ModelDB: Human Cortical L5 Pyramidal Cell (Rich et al. 2021)

proc turnclampoff() {
	Iclamp = 0
	ic_clamp.amp=Iclamp
}

proc turnclampon() {
	Iclamp= PARAM_ic_clamp_amp
	ic_clamp.amp=Iclamp
}

proc setclamp() {
	Iclamp= $1
	ic_clamp.amp=Iclamp
}

proc setclampdur() {
	PARAM_ic_clamp_dur= $1
	ic_clamp.dur = PARAM_ic_clamp_dur
}

proc block() {
	gIhbar_opt=0
	gSKv3_1bar_opt=0
	gK_Pstbar_opt=0
	gImbar_opt=0
	gSK_E2bar_opt=0
	gK_Tstbar_opt=0
	gCa_LVAstbar_opt=0
	gCa_HVAbar_opt=0
	gNa_Et2_opt=0
	gNaTa_t_soma_opt=0
	gNaTa_t_apical_opt=0
	reset()
}

proc unblock() {
	gIhbar_opt=PARAM_gIhbar
	gSKv3_1bar_opt=PARAM_gSKv3_1bar
	gK_Pstbar_opt=PARAM_gK_Pstbar
	gImbar_opt=PARAM_gImbar
	gSK_E2bar_opt=PARAM_gSK_E2bar
	gK_Tstbar_opt=PARAM_gK_Tstbar
	gCa_LVAstbar_opt=PARAM_gCa_LVAsshiftbar
	gCa_HVAbar_opt=PARAM_gCa_HVAbar
	gNa_Et2_opt=PARAM_Nap_Et2
	gNaTa_t_soma_opt=PARAM_NaTa_t_soma
	gNaTa_t_apical_opt=PARAM_NaTa_t_apical
	reset()
}

proc block_Na() {
	gNa_Et2_opt=0
	gNaTa_t_soma_opt=0
	gNaTa_t_apical_opt=0
	reset()
}

proc block_Ca() {
	gCa_LVAstbar_opt=0
	gCa_HVAbar_opt=0
	reset()
}

proc block_K() {
	gSKv3_1bar_opt=0
	gK_Pstbar_opt=0
	gImbar_opt=0
	gSK_E2bar_opt=0
	gK_Tstbar_opt=0
	reset()
}

proc block_Ih() {
	gIhbar_opt=0
	reset()
}

proc setizap() {
	tstop=$1+$2

	setclamp(0)
	access filament_100000042[0]
	Zap= new Izap(0.5)

	Zap.del=$1
	Zap.dur=$2
	Zap.f0=$3
	Zap.f1=$4
	Zap.amp=$5

	load_file("VoltageAndCurrentTrace_zap.ses")

}

proc recordizap() {
	setizap($1,$2,$3,$4,$5)

	time= new Vector()
	voltage= new Vector()
	zapcurrent= new Vector()

	time.record(&t)
	voltage.record(&filament_100000042[0].v(0.5))
	zapcurrent.record(&Zap.i)

	run()

	save_time= new File()
	save_voltage= new File()
	save_zapcurrent= new File()

	sprint(title_time, "ZapData_time_%d_%d_%d_%d.csv", Zap.f0, Zap.f1, Zap.amp*100, Zap.dur)
	sprint(title_voltage, "ZapData_voltage_%d_%d_%d_%d.csv", Zap.f0, Zap.f1, Zap.amp*100, Zap.dur)
	sprint(title_zapcurrent, "ZapData_zapcurrent_%d_%d_%d_%d.csv", Zap.f0, Zap.f1, Zap.amp*100, Zap.dur)


	save_time.wopen(title_time)
	save_voltage.wopen(title_voltage)
	save_zapcurrent.wopen(title_zapcurrent)

	time.printf(save_time)
	voltage.printf(save_voltage)
	zapcurrent.printf(save_zapcurrent)

	save_time.close()
	save_voltage.close()
	save_zapcurrent.close()

	tstop=PARAM_tstop
}

proc noiserun() {
	cvode.active(0)
	dt= $2
	tstop=$3
	numstep=tstop/dt

	NoiseFile= new File()
	NoiseVector= new Vector(numstep)
	NoiseVector

	sprint(noiseinput, "%s.dat", $s1)
	NoiseFile.ropen(noiseinput)

	for i=1, numstep {
		NoiseVector.x[i-1]=$4+NoiseFile.scanvar()
	}

	ic_clamp.del=0
	ic_clamp.dur=1e9
	NoiseVector.play(&ic_clamp.amp, dt)

