//genesis
//HookUp.g
//Can give pattern of current injection and/or pattern of pre-syn stim, allowing STDP, HFS, Theta, etc
//pulse>=1 and numtrains>=1 else there will be NO pre-syn stim (good for evaluating AP alone)
//AND preStimPct>0, else there will be NO pre-syn stim
//inject=0 will give pre-syn stim alone, without triggered AP (e.g. hfs or theta)
//set TooFast = 100 will revert to stimulating just one spine, even for 50 Hz stimulation
//If no synaptic stimulation StimComp is where one specifies which spine output to save
/*Commented out lines allow giving a pulse before and after, to test the plasticity
and also repeating the pairings. BUT, these will mess up the alignment of the
pre-synaptic stim and the post-synaptic depol. So, fix the pulse generators when you uncomment them */
function connect_synapse(input,spikegen,stimname,name)
str input,spikegen,stimname,name
if ({exists {stimname}/{name}})
addmsg {input}/{spikegen} {stimname}/{name} SPIKE
else
echo could not find {stimname}/{name}
end
end
function set_timetable(input_name,fname_base,i,maxt,fnam, spikegen,StimComp, spike_history)
str input_name, fnam, fname_base, spikegen, StimComp, spike_history
int i
float maxt
str stimname
pushe /
create timetable {input_name}[{i}]
echo {input_name}[{i}] {StimComp} "max time" {maxt}
setfield {input_name}[{i}] maxtime {maxt} \
method 4 \
act_val 1.0 \
fname {fname_base}
call {input_name}[{i}] TABFILL
create spikegen {input_name}[{i}]/{spikegen}
setfield {input_name}[{i}]/{spikegen} output_amp 1 thresh 0.5 abs_refract 0.0001
addmsg {input_name}[{i}] {input_name}[{i}]/{spikegen} INPUT activation
create spikehistory {spike_history}[{i}].history
setfield {spike_history}[{i}].history ident_toggle 1 filename {fnam} initialize 1 leave_open 1 flush 1
addmsg {input_name}/spikes {spike_history}[{i}].history SPIKESAVE
reset
pope
end
//pass the name of the paradigm, because it is used in naming spine stimulation files
function HookUp(PreStim, paradigm, timing, StimComp, file,numAP,inj,dur,interval, isi, pulseFreq, pulses, burstFreq, numbursts, trainFreq, numtrains, jitter, ChanString)
int PreStim
str StimComp,file, compt, paradigm, timing,ChanString
//These are parameters related to both pre-and post-synaptic AP (EPSP) pattern
int numbursts, numtrains
float trainFreq, burstFreq
float isi //interval between onset of EPSP and onset of AP
//These are parameters related to pre-synaptic stimulation - pulses in a burst
int pulses
float pulseFreq
//These parameters describe post-synaptic stimulation - AP in a burst
int numAP
float inj, dur, interval, interpulse=0, bufpos
str spikegen = "spikes", bufStrTmp, whereStim
// Determine the interpulse intervals for pre-synaptic stimulation
if ({pulses}>1)
interpulse=1./{pulseFreq}
end
// Determine the interburst and intertrain intervals for pre- and post- stimulation
float intertrain=0, interburst=0
interburst = 1.0/{burstFreq}
intertrain = 1.0/{trainFreq}
int pulse, train, burst
str spines_to_hook_up = "1"
//delay refers to onset of current injection relative to first pulse, which occurs at initSim
//float TooFast = 30 //if pre-syn pulses in burst are too fast, distribute them among multiple spines
if ({pulseYN})
float AP_delay= {2*initSim + isi}//+ (pulses-1)*interpulse}
else
float AP_delay = {initSim + isi}// + (pulses-1)*interpulse}
end
if ({isi} > 0)
AP_delay = {AP_delay}
else
AP_delay = {AP_delay} - ({numAP}-1)*{interval}
end
echo "APdelay" {AP_delay}
//parameters for post-synaptic spike generators
if ({interval} == 0 )
echo "Wrong paradigm chosen. You can choose: P_and_K (Pawlak and Kerr), K_and_P (Kerr and Plenz), Shindou, Shen and IF (IF curves)"
return
end
if ({interval}<{dur})
echo "please define lower AP frequency"
end
//**********set the filenames, and
//set up presynaptic element for stimulating
float maxt = {numtrains/trainFreq+2*initSim}
str filenam={file}
if ({GABAYesNo})
filenam={file}@"_gaba_delay_"@{GABAdelay}@"_"
if ({GABAstim} == "")
GABAstim = {StimComp}
end
bufStrTmp = {StimComp}
bufpos = 0
str gaba_file = {paradigm}@"_"@{timing}@"_gaba"
int i = 0
while ({bufpos} > -1)
bufpos = {findchar {bufStrTmp} ,}
if ({bufpos} == -1)
whereStim = {bufStrTmp}
else
whereStim = {substring {bufStrTmp} 0 {bufpos-1}}
bufStrTmp = {substring {bufStrTmp} {bufpos+1}}
end
filenam = {filenam}@"_"@whereStim@"_"@"GABAtau2"@{GABAtau2}@"_"
