// genesis
int i,n
str hstr // string for findsolvefield operations
/********************************************************************
** Modified by Carson Roberts 09/2004 From Dieter Jaeger's GP simulations
** (05/2000) for use in gnrh neurons.
** In its present form, it uses the scripts:
** gnrh_const.g, gnrh_actcomps.g, gnrh_chansave.g, gnrh_syns.g,
** and gnrh_current_inject.g
*******************************************************************/
setenv SIMPATH {getenv SIMPATH} ./prototypes
/* always include these default definitions! */
include defaults
//include userprefs
/* simulation constants */
include gnrh_const.g
/*****************************************************************************
** The above file, "gnrh_const.g" holds settings for ELEAK, EREST_ACT,
** The Tabchannel xmin and xmax etc, default values CM,RM,RA (which may be over-
** written by values read in from a "parameter.asc" file). It is also the place
** to set the densities of active channels and synapses
******************************************************************************/
echo data_fname {data_fname}
echo gsyn_AMPA_fname {gsyn_AMPA_fname}
echo gsyn_GABA_fname {gsyn_GABA_fname}
/* Skip input of parameters, take values from "gnrh_const" */
/************************************************************/
echo Cell Parameters are: RMs {RMs}, CM {CM}, RA {RA} RMd {RMd}
/* scripts to create the prototypes */
include gnrh_actcomps.g
/********************************************************************************
** Sets up prototype Soma, Dendrite and Axon compartments. Differences in channel
** Types and Densities should be set up in this script.
*********************************************************************************/
//include gnrh_chanload.g // This line for already saved channels
include gnrh_chansave.g // This line to initially generate Table Channels
/******************************************************************************
** The two lines above will contain the actual kinetic equations for whatever
** channels are included in the model.
********************************************************************************/
include gnrh_syns.g // This script contains the definitions for various synapses
include gnrh_current_inject.g // This script contains codes for various current injections
/* Create the output elements */
//Create Output element for Membrane Potential
create asc_file /out
setfield /out filename {data_fname} initialize 1 flush 0 append 1 leave_open 1
useclock /out 9
silent -1
/* To ensure that all subsequent elements are made in the library */
ce /library
//These make the prototypes of channels and compartments that can be
// invoked in .p files
make_Kdr_gnrh // function in gnrh_chansave.g
make_NaF_gnrh // function in gnrh_chansave.g
make_CaL_gnrh // function in gnrh_chansave.g
make_gnrh_comps // function in gnrh_actcomps.g
/* create the model and set up the run cell mode */
// read cell data from .p file AND set the cell itself up as the hsolve element
readcell {dotp} {cellpath} -hsolve
echo done reading cell
/* Set the clocks */
for (i=0; i<=8; i=i+1)
setclock {i} {dt}
end
setclock 9 1.0e-4
// Add Synapses
//create input element tree outside of the cell path
if (!{exists /inputs})
create neutral /inputs
end
create neutral /inputs/AMPAs
create neutral /inputs/GABAs
/******************************************************************/
/* Block of code to create AMPA Synapses, and set up timetables */
/* to drive them. */
/******************************************************************/
/* Generate the prototype AMPA synapse, as defined in gnrh_syns */
make_gnrh_AMPA
randseed = 1234567
/* create a large number of independant synapses, */
/* receiving activation info from timetables */
/*AMPA synapses*/
create neutral /inputs/AMPAs/{syn_compt}
for (i=0; i<{num_AMPA_syns}; i=i+1)
copy /library/AMPA {cellpath}/{syn_compt}/AMPAs{i}
addmsg {cellpath}/{syn_compt}/AMPAs{i} {cellpath}/{syn_compt} CHANNEL Gk Ek
addmsg {cellpath}/{syn_compt} {cellpath}/{syn_compt}/AMPAs{i} VOLTAGE Vm
create timetable /inputs/AMPAs/{syn_compt}/AMPAtt{i}
// set properties of spike timing
setfield /inputs/AMPAs/{syn_compt}/AMPAtt{i} \
maxtime 10 \ // Max. Time up to which table is filled