	time= new Vector()
	voltage= new Vector()
	current= new Vector()

	time.record(&t)
	voltage.record(&filament_100000042[0].v(0.5))
	current.record(&ic_clamp.i)

	run()

	save_time= new File()
	save_voltage= new File()
	save_current= new File()

	sprint(title_time, "NoiseData_time_%s.csv", $s1)
	sprint(title_voltage, "NoiseData_voltage_%s.csv", $s1)
	sprint(title_current, "NoiseData_current_%s.csv", $s1)

	save_time.wopen(title_time)
	save_voltage.wopen(title_voltage)
	save_current.wopen(title_current)

	time.printf(save_time)
	voltage.printf(save_voltage)
	current.printf(save_current)

	save_time.close()
	save_voltage.close()
	save_current.close()


	cvode.active(1)
	tstop=PARAM_tstop
	NoiseVector.play_remove()
	ic_clamp.del = PARAM_ic_clamp_del
	ic_clamp.dur = PARAM_ic_clamp_dur
	ic_clamp.amp = Iclamp
}

proc multnoiseruns() {
	pw= new PWManager()
	while (pw.count()>2) {
		pw.close(pw.count()-1)
	}

	xopen("VoltageAndCurrentTrace_noise_full.ses")

	for j=1,60 {
		sprint(noiseinputmult, "%d_%s", j, $s1)
		print noiseinputmult
		noiserun(noiseinputmult,.01, 2500, 0.031)
		print j
	}
}

proc setizap_supra() {
	tstop=$1+$2

	setclamp(0)
	access filament_100000042[0]
	Zap= new Izap(0.5)

	Zap.del=$1
	Zap.dur=$2
	Zap.f0=$3
	Zap.f1=$4
	Zap.amp=$5

	load_file("VoltageAndCurrentTrace_zap.ses")
}

proc recordizap_supra() {
	setizap_supra($1,$2,$3,$4,$5)

	cvode.active(0)
	dt=.01
	numstep=tstop/dt


	time= new Vector()
	voltage= new Vector()
	zapcurrent= new Vector()

	time.record(&t)
	voltage.record(&filament_100000042[0].v(0.5))
	zapcurrent.record(&Zap.i)

	run()

	save_time= new File()
	save_voltage= new File()
	save_zapcurrent= new File()

	sprint(title_time, "ZapData_time_%d_%d_%d_%d.csv", Zap.f0, Zap.f1, Zap.amp*100, Zap.dur)
	sprint(title_voltage, "ZapData_voltage_%d_%d_%d_%d.csv", Zap.f0, Zap.f1, Zap.amp*100, Zap.dur)
	sprint(title_zapcurrent, "ZapData_zapcurrent_%d_%d_%d_%d.csv", Zap.f0, Zap.f1, Zap.amp*100, Zap.dur)


	save_time.wopen(title_time)
	save_voltage.wopen(title_voltage)
	save_zapcurrent.wopen(title_zapcurrent)

	time.printf(save_time)
	voltage.printf(save_voltage)
	zapcurrent.printf(save_zapcurrent)

	save_time.close()
	save_voltage.close()
	save_zapcurrent.close()

	cvode.active(1)
	tstop=PARAM_tstop
}

proc setizap_distal() {
	tstop=$1+$2

	setclamp(0)
	access filament_100000042[203]
	Zap= new Izap(0.5)

	Zap.del=$1
	Zap.dur=$2
	Zap.f0=$3
	Zap.f1=$4
	Zap.amp=$5

	load_file("VoltageAndCurrentTrace_zap.ses")
}

proc recordizap_distal() {
	setizap_distal($1,$2,$3,$4,$5)

	time= new Vector()
	voltage= new Vector()
	zapcurrent= new Vector()

	time.record(&t)
	voltage.record(&filament_100000042[203].v(0.5))
	zapcurrent.record(&Zap.i)

	run()

	save_time= new File()
	save_voltage= new File()
	save_zapcurrent= new File()

	sprint(title_time, "ZapData_time_%d_%d_%d_%d.csv", Zap.f0, Zap.f1, Zap.amp*100, Zap.dur)
	sprint(title_voltage, "ZapData_voltage_%d_%d_%d_%d.csv", Zap.f0, Zap.f1, Zap.amp*100, Zap.dur)
	sprint(title_zapcurrent, "ZapData_zapcurrent_%d_%d_%d_%d.csv", Zap.f0, Zap.f1, Zap.amp*100, Zap.dur)

