar_nap = 0.0}
if (ismembrane("k2")) {gbar_k2 = 0.0}
if (ismembrane("km")) {gbar_km = 0.0}
if (ismembrane("kahp")) {gbar_kahp = 0.0}
if (ismembrane("kahp_slower")) {gbar_kahp_slower = 0.0}
if (ismembrane("cat")) {gbar_cat = 0.0}
if (ismembrane("ar")) {gbar_ar = 0.0}
}
}
endtemplate deepaxax