act_val 1.0 \ // Value of Activation when set to ON
method 2 \ // Gamma Dist. for Inter Time Intervals
meth_desc1 {1/{AMPA_freq}} \ //mean Inter Time Interval (method 2)
meth_desc2 0.003 \ //absolute refractory period of 3 ms (method 2)
meth_desc3 2 //Order of Gamma Dist. (method 2)
call /inputs/AMPAs/{syn_compt}/AMPAtt{i} TABFILL
// addmsg /inputs/AMPAs/{syn_compt}/AMPAtt{i} {cellpath}/{syn_compt}/AMPAs{i} ACTIVATION activation
//set up spikegen
create spikegen /inputs/AMPAs/{syn_compt}/spiker{i}
setfield /inputs/AMPAs/{syn_compt}/spiker{i} \
output_amp 1 \
thresh 0.5
//connect timetables to AMPA synapses
addmsg /inputs/AMPAs/{syn_compt}/AMPAtt{i} \
/inputs/AMPAs/{syn_compt}/spiker{i} INPUT activation
addmsg /inputs/AMPAs/{syn_compt}/spiker{i} \
{cellpath}/{syn_compt}/AMPAs{i} SPIKE
end
echo we have made {num_AMPA_syns} AMPA syns
/******************************************************************/
/* Block of code to create GABA Synapses, and set up timetables */
/* to drive them. */
/******************************************************************/
/* Generate the prototype GABA synapse, as defined in gnrh_syns */
make_gnrh_GABA
randseed = 2345671
/* create a large number of independant synapses, */
/* receiving activation info from timetables */
/*GABA synapses*/
create neutral /inputs/GABAs/{syn_compt_GABA}
for (i=0; i<{num_GABA_syns}; i=i+1)
copy /library/GABA {cellpath}/{syn_compt_GABA}/GABAs{i}
addmsg {cellpath}/{syn_compt_GABA}/GABAs{i} {cellpath}/{syn_compt_GABA} CHANNEL Gk Ek
addmsg {cellpath}/{syn_compt_GABA} {cellpath}/{syn_compt_GABA}/GABAs{i} VOLTAGE Vm
create timetable /inputs/GABAs/{syn_compt_GABA}/GABAtt{i}
// set properties of spike timing
setfield /inputs/GABAs/{syn_compt_GABA}/GABAtt{i} \
maxtime 10 \ // Max. Time up to which table is filled
act_val 1.0 \ // Value of Activation when set to ON
method 2 \ // Gamma Dist. for Inter Time Intervals
meth_desc1 {1/{GABA_freq}} \ //mean Inter Time Interval (method 2)
meth_desc2 0.003 \ //absolute refractory period of 3 ms (method 2)
meth_desc3 3 //Order of Gamma Dist. (method 2)
// for the last variable, use "meth_desc3 3" for inputs independant of the AMPA synapses, and
// use "meth_desc3 2" for GABA inputs coincident with AMPA ones.
call /inputs/GABAs/{syn_compt_GABA}/GABAtt{i} TABFILL
// addmsg /inputs/GABAs/{syn_compt_GABA}/GABAtt{i} \
// {cellpath}/{syn_compt_GABA}/GABAs{i} ACTIVATION activation
//set up spikegen
create spikegen /inputs/GABAs/{syn_compt_GABA}/spiker_GABA{i}
setfield /inputs/GABAs/{syn_compt_GABA}/spiker_GABA{i} \
output_amp 1 \
thresh 0.5
//connect timetables to GABA synapses
addmsg /inputs/GABAs/{syn_compt_GABA}/GABAtt{i} \
/inputs/GABAs/{syn_compt_GABA}/spiker_GABA{i} INPUT activation
addmsg /inputs/GABAs/{syn_compt_GABA}/spiker_GABA{i} \
{cellpath}/{syn_compt_GABA}/GABAs{i} SPIKE
end
echo we have made {num_GABA_syns} GABA syns
// make_gnrh_GABA
// copy GABA {cellpath}/soma/GABA
// addmsg {cellpath}/soma/GABA {cellpath}/soma CHANNEL Gk Ek
// addmsg {cellpath}/soma {cellpath}/soma/GABA VOLTAGE Vm
// addmsg /input/Apulse/spiketrain {cellpath}/soma/GABA SPIKE
//set up current injection
/****************************************************************************
* This is a bit of a hack, to get around a Genesis bug involving injecting *
* current into a cell that has been taken over by the Hines solver. The *
* Manual says to use code like: *
* setfield {cellpath}/soma inject {curr} *
* call {cellpath} HPUT {cellpath}/soma *
* But, it turns out that there is a disturbance in the membrane potential *
* every time the HPUT command is excecuted. The solution (as implemented *
* here) is to set up a "pulse" that is actually a DC current injection, and *
* in the run code for current injections to use commands like: *
* setfield /pulse level1 {curr} *
* step 0.05 -time *
* setfield /pulse level1 0 *
* to generate a pulse. The injections are set up and run from the script *
* "gnrh_current_inject.g *
****************************************************************************/
create pulsegen /pulse
setfield /pulse \
level1 0 \
width1 0.1 \
delay1 0 \
delay2 0 \
baselevel 0 \
trig_mode 0
addmsg /pulse {cellpath}/soma INJECT output
/****************************
* SETUP THE HINES SOLVER *
****************************/
echo preparing hines solver...