	save_time.wopen(title_time)
	save_voltage.wopen(title_voltage)
	save_zapcurrent.wopen(title_zapcurrent)

	time.printf(save_time)
	voltage.printf(save_voltage)
	zapcurrent.printf(save_zapcurrent)

	save_time.close()
	save_voltage.close()
	save_zapcurrent.close()

	tstop=PARAM_tstop
}

proc SwapToKole() {
	forsec Soma {
		insert Ih_mod
		gIhbar_Ih= 0
		gbar_Ih_mod= gIhbar_opt
	}

	forsec Apical {
		dist=distance(.5)
		insert Ih_mod
 		gbar_Ih_mod=gIhbar_opt*(-0.8696+2.0870*exp(3.6161*(dist/decay)))
		gIhbar_Ih= 0
	}

	forsec Basilar {
		insert Ih_mod
		gIhbar_Ih=0
		gbar_Ih_mod=gIhbar_opt
	}
}

proc ResetHChannel() {
	forsec Soma {
		gIhbar_Ih= gIhbar_opt
		gbar_Ih_mod= 0
	}

	forsec Apical {
		dist=distance(.5)
 		gbar_Ih_mod= 0
		gIhbar_Ih= gIhbar_opt*(-0.8696+2.0870*exp(3.6161*(dist/decay)))
	}

	forsec Basilar {
		gIhbar_Ih= gIhbar_opt
		gbar_Ih_mod=0
	}

}

proc changepassive() {
    	forall {
        	cm = $1
        	Ra = $2
        	g_pas = $3
        	e_pas = -$4
    	}
}

proc setizap_DC() {
	tstop=$1+$2

	setclamp($6)
	ic_clamp.del=0
	ic_clamp.dur=tstop

	access filament_100000042[0]
	Zap= new Izap(0.5)

	Zap.del=$1
	Zap.dur=$2
	Zap.f0=$3
	Zap.f1=$4
	Zap.amp=$5

	load_file("VoltageAndcurrentTrace_zap_laptop.ses")

}

proc recordizap_DC() {
	setizap_DC($1,$2,$3,$4,$5,$6)

	time= new Vector()
	voltage= new Vector()
	zapcurrent= new Vector()

	time.record(&t)
	voltage.record(&filament_100000042[0].v(0.5))
	zapcurrent.record(&Zap.i)

	run()

	save_time= new File()
	save_voltage= new File()
	save_zapcurrent= new File()

	sprint(title_time, "ZapData_time_%d_%d_%d_%d_%d.csv", Zap.f0, Zap.f1, Zap.amp*100, Zap.dur, ic_clamp.amp*100)
	sprint(title_voltage, "ZapData_voltage_%d_%d_%d_%d_%d.csv", Zap.f0, Zap.f1, Zap.amp*100, Zap.dur, ic_clamp.amp*100)
	sprint(title_zapcurrent, "ZapData_zapcurrent_%d_%d_%d_%d_%d.csv", Zap.f0, Zap.f1, Zap.amp*100, Zap.dur, ic_clamp.amp*100)


	save_time.wopen(title_time)
	save_voltage.wopen(title_voltage)
	save_zapcurrent.wopen(title_zapcurrent)

	time.printf(save_time)
	voltage.printf(save_voltage)
	zapcurrent.printf(save_zapcurrent)

	save_time.close()
	save_voltage.close()
	save_zapcurrent.close()

	tstop=PARAM_tstop
}


proc recordclamp_TTX() {
	tstop=4080.6
	block_Na()
	tstop=4080.6

	ic_clamp.del=$1
	ic_clamp.dur=$2
	ic_clamp.amp=$3

	time= new Vector()
	voltage= new Vector()

	time.record(&t)
	voltage.record(&filament_100000042[0].v(0.5))

	run()

	save_time= new File()
	save_voltage= new File()

	sprint(title_time, "CurrentClampData_TTX_time_%d_%d_%d.csv", ic_clamp.del, ic_clamp.dur, ic_clamp.amp*100)
	sprint(title_voltage, "CurrentClampData_TTX_voltage_%d_%d_%d.csv", ic_clamp.del, ic_clamp.dur, ic_clamp.amp*100)

	save_time.wopen(title_time)
	save_voltage.wopen(title_voltage)

	time.printf(save_time)
	voltage.printf(save_voltage)

	save_time.close()
	save_voltage.close()

