//genesis
// MSsimSyn.g
/*************************** MS Model, Version 12 ***************/
//*********** includes - functions for constructing model and outputs, and doing simulations
include SimParams.g //simulation control parameters, can be overridden in this file
include MScell/globals.g
include MScell/Ca_constants.g
include MScell/SynParamsCtx.g
include MScell/spineParams.g
include MScell/MScellSynSpines // access make_MS_cell
include InOut/add_output.g //functions for ascii file output
include InOut/IF.g //function to create pulse generator for current injection, also IF & IV curves
include InOut/HookUp.g //run STDP protocols - single PSP with current injection
//include InOut/SpikeMakerFunctions.g //functions to create randomspikes and connect to synapes
//include InOut/PreSynSync.g //functions for setting up synchronous pre-synaptic stimulation
//include InOut/UpState.g //run upstate simulations - asynchronous synaptic stimulation
//include InOut/UpStateSTDP.g //run upstate simulations
//include InOut/PlasStim.g //run plasticity protocols - pattern of PSPS, no current injection
/*//include InOut/ConstrainUp.g
//include RebekahSims/Store_Parameters.g
//include graphics7.g
//set random seed so for each simulation the randomspike train will be the same
//3 = 5757538
//5 = 9824501
//4 = 2394075
//6 = 492
//7 = 2370
//int seedvalue= 5757538
//**************** end of parameters, now contruct model and do simulations*/
setclock 0 {simdt}
setclock 1 {outputclock}
echo Paradigm list: Fino, Shen, P_and_K (Pawlak and Kerr), K_and_P (Kerr and Plenz), Shindou, 3_AP (just the soma injections from Shindou), 1_AP, 1_PSP
str DA = {input "MSN type:" "UI"}
str Protocol = {input "Protocol:" "P_and_K"}
str Timing = {input "Timing:" "Pre"}
str Location = {input "Location:" "tertdend1_1"}
str jitter = {input "With jitter:" "No"}
int seedvalue = {input "Random seed:" 5757538}
echo "DA" {DA}
echo "Protocol" {Protocol}
echo "Timing" {Timing}
echo "Jitter" {jitter}
if ({Protocol}=="P_and_K")
str pname = "PandK"
elif ({Protocol}=="P_and_K_1_AP")
str pname = "PandK1AP"
elif ({Protocol}=="K_and_P")
str pname = "KandP"
else
str pname = {Protocol}
end
int jitter_int = 0
if (({jitter}!="No") && ({jitter}!="no"))
jitter_int = 1
end
str diskpath="SimData/"@{pname}@"_"@{DA}@"_"@{Timing}@"_randseed_"@{seedvalue}@"_high_res"
if ({GABAtonic})
diskpath = {diskpath}@"_tonic_gaba"
end
if ({calciumtype})
diskpath = {diskpath}@"_simple_calcium"
end
//include PSim_Params.g
int totspine={make_MS_cell_SynSpine {neuronname} {pfile} {spinesYesNo} {DA}} // MS_cell.g
reset
/*uncomment the following lines (and one line in MScell.g) to use the hsolver
setfield {neuronname} chanmode 1
call {neuronname} SETUP
setmethod 11
*/
//Store_Parameters
echo {Vmfile}
//Set up asc_file outputs and get headers for the files
if ( {calciumdye} == 0)
Vmfile = {Vmfile}
elif ( {calciumdye} == 1)
Vmfile = {Vmfile}@"_Ca_Fura_2"
elif ( {calciumdye} == 2)
Vmfile = {Vmfile}@"_Ca_Fluo_5f"
elif ( {calciumdye} == 3)
Vmfile = {Vmfile}@"_Ca_Fluo_4"
else
Vmfile = {Vmfile}@"_Ca_unnkown_dye"
end
Vmhead={add_outputVm {comps} {Vmfile} {neuronname}}
if ({CaOut})
if ( {calciumdye} == 0)
Cafile = "Ca"
elif ( {calciumdye} == 1)
Cafile = "Ca_Fura_2"
elif ( {calciumdye} == 2)
Cafile = "Ca_Fluo_5f"
elif ( {calciumdye} == 3)
Cafile = "Ca_Fluo_4"
else
Cafile = "Ca_unnkown_dye"
end
if ({plastYesNo})
Cafile = {Cafile}@"_plasticity"
end
