//genesis
float dt = 20e-6
str disk = "results/"
int amp = {1 / dt} // {1 / dt + 1}
str a = (amp)
int i, k, l
str el, name
float t
/*********************************************************************
** Simple Granule cell model script (#1)
** Carl Piaf BBF 1994
*********************************************************************/
// str filename = (disk) @ "G_soma-injectIh0"
// str filename = (disk) @ "G_soma-AMPA30dend3"
str filename = (disk) @ "G_soma-inject10"
/* always include these default definitions! */
include defaults
str cellpath = "/Golgi"
/* Golgi cell constants */
include Golg_const.g
/* special scripts to create the prototypes */
//include Golg_chan.g
include Golg_chan_tab.g
include Golg_synchan.g
// include Golg_comp_soma_dend.g
include Golg_comp_passivedend.g
/* Set the clocks */
for (i = 0; i <= 7; i = i + 1)
setclock {i} {dt}
end
setclock 8 4e-5 // 2e-5 // 4.0e-5
setclock 9 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_Golgi_chans
make_Golgi_syns
make_Golgi_comps_soma_dend
/*
call Gran_InNa TABSAVE tabInNa37.data
call Gran_KDr TABSAVE tabKDr37.data
call Gran_KA TABSAVE tabKA37.data
call Gran_CaHVA TABSAVE tabCaHVA37.data
call Gran_H TABSAVE tabH37.data
call Moczyd_KC TABSAVE tabKCa37.data
*/
//make_Vmgraph
/* create the model and set up the run cell mode */
// read cell data from .p file
echo STARTING READ CELL
// readcell Golg1M0_dend.p {cellpath}
readcell Stc_3D.p {cellpath}
// setfield /Golgi/soma/InNa Gbar {{getfield /Golgi/soma/InNa Gbar} * 6.0}
// setfield /Golgi/soma/KDr Gbar {{getfield /Golgi/soma/KDr Gbar} * 6.0}
create neutral /library/interneuron/soma/mf_presyn
disable /library/interneuron/soma/mf_presyn
setfield /library/interneuron/soma/mf_presyn z 0
// Comment out whichever one to switch it off
//addmsg /library/interneuron/soma/mf_presyn /Golgi/soma/GABAA ACTIVATION z
//addmsg /library/interneuron/soma/mf_presyn /Golgi/soma/mf_NMDA ACTIVATION z
//addmsg /library/interneuron/soma/mf_presyn /Golgi/soma/pf_AMPA ACTIVATION z
addmsg /library/interneuron/soma/mf_presyn /Golgi/dend3[8]/pf_AMPA ACTIVATION z
//read_hines -vm -method 11 Gran1M0.p {cellpath}
/* Create the output element */
create asc_file /output/plot_out
//create disk_out /output/plot_out
useclock /output/plot_out 8
enable /output
enable /output/plot_out
ce {cellpath}
// setup the hines solver
echo preparing hines solver...
create hsolve solve
ce solve
// if this is set then reset will NOT change Vm in Hines
setfield . path "../##[][TYPE=compartment]" comptmode 1 chanmode 4
/* Vm_reset 1 !! geeft foutboodschap cannot find field 'Vm_reset'
on '/Golgi/solve' */
call . SETUP
setfield . computeIm 1
setmethod 11
/*
el = ({findsolvefield {cellpath}/solve soma/H Ik})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#2
el = ({findsolvefield {cellpath}/solve soma/Ca_pool Ca})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#3
*/
el = ({findsolvefield {cellpath}/solve soma Vm}) //#4
addmsg {cellpath}/solve /output/plot_out SAVE {el}
/*
el = ({findsolvefield {cellpath}/solve soma/pf_AMPA Gk})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#9
el = ({findsolvefield {cellpath}/solve soma/pf_AMPA Ik})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#9
*/
/*
el = ({findsolvefield {cellpath}/solve dend[0] Vm}) //#4
addmsg {cellpath}/solve /output/plot_out SAVE {el}
el = ({findsolvefield {cellpath}/solve dend[1] Vm}) //#4
addmsg {cellpath}/solve /output/plot_out SAVE {el}
el = ({findsolvefield {cellpath}/solve dend[2] Vm}) //#4
addmsg {cellpath}/solve /output/plot_out SAVE {el}
el = ({findsolvefield {cellpath}/solve dend[3] Vm}) //#4
addmsg {cellpath}/solve /output/plot_out SAVE {el}
el = ({findsolvefield {cellpath}/solve dend[4] Vm}) //#4
addmsg {cellpath}/solve /output/plot_out SAVE {el}
*/
/*
el = ({findsolvefield {cellpath}/solve soma/Moczyd_KC Ik})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#5
el = ({findsolvefield {cellpath}/solve soma/KDr Ik})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#6
el = ({findsolvefield {cellpath}/solve soma/InNa Ik})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#7
el = ({findsolvefield {cellpath}/solve soma/KA Ik})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#8
el = ({findsolvefield {cellpath}/solve soma/CaHVA Ik})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#9
el = ({findsolvefield {cellpath}/solve soma/Moczyd_KC Gk})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#5
el = ({findsolvefield {cellpath}/solve soma/CaHVA Gk})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#9
el = ({findsolvefield {cellpath}/solve dend[4]/mf_AMPA Ik})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#10
el = ({findsolvefield {cellpath}/solve dend[4]/mf_AMPA Gk})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#10
el = ({findsolvefield {cellpath}/solve soma/mf_NMDA Ik})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#11
el = ({findsolvefield {cellpath}/solve soma/Mg_BLOCK Ik})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#12
el = ({findsolvefield {cellpath}/solve soma/Mg_BLOCK Gk})
addmsg {cellpath}/solve /output/plot_out SAVE {el} //#13
*/
setfield /output/plot_out filename {filename} initialize 1 leave_open 1 \
flush 1
echo Output to {filename}
//check
reset
step 1.2 -time
call {cellpath}/solve HGET {cellpath}/soma
setfield {cellpath}/soma inject 5e-12 // -5e-12 // -12e-12
call {cellpath}/solve HPUT {cellpath}/soma
step 0.0 -t
call {cellpath}/solve HGET {cellpath}/soma
setfield {cellpath}/soma inject 10e-12 // -22e-12
call {cellpath}/solve HPUT {cellpath}/soma
step 0.0 -t
call {cellpath}/solve HGET {cellpath}/soma
setfield {cellpath}/soma inject 0 // -10e-12 // -22e-12
call {cellpath}/solve HPUT {cellpath}/soma
step 0.0 -t
// Synaptic stimulation protocol
/*
call {cellpath}/solve HGET {cellpath}/soma
setfield {cellpath}/soma inject -15e-12 // -5e-12 // -12e-12
call {cellpath}/solve HPUT {cellpath}/soma
step 0.2 -t
setfield /library/interneuron/soma/mf_presyn z {amp}
step 1
setfield /library/interneuron/soma/mf_presyn z 0
step 425e-3 -time
*/
// Current injection protocol
/*
step 0.5 -time
call {cellpath}/solve HGET {cellpath}/soma
setfield {cellpath}/soma inject 20e-12
call {cellpath}/solve HPUT {cellpath}/soma
step 0.5 -time
call {cellpath}/solve HGET {cellpath}/soma
setfield {cellpath}/soma inject 0e-12
call {cellpath}/solve HPUT {cellpath}/soma
step 0.5 -time
*/
/*
call {cellpath}/solve HGET {cellpath}/soma
setfield {cellpath}/soma inject -22.5e-12
call {cellpath}/solve HPUT {cellpath}/soma
step 0.5 -time
*/