/**********************************************************************
// Taken from dendritica, settings.hoc
//
Copyright (C) 2001 Philipp Vetter, Arnd Roth and Michael Hausser
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
**********************************************************************/
spinescale = 1
dendscale = 1
objref stim, biasStim
proc reset() { /* set the whole environment to its standard settings */
active_set()
passive_set()
}
/**********************************************************************/
proc active_set() { /* set active model parameters */
/* $1 gbar_na */
/* $2 gbar_kv */
/* $3 gbar_na (node) */
/* $4 g_qq */
/* $5 qq_end */
/* $6 qq_steep */
/* $7 qq_half */
n = numarg()
if (n>0) g_na = $1 else g_na = G_na
if (n>1) g_kv = $2 else g_kv = G_kv
if (n>2) g_nanode = $3 else g_nanode = G_nanode
if (n>3) g_kvnode = $4 else g_kvnode = G_kvnode
if (n>4) g_qq = $5 else g_qq = G_qq
if (n>5) qq_end = $6 else qq_end = Qq_end
if (n>6) qq_steep = $7 else qq_steep = Qq_steep
if (n>7) qq_half = $8 else qq_half = Qq_half
if (Iq_current) forsec all \
gbar_qq=qq_end+(g_qq-qq_end)/(1+exp((distance(0)-qq_half)/qq_steep))
forsec "soma" { gbar_na = g_na
gbar_kv = g_kv }
forsec "myelin" gbar_na = g_na
forsec "node" { gbar_na = g_nanode
gbar_kv = g_kvnode}
forsec "hill" { gbar_na = g_nanode
gbar_kv = g_kvnode }
forsec "iseg" { gbar_na = g_nanode
gbar_kv = g_kvnode }
// Vetter et al used different settings here for spines vs. dendrites
forsec dendritic { gbar_kv = g_kv*dendscale
gbar_na = g_na*dendscale
if (Iq_current) gbar_qq *= dendscale
}
}
/**********************************************************************/
proc passive_set() { /* set passive properties */
/* $1 rm */
/* $2 rax */
/* $3 c_m */
/* $4 cm_myelin */
/* $5 qq_end */
/* $6 qq_steep */
/* $7 qq_half */
n = numarg()
if (n>0) rm = $1 else rm = Rm
if (n>1) rax = abs($2) else rax = Rax
if (n>2) c_m = $3 else c_m = C_m
if (n>3) cm_myelin = $4 else cm_myelin = Cm_myelin
if (n>4) rm_node = $5 else rm_node = Rm_node
if (n>5) rm_end = $6 else rm_end = Rm_end
if (n>6) rm_steep = $7 else rm_steep = Rm_steep
if (n>7) rm_half = $8 else rm_half = Rm_half
if (!nonuniform_Rm) rm_end = rm /* only nonuniform distr if nonuniform_Rm==1 */
//origin.sec distance(0,originx)
forall {if (rm-rm_end==0) g_pas =1/rm else \
g_pas = 1/(rm+(rm-rm_end)/(1+exp((distance(0)-rm_half)/rm_steep)))
cm = c_m
Ra = rax
}
forsec "myelin" cm = cm_myelin
forsec "node" g_pas = 1/rm_node
forsec "iseg" g_pas = 1/rm /* make sure iseg & hill have uniform rm */
forsec "hill" g_pas = 1/rm
/****
forsec dendritesI { cm *= spinescale // spine corrections
g_pas *= spinescale }
forsec dendritesII { cm *= spinescaleII // spine corrections
g_pas *= spinescaleII }
forsec dendritesIII { dendarea = 0 // spine corrections Rapp
for(x) dendarea+= area(x)
spinarea = 10*L
spinescaleIII = (spinarea+dendarea)/dendarea
cm *= spinescaleIII
g_pas *= spinescaleIII }
****/
}
/**********************************************************************/
proc get_standard() { /* standard settings, implemented substitutively, whenever a neuron is loaded */
Iq_current = 0 /* substitutively no Iq_current */
Ca_current = 0 /* substitutively no Ca_current */
KCa_current = 0 /* substitutively no KCa_current */
Km_current = 0 /* substitutively no Km_current */
nonuniform_Rm = 0 /* substitutively no nonuniform Rm */
electrotonicL = 0 /* substitutively physical lengths */
activespine = 1 /* model spines with active membrane */
currentdist = 1 /* status for which distlist to use*/
currentcell = 0 /* number of currently active cell */
simMode = 0 /* 0 IClamp 1 Vclamp simulation */
celsius = 37 /* general settings */
originx = 0.5 /* where to add axon */
Ek = -90
Ena = 60
cells = 1
swc = 0 /* flag is turned on for Duke Southampton files */
synthetic = 0 /* synthetic neurons need longer simulation time */
St_del = 0 /* stimulation (duration,delay,amplitude) */
St_amp = 1
St_dur = 9999
Sim_durI = 0 /* simulation (duration & dt) */
Sim_dtI = 0.25 /* run for Sim_durI with Sim_dtI,
then Sim_dur with Sim_dt */
Sim_dur = 15
Sim_dt = 0.025
Rec_del = Sim_durI /* recording options (for display) */
Rec_dur = Sim_dur
Rec_dt = Sim_dt
/* passive membrane properties, which aren't being changed in general */
Rm_node = 50
Cm_myelin = 0.04
G_ca = .3 /* 13.8.98 */
G_kca = .1
G_km = 3
Rm_end = Rm_half = Rm_steep = 0
G_qq = 0.02 /* Iq settings */
Qq_end = 20
Qq_steep = 439
Qq_half = 50
}
proc act0_set() { /* Zach Nature standard (kvz|naz) */
Rax = 150 /* passive membrane properties */
Rm = 12000
C_m = 1
G_kv = 30 /* active membrane properties */
G_kvnode = 500
G_na = 35
G_nanode = 35000
insert_channels()
}
proc pass0_set() { /* Zach Nature standard (kvz|naz) */
Rax = 150 /* passive membrane properties */
Rm = 12000
C_m = 1
G_kv = 30 /* active membrane properties */
G_kvnode = 500
G_na = 35
G_nanode = 35000
}
proc init_model() {
get_standard() // initialize standard settings (T, activespine ...)
act0_set() // just use the Vetter et al default
reset()
}
proc init_iclamps() {
stim = new IClamp(0.5)
stim.del = 0
stim.dur = 0
stim.amp = 0
biasStim = new IClamp(0.5)
biasStim.del = 0
biasStim.dur = 1e5
biasStim.amp = 0
}
proc init_passive_model() {
get_standard() // initialize standard settings (T, activespine ...)
pass0_set()
insert_passive()
passive_set()
}
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