Cahead={add_outputCal {comps} {CaBufs} {Cafile} {neuronname}}
else
Cafile="Unknown_Ca"
if ({plastYesNo})
Cafile = {Cafile}@"_plasticity"
end
Cahead=""
end
if ({GkOut})
Gkfile="Gk"
if ({plastYesNo})
Gkfile = {Gkfile}@"_plasticity"
end
if ( {calciumdye}== 0)
Gkfile = {Gkfile}
elif ( {calciumdye}== 1)
Gkfile = {Gkfile}@"_Ca_Fura_2"
elif ( {calciumdye}== 2)
Gkfile = {Gkfile}@"_Ca_Fluo_5f"
elif ( {calciumdye}== 3)
Gkfile = {Gkfile}@"_Ca_Fluo_4"
else
Gkfile = {Gkfile}@"_Ca_unnkown_dye"
end
Gkhead={add_outputGk {comps} {chans} {Gkfile} {neuronname}}
else
Gkfile="Unknown_Gk"
if ({plastYesNo})
Gkfile = {Gkfile}@"_plasticity"
end
if ( {calciumdye}== 0)
Gkfile = {Gkfile}
elif ( {calciumdye}== 1)
Gkfile = {Gkfile}@ "_Ca_Fura_2"
elif ( {calciumdye}== 2)
Gkfile = {Gkfile}@"_Ca_Fluo_5f"
elif ( {calciumdye}== 3)
Gkfile = {Gkfile}@"_Ca_Fluo_4"
else
Gkfile = {Gkfile}@"_Ca_unnkown_dye"
end
Gkhead=""
end
str stimcomp= {Location}
str spinefile="spine"
if ({plastYesNo})
spinefile = {spinefile}@"_plasticity"
end
if ( {calciumdye} == 0)
spinefile = {spinefile}
elif ( {calciumdye} == 1)
spinefile = {spinefile}@"_Ca_Fura_2"
elif ( {calciumdye} == 2)
spinefile = {spinefile}@"_Ca_Fluo_5f"
elif ( {calciumdye} == 3)
spinefile = {spinefile}@"_Ca_Fluo_4"
else
spinefile = {spinefile}@"_Ca_unnkown_dye"
end
ce /
/***************************** Simulations of STDP */
if ({Protocol}=="Shen")
include InOut/Shen.g
if ({DA} == "D1")
inject = 1.45e-9
elif ({DA} == "D2")
inject = 1.3e-9
end
elif ({Protocol}=="P_and_K")
include InOut/P_K.g
elif ({Protocol}=="P_and_K_1_AP")
include InOut/P_K_1_AP.g
elif ({Protocol}=="Fino")
include InOut/Fino.g
elif ({Protocol}=="Shindou")
include InOut/Shindou.g
elif ({Protocol}=="K_and_P")
include InOut/Kerr_and_Plenz.g
elif ({Protocol}=="3_AP")
include InOut/3_AP.g
elif ({Protocol}=="1_AP")
include InOut/1_AP.g
elif ({Protocol}=="1_PSP")
include InOut/1_PSP.g
elif ({Protocol}=="no_stim")
include InOut/no_stim.g
elif ({Protocol}=="IF")
//setclock 1 {outputclock}
setclock 0 {simdt}
setclock 1 {simdt}
numcurr = 5
injectstart = .1e-9
IFcurve {injectstart} {inc} {numcurr} {delay} {duration} {diskpath}
end
// if ({Protocol}!="IF")
// float newTrainFreq = {burstFreq}/{numbursts}
// echo {newTrainFreq}
// echo {prestim} {Protocol} {Timing} {stimcomp} {diskpath} {numAP} {inject} {AP_durtime} {APinterval} {ISI} {pulseFreq} {pulses} {burstFreq} {numbursts} {newTrainFreq} 1 {jitter_int}
// HookUp {prestim} {Protocol} {Timing} {stimcomp} {diskpath} {numAP} {inject} {AP_durtime} {APinterval} {ISI} {pulseFreq} {pulses} {burstFreq} {numbursts} {newTrainFreq} 1 {jitter_int}
// step 2.6 -time
// fileFLUSH {Vmfile}
// fileFLUSH {Cafile}
// fileFLUSH {Gkfile}
// fileFLUSH {spinefile}
// fileFLUSH {somainjfile}
// end
reset
if ({numtrains}>1)
reset
//uncomment the following lines (and one line in MScell.g) to use the hsolver
//setfield {neuronname} chanmode 1
//call {neuronname} SETUP
//setmethod 11
ce /
setclock 0 {simdt}
setclock 1 {outputclock}
str diskpath="SimData/"@{pname}@"_"@{DA}@"_"@{Timing}@"_randseed_"@{seedvalue}@"_low_res"
if ({Protocol}!="IF")
HookUp {prestim} {Protocol} {Timing} {stimcomp} {diskpath} {numAP} {inject} {AP_durtime} {APinterval} {ISI} {pulseFreq} {pulses} {burstFreq} {numbursts} {trainFreq} {numtrains} {jitter_int}
step {numtrains/trainFreq} -time
fileFLUSH {Vmfile}
fileFLUSH {Cafile}
fileFLUSH {Gkfile}
fileFLUSH {spinefile}
fileFLUSH {somainjfile}
end
end
| 