//create hsolve {cellpath}
// The hsolve element has already been created.... It is the cell itself
setfield {cellpath} \
path {cellpath}/##[][TYPE=compartment] \
comptmode 1 \ // uses less memory, and a bit slower than comptmode 1
chanmode 4 \ // Mode for efficient saving of multiple compartment values
calcmode 0 \ // no linear interpolation of values from lookup tables
outclock 9 \ // clock to be used for element updates
storemode 2 // Total Conductances are stored
call {cellpath} SETUP
setmethod 11 // Crank-Nicholson Method
/********************************
* OUTPUT *
********************************/
/* Output of Soma trace only: */
hstr ={findsolvefield {cellpath} {cellpath}/soma Vm}
addmsg {cellpath} /out SAVE {hstr}
hstr ={findsolvefield {cellpath} {cellpath}/p0[196] Vm}
addmsg {cellpath} /out SAVE {hstr}
/* uncomment above line to save only one Vm trace (for simple graphs) */
/************************************************************************/
/* Save Vm of all compartments to a file for use in making movie frames */
/* Uncomment block below for saving stuff for making movies */
/************************************************************************/
//int n
//str readcompartment
//openfile {outputcompsfname} r
//readcompartment = {readfile {outputcompsfname}}
//while (! {eof {outputcompsfname}})
// hstr ={findsolvefield {cellpath} {cellpath}/{readcompartment} Vm}
// addmsg {cellpath} /out SAVE {hstr}
// readcompartment = {readfile {outputcompsfname}}
//end
//closefile {outputcompsfname}
//
/* ****************************************************************************/
/* Block of code to output synaptic conductances: leave uncommented if not */
/* desired, to save time in repeated simulations (actually, it does not seem */
/* to save much time at all...... */
/******************************************************************************/
/* Create Output element for AMPA synaptic conductances */
if ({num_AMPA_syns} >0)
create asc_file /out2
setfield /out2 filename {gsyn_AMPA_fname} initialize 1 flush 0 append 1 leave_open 1
useclock /out2 9
silent -1
/* Loop through and save each AMPA conductance in the output file */
for (i=0; i<{num_AMPA_syns}; i=i+1)
hstr ={findsolvefield {cellpath} {cellpath}/{syn_compt}/AMPAs{i} Gk}
addmsg {cellpath} /out2 SAVE {hstr}
end
end
/* Create Output element for GABA synaptic conductances */
if ({num_GABA_syns}>0)
create asc_file /out3
setfield /out3 filename {gsyn_GABA_fname} initialize 1 flush 0 append 1 leave_open 1
useclock /out3 9
silent -1
/* Loop through and save each GABA conductance in the output file */
for (i=0; i<{num_GABA_syns}; i=i+1)
hstr ={findsolvefield {cellpath} {cellpath}/{syn_compt_GABA}/GABAs{i} Gk}
addmsg {cellpath} /out3 SAVE {hstr}
end
end
/* Create Output element for Injected Currents */
create asc_file /out4
setfield /out4 filename {current_data_fname} initialize 1 flush 0 append 1 leave_open 1
useclock /out4 9
silent -1
hstr ={findsolvefield {cellpath} {cellpath}/soma inject}
addmsg {cellpath} /out4 SAVE {hstr}
/****************************************************************************/
/* End of block for saving all voltages and synapses for movie */
/****************************************************************************/
/*************************************/
/* Start running the simulation */
/*************************************/
reset
/*********************************************/
/* Restore a saved snapshot of the cell */
/* See code below for saving the snapshot */
/* Uncomment the two lines below to restore */
/*********************************************/
restore {snapshotname}
call {cellpath} HRESTORE
/**********************/
/* Run for some time */
/**********************/
/*********************************************************************************/
/* Use the line below to run for some time and with synapses, etc, as set up in */
/* "gnrh_const.g"... Comment it out for current injection simulations. */
/*********************************************************************************/
// step {run_time} -time
/*********************************************************************************/
/* Use the line below to run for current injection protocols to match */
/* experiments as set up in "gnrh_current_inject.g.... */
/* Comment it out for synaptic activation simulations. */
/*********************************************************************************/
do_current_injections
/**************************************************/
/* Take a snapshot of the cell for RESTORE */
/* Uncomment the lines below to take the snapshot */
/**************************************************/
// call {cellpath} HSAVE
/* This updates all compartments from the hsolve element */
// save {cellpath}/##[] {snapshotname}
/* This saves all values for all elements in the file "test.save" */
/* NOTE: Just using the wildcard /## will only save elements of the type "p0[XX]" */
/* but WILL NOT save elements of the type "p1[XX]" */
quit // exits Genesis