	tstop=PARAM_tstop
}

proc recordclamp() {
	tstop=4080.6
	unblock()
	tstop=4080.6

	ic_clamp.del=$1
	ic_clamp.dur=$2
	ic_clamp.amp=$3

	time= new Vector()
	voltage= new Vector()

	time.record(&t)
	voltage.record(&filament_100000042[0].v(0.5))

	run()

	save_time= new File()
	save_voltage= new File()

	sprint(title_time, "CurrentClampData_time_%d_%d_%d.csv", ic_clamp.del, ic_clamp.dur, ic_clamp.amp*100)
	sprint(title_voltage, "CurrentClampData_voltage_%d_%d_%d.csv", ic_clamp.del, ic_clamp.dur, ic_clamp.amp*100)

	save_time.wopen(title_time)
	save_voltage.wopen(title_voltage)

	time.printf(save_time)
	voltage.printf(save_voltage)

	save_time.close()
	save_voltage.close()

	tstop=PARAM_tstop
}


proc reset() {
filament_100000042[0] distance()

    	forall {
        	insert pas
        	cm = cm_opt
        	Ra = Ra_opt
        	g_pas = g_pas_opt
        	e_pas = -e_pas_opt
    	}

	forsec Soma {
		insert Ca_LVAst
	  	insert Ca_HVA
		insert SKv3_1
		insert K_Pst
		insert K_Tst
		insert SK_E2
		insert CaDynamics_E2
		// insert Im
		insert Ih

		insert Nap_Et2
	  	insert NaTa_t


  		gCa_LVAstbar_Ca_LVAst = gCa_LVAstbar_opt
  		gCa_HVAbar_Ca_HVA = gCa_HVAbar_opt
		decay_CaDynamics_E2= 460.0
		gamma_CaDynamics_E2= 0.000501
		gSKv3_1bar_SKv3_1= gSKv3_1bar_opt
		gK_Pstbar_K_Pst= gK_Pstbar_opt
		gK_Tstbar_K_Tst= gK_Tstbar_opt
		gSK_E2bar_SK_E2= gSK_E2bar_opt
		// gImbar_Im= gImbar_opt
		gIhbar_Ih= gIhbar_opt

		gNap_Et2bar_Nap_Et2= gNa_Et2_opt
		gNaTa_tbar_NaTa_t= gNaTa_t_soma_opt

		cm=1
	}

	forsec Apical {
		insert Ca_LVAst
	  	insert Ca_HVA
		insert SKv3_1
		// insert K_Pst
		// insert K_Tst
		insert SK_E2
		insert CaDynamics_E2
		insert Im
		insert Ih

  		insert NaTa_t

		decay_CaDynamics_E2= 460.0
		gamma_CaDynamics_E2= 0.000501
		gSKv3_1bar_SKv3_1= gSKv3_1bar_opt
		// gK_Pstbar_K_Pst= gK_Pstbar_opt
		gSK_E2bar_SK_E2= gSK_E2bar_opt
		gImbar_Im= gImbar_opt

		// gIhbar_Ih= gIhbar_opt
		dist=distance(.5)
		// gIhbar_Ih=gIhbar_opt*exp(-1*dist/decay)
		gIhbar_Ih=gIhbar_opt*(-0.8696+2.0870*exp(3.6161*(dist/decay)))

  		// gCa_LVAstbar_Ca_LVAst = gCa_LVAstbar_opt
  		// gCa_HVAbar_Ca_HVA = gCa_HVAbar_opt
		//if (dist>685 && dist<885) {
		if (dist>360 && dist<600) {
  			gCa_LVAstbar_Ca_LVAst = 100*gCa_LVAstbar_opt
  			gCa_HVAbar_Ca_HVA = 10*gCa_HVAbar_opt
		} else{
			gCa_LVAstbar_Ca_LVAst = gCa_LVAstbar_opt
  			gCa_HVAbar_Ca_HVA = gCa_HVAbar_opt
		}

		gNaTa_tbar_NaTa_t=gNaTa_t_apical_opt
	}

	forsec Basilar {
		// insert Ca_LVAst
	  	// insert Ca_HVA
		// insert SKv3_1
		// insert K_Pst
		// insert K_Tst
		// insert SK_E2
		// insert CaDynamics_E2
		// insert Im
		insert Ih

		// decay_CaDynamics_E2= 460.0
		// gamma_CaDynamics_E2= 0.000501
		// gSKv3_1bar_SKv3_1= gSKv3_1bar_opt
		// gK_