set_timetable {GABA_input} {gaba_file} {i} {maxt} {filenam} {spikegen} {whereStim} "GABASynTimes"
str stimname = {neuronname}@"/"@{whereStim}
connect_synapse {GABA_input}[{i}] {spikegen} {stimname} {GABAname}
i = i + 1
end
else
if ({GABAtonic}==0)
filenam={file}@"_no_gaba_"
end
end
if ({jitter} == 1)
filenam = {filenam}@"jitter_"
end
if ({abs {isi}}<{SMALLNUMBER})
isi=0
end
//Used for stimulation during simulation
filenam={filenam}@"Stim_"@{StimComp}@"_AP_"@{numAP}@"_ISI_"@{isi}@"_PSP_"@{pulses}@"_interpulse_"@{interpulse}
if ({spinesYesNo})
if ({PreStim}>0)
echo "before pulseFreq entry pulseFreq" {pulseFreq} {TooFast} {pulses}
str fname_base = paradigm@"_"@timing@"_stimulation_spine_"
int dendPos = 0
str dendBuf = {StimComp}
str whichSegment
str stimname
if ({pulses} == 1)
int help = {findchar {whichSpines} ,}
spines_to_hook_up = {substring {whichSpines} 0 {help-1}}
else
spines_to_hook_up = {whichSpines}
end
int i = 0
while ({dendPos} >-1)
dendPos = {findchar {dendBuf} ,}
if ({dendPos} == -1)
whichSegment = {dendBuf}
else
whichSegment = {substring {dendBuf} 0 {dendPos-1}}
dendBuf = {substring {dendBuf} {dendPos+1}}
end
bufpos =0
bufStrTmp = spines_to_hook_up
str whichSpine
while ({bufpos} > -1)
bufpos = {findchar {bufStrTmp} ,}
if ({bufpos} == -1)
whichSpine = {bufStrTmp}
else
whichSpine = {substring {bufStrTmp} 0 {bufpos-1}}
bufStrTmp = {substring {bufStrTmp} {bufpos+1}}
end
str fnam = {filenam}@"_spikes_"@{whichSpine}
str spikegen_file = {fname_base}@{whichSpine}
set_timetable {input_name} {spikegen_file} {i} {maxt} {fnam} {spikegen} {whichSegment} "SynTimes"
stimname = {neuronname}@"/"@{whichSegment}@"/spine_"@{whichSpine}@"/"@{spcomp1}
connect_synapse {input_name}[{i}] {spikegen} {stimname} {NMDAname}
connect_synapse {input_name}[{i}] {spikegen} {stimname} {AMPAname}
i = {i+1}
end
end
end
end
/* //Does not really work, should be rewritten
str stimname={StimComp}
create timetable {input_name}
set_timetable {input_name} {numtrains}/{trainFreq} {filename}
connect_synapse {input_name} {NMDAname} {neuronname} {stimname}
connect_synapse {input_name} {AMPAname} {neuronname} {stimname}
end
*/
echo "################ simulating STDP, " {numAP} "AP, ISI: " {isi}
//set-up file names, post-synaptic spike generators
if ({spinesYesNo})
spinehead={add_output_hook_up {spinefile} {neuronname} {StimComp} {spines_to_hook_up} {ChanString} {PreStim}}
//echo {spinehead}
end
setfilename {Vmfile} {filenam} 1 {Vmhead}
setfilename {Cafile} {filenam} 1 {Cahead}
setfilename {Gkfile} {filenam} 1 {Gkhead}
setfilename {spinefile} {filenam} 1 {spinehead}
int go = 1
float width_burst = {numAP}*{interval}
float width_train = {numbursts}/{burstFreq}
float very_big_number = {1e9}
float exp_duration = {numtrains}/{trainFreq}
if ({dur} > {interval})
go = 0
echo "The AP is wider than the inter AP interval"
else
if ({width_burst} > {interburst})
if (({numbursts} == 1) && ({numtrains} == 1))
interburst = 2*{width_burst}
width_train = {interburst}
if ({width_train} > {intertrain})
echo "Train frequency smaller than duration of all bursts"
intertrain = 2*{width_train}
exp_duration = 2*{width_train}
end
end
else
if ({width_train} > {intertrain})
if ({numtrains} == 1)
intertrain = 2*{width_train}
exp_duration = 1.2*{width_train}
echo "Train frequency smaller than duration of all bursts"
else
go = 0
echo "The train is wider than the intertrain interval"
end
end
end
end
echo go {go}
if ({go} == 1)
//onset of the injections jitter (shift lower than 1 ms):
if ({jitter} == 1)
AP_delay = {AP_delay} + {rand 0 0.0005}
//amplitude jitter
inj = {inj} + {rand 0 {inj}/20.}
//width jitter
dur = {dur} + {rand 0 0.0005}
end
echo AP_delay {AP_delay} inj {inj} AP_duration {dur}
createPulseGen {inj} {basal_current} 0 {interval} {dur} {neuronname}/soma {injectName} 2 "INJECT"
createPulseGen {inj} {basal_current} 0 {interburst} {width_burst} {injectName} {injectName}/burst_gate 2 "INPUT"
createPulseGen {inj} {basal_current} 0 {intertrain} {width_train} {injectName}/burst_gate {injectName}/train_gate 2 "INPUT"
createPulseGen {inj} {basal_current} {AP_delay} {very_big_number} {exp_duration} {injectName}/train_gate {injectName}/experiment_gate 0 "INPUT"
if ({somainjout})
str inj_header
inj_header = {add_outputPulseGen {somainjfile} {injectName}}
setfilename {somainjfile} {filenam} 1 {inj_header}
else
inj_header = ""
somainjfile = "X"
end
end
reset
end
