//genesis 2.0
// This new version of the defaults.g file uses compiled code
// instead of Script Language functions to set up tabchannels.
/***********************************************************************
** **
** DEFAULTS.G : defaults definition file, neuron builder kit. **
** **
** By E. De Schutter, Nov 1990 **
** Modified by Upi Bhalla and D. Beeman, June 1992 for GENESIS 1.4 **
************************************************************************/
/* DO NOT EDIT THIS FILE: it is the default. Customize by making a
** copy of the 'userprefs.g' file and put that in your working
** directory (each directory can contain a different userpref file).
** In userprefs.g you can change the value of the user_values and
** other globals and create your own specific library.
** Do cd to your working directory before starting Neurokit. */
/**********************************************************************/
/* DEFAULT USER_VALUES AND CELL_PARSER VALUES */
/* THESE GLOBAL VALUES SHOULD ALWAYS BE DEFINED! */
float PI = 3.14159
/* VARIABLES USED BY ACTIVE COMPONENTS */
int EXPONENTIAL = 1
int SIGMOID = 2
int LINOID = 3
/* VARIABLES ASSUMED DEFINED BY CELL_PARSER */
float CM = 0.01 // Farads/m^2
float RA = 0.5 // Ohms m
float RM = 0.2 // Ohms m^2
float EREST_ACT = -0.070 // Volts
/* Set the user_variables: all these variables must be declared,
** even if they are not used! */
str user_help = "./README" /* help file name */
/* xcell widget */
float user_wx = 1.4e-3 //wx, wy, cx, cy, cz for the draw widget
float user_wy = 1.4e-3
float user_cx = 0.0
float user_cy = 0.0
float user_cz = 0.2e-3
str user_field1 = "Vm"
str user_path1 = "."
float user_colmin1 = -0.10
float user_colmax1 = 0.05
float user_fatrange1 = -20.0
int user_fatfix1 = 1
int user_colfix1 = 0
int user_numxouts = 1 /* show 1 or 2 xout and graph windows */
str user_field2 = "Vm"
str user_path2 = "."
float user_colmin2 = -0.10
float user_colmax2 = 0.05
float user_fatrange2 = -20.0
int user_fatfix2 = 1
int user_colfix2 = 0
/* xgraph widget */
float user_xmax1 = 0.5
float user_ymin1 = -0.1
float user_ymax1 = 0.05
float user_yoffset1 = 0.10
float user_xmax2 = 0.5
float user_ymin2 = -0.1
float user_ymax2 = 0.05
float user_yoffset2 = 0.10
/* cell_run_control widget */
/* integration */
int user_symcomps = 0 /* boolean, default is asymmetric comps */
int user_intmethod = 0
float user_runtime = 0.5
/* electrophysiology */
float user_inject = 1.0 //nA
float user_clamp = 0.0
float user_rate = 100.0
float user_weight = 1.0
float user_activ = 1000.0
float user_spike = 1.0
str user_syntype1 = "glu"
str user_syntype2 = "GABA"
/* simulation output : file_IO widget */
str user_filepath = "."
str user_restorefile = "restore_camit"
str user_filefield = "Vm"
str user_filefieldpath = "soma"
str user_filename = "testVm"
float user_dt = 1.0e-5
float user_refresh = 10.0
/* Cell specifications : file_form widget */
str user_cell = "/camit"
str user_pfile = "camit.p"
str user_name = "Me"
/* Set screen width preferences here.
** Decstation 5000/200 : 1280
** SUN workstations : 1150
*/
int user_screenwidth = 1024
if ({exists /xproto})
/* appropriate for black and white printing */
xps -mingray 255 -maxgray 256 -inverse 0
/* appropriate for printing out shades of grey */
xps -mingray 20 -maxgray 120 -inverse 0
end
/* predefine some neurokit variables so they can be used in
** functions defined in userprefs.g */
str cellname = "camit"
str comptname = "soma"
str channelname = "glu"
str cellpath = "/new"
str comptpath = "/new/soma"
str channelpath = "/new/soma/glu"
str analysis_level = "new"
/***********************************************************************/
/**********************************************************************
**
** Creating the library
**
**********************************************************************/
if (!{exists /library})
