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//genesis
// Cable.g - main script
//==================================================
// global variables used in the simulation
//==================================================
// start with no passive cable compartments
int NCableSects = 0
// use the Crank-Nicholson numerical integration method
int IntegMethod = 11
// start with injection to soma (comp 0)
int InjComp = 0
// start with synaptic input to soma (comp 0)
int SynComp = 0
// default time to run simulation (msecs)
float tmax = 50
// default integration time step (msecs)
float dt = 0.01
float PI = 3.14159
// resting membrane potential
float EREST = 0
// Specific resistances and capacitance
// Kohm-cm^2
float RM = 10.0
// uF/cm^2
float CM = 1.0
// Kohm-cm
float RA = 0.1
// compartment dimensions (cm.)
float soma_l = 50e-4
float soma_d = 50e-4
float dend_l = 50e-4
float dend_d = 1e-4
// default (initial) parameters for current injection
// msec
float injwidth = 10
float injdelay = 0
// uA (200 nA)
float injcurrent = 2e-4
// default (initial) parameters synaptic input
// msec
float syndelay = 0
// choose width and interval to give a single spike
float synwidth = 1000
float syninterval = 100000
// milliSiemen
float gsyn = 1e-5
// milliseconds
float tsyn = 1
// mV above resting potential (defined as zero)
float Vsyn = 50
// for comparison
// Vsyn = 125 ==> Na channel (+55 mV with Erest = -70)
// Vsyn = -12 ==> K channel (-82 mV with Erest = -70)
// While simulation is being loaded, put up some credits
echo " "
echo "*************************************************"
echo "* *"
echo "* Cable *"
echo "* *"
echo "* A simulation of a simple dendritic cable *"
echo "* *"
echo "* (version 2.0) *"
echo "* *"
echo "* D. Beeman *"
echo "* *"
echo "* UNIVERSITY OF COLORADO *"
echo "* *"
echo "*************************************************"
echo " "
echo "Loading simulation ....."
//==================================================
// STARTUP SCRIPTS
//==================================================
include compartment.g
include methods.g // sets integration method and creates hsolver
include inputs.g // functions for injection and synaptic input
include logifier.g // constructs lookup tables for log plots
// include view.g // graphics for propagation along the cable
include addcable.g // functions to add and delete cable sections
include forms.g // Control Panel and Graphs
include setcolors.g // function colorize sets widget colors
//=========================================================================
// Some functions used in the main script
// SendPlotMsgs - sends messages to the graphics forms
// ResetGlobals - resets the values of the global variables to defaults
// ResetDefaults - similar to the main script, but graph forms pre-exist
//=========================================================================
function SendPlotMsgs
pushe /output/somagraphs
addmsg /cell/soma somaVm_grf PLOT Vm *soma *black
addmsg /cell/soma /logtable INPUT Vm
addmsg /logtable loggraph PLOT output *soma *black
addmsg /cell/syn_channel /output/condgraphs/channel_Gk PLOT Gk *Gk \
*blue
pope
end// SendPlotMsgs
function ResetGlobals
// start with no passive cable compartments
NCableSects = 0
IntegMethod = 11
// start with injection to soma (comp 0)
InjComp = 0
// start with synaptic input to soma (comp 0)
SynComp = 0
// default time to run simulation (msecs)
tmax = 50
// default integration time step (msecs)
dt = 0.01
// Kohm-cm^2
RM = 10.0
// uF/cm^2
CM = 1.0
// Kohm-cm
RA = 0.1
soma_l = 50e-4
soma_d = 50e-4
dend_l = 50e-4
dend_d = 1e-4
end
function ResetDefaults
stop
// in case we are plotting cable sections
remove_cable_plots
delete /cell
delete /input
delete /output/control
delete /output/param_menu
delete /output/inject_menu
delete /output/synapse_menu
delete /output/method_menu
delete /output/plot_menu
deletemsg /logtable 0 -outgoing
// re-initialize global constants
ResetGlobals
// simulation time step in msec
setclock 0 {dt}
create neutral /cell
makecompartment /cell/soma {soma_l} {soma_d} {EREST}
// inputs.g
makeinputs
load_menus
SendPlotMsgs
// check
colorize
reset
end
//=========================================================================
// MAIN SCRIPT - Cable
//=========================================================================
//==================================================
// check and initialize the simulation
//==================================================
// set the prompt
setprompt "Cable !"
// simulation time step in msec
setclock 0 {dt}
// max size for reasonable accuracy
// output interval
setclock 1 0.05
create neutral /cell
makecompartment /cell/soma {soma_l} {soma_d} {EREST}
makeinputs // inputs.g
loadgraphs // in forms.g (This is done after the elements are created)
load_menus
loadhelp
SendPlotMsgs
// check
colorize
reset
echo ==================
echo Simulation loaded.
echo ==================
|