create neutral /library
/* We don't want the library to try to calculate anything,
** so we disable it */
disable /library
end
/**********************************************************************
**
** Creating the voltage clamp circuit for the library
**
**********************************************************************/
include vclamp
ce /library
make_Vclamp
ce /
/**********************************************************************
**
** Some utility functions for tabulated channels
**
**********************************************************************/
int TAB_XDIVS = 3000
float TAB_XMIN = -0.1
float TAB_XMAX = 0.05
/*
** These SLI functions been replaced by compiled functions with
** clearer names. The aliases defined below are just for
** backwards compatibility. They replace the script functions below.
*/
addalias setup_table2 setupgate // aka setupgate
// The usage of this has changed, so "setupgate" should be used instead
addalias tweak_tabchan tweakalpha // aka tweakalpha
addalias tau_tweak_tabchan tweaktau // aka tweaktau
addalias setup_tabchan setupalpha // aka setupalpha
addalias setup_tabchan_tau setuptau // aka setuptau
function setup_table3(gate, table, xdivs, xmin, xmax, A, B, C, D, F)
setup_table2 {gate} {table} {A} {B} {C} \
{D} {F} -size {xdivs} -range {xmin} {xmax} -noalloc
end
function setup_table(gate, table, xdivs, A, B, C, D, F)
setup_table2 {gate} {table} {A} \
{B} {C} {D} {F} -size {xdivs} -range {TAB_XMIN} {TAB_XMAX}
end
// settab2const sets a range of entries in a tabgate table to a constant
function settab2const(gate, table, imin, imax, value)
str gate
str table
int i, imin, imax
float value
for (i = (imin); i <= (imax); i = i + 1)
setfield {gate} {table}->table[{i}] {value}
end
end
/* The following "commented-out" functions were replaced by more
efficient compiled functions in GENESIS ver. 1.4. The older GENESIS
Script Language implementations are included here in order to illustrate
what they do.
function setup_table3(gate,table,xdivs,xmin,xmax,A,B,C,D,F)
str gate,table
int xdivs
float xmin,xmax,A,B,C,D,F
int i
float x,dx,y
dx = xdivs
dx = (xmax - xmin)/dx
x = xmin
for (i = 0 ; i <= {xdivs} ; i = i + 1)
y = (A + B * x) / (C + {exp({(x + D) / F})})
setfield {gate} {table}->table[{i}] {y}
x = x + dx
end
end
function setup_table2(gate,table,xdivs,xmin,xmax,A,B,C,D,F)
str gate,table
int xdivs
float xmin,xmax,A,B,C,D,F
if (xdivs <= 9)
echo must have at least 9, preferably over 100 elements in table
return
end
call {gate} TABCREATE {table} {xdivs} {xmin} {xmax}
setup_table3({gate},{table},{xdivs},{xmin},{xmax},{A},{B},{C},{D},{F})
end
function setup_table(gate,table,xdivs,A,B,C,D,F)
str gate,table
int xdivs
float A,B,C,D,F
setup_table2({gate},{table},{xdivs},-0.1,0.1,{A},{B},{C},{D},{F})
end
// Alters the values in the B arrays of tabchan to 1/tau
function tweak_tabchan(chan,gate)
str chan,gate
str tabA = {gate}+"_A"
str tabB = {gate}+"_B"
int xdivs,i
float A,B
xdivs = get({chan},{tabA}->xdivs)
for (i = 0 ; i <= xdivs ; i = i + 1)
A = get({chan},{tabA}->table[{i}])
B = get({chan},{tabB}->table[{i}])
setfield {chan} {tabB}->table[{i}] {A + B}
end
end
// Alters the values in the A and B arrays of tabchan to A and 1/tau,
// from tau and minf
function tau_tweak_tabchan(chan,gate)
str chan,gate
str tabA = {gate}+"_A"
str tabB = {gate}+"_B"
int xdivs,i
float A,B
float T,M
xdivs = get({chan},{tabA}->xdivs)
for (i = 0 ; i <= xdivs ; i = i + 1)
T = get({chan},{tabA}->table[{i}])
M = get({chan},{tabB}->table[{i}])
A = M / T
B = 1.0/T
setfield {chan} {tabA}->table[{i}] {A}
setfield {chan} {tabB}->table[{i}] {B}
end
end
// Sets up a tabchan with hh params, with the non-interp option in
// a table of 3000 entries
function setup_tabchan(chan,gate,AA,AB,AC,AD,AF,BA,BB,BC,BD,BF)
str chan,gate
str tabA = {gate}+"_A"
str tabB = {gate}+"_B"
float AA,AB,AC,AD,AF,BA,BB,BC,BD,BF
call {chan} TABCREATE {gate} 49 -0.1 0.05
setup_table3({chan},{tabA},49,-0.1,0.05,{AA},{AB},{AC},{AD},{AF})
setup_table3({chan},{tabB},49,-0.1,0.05,{BA},{BB},{BC},{BD},{BF})
tweak_tabchan({chan},{gate})
setfield {chan} {tabA}->calc_mode 0 {tabB}->calc_mode 0
call {chan} TABFILL {gate} 3000 0
end
// Sets up a tabchan with hh params, with the non-interp option in
// a table of 3000 entries.
// This version uses parameters for tau and minf instead
// of alpha and beta
function setup_tabchan_tau(chan,gate,TA,TB,TC,TD,TF,MA,MB,MC,MD,MF)
str chan,gate
str tabA = {gate}+"_A"
str tabB = {gate}+"_B"
float TA,TB,TC,TD,TF,MA,MB,MC,MD,MF
call {chan} TABCREATE {gate} 49 -0.1 0.05
setup_table3({chan},{tabA},49,-0.1,0.05,{TA},{TB},{TC},{TD},{TF})
setup_table3({chan},{tabB},49,-0.1,0.05,{MA},{MB},{MC},{MD},{MF})
tau_tweak_tabchan({chan},{gate})
setfield {chan} {tabA}->calc_mode 0 {tabB}->calc_mode 0
call {chan} TABFILL {gate} 3000 0
end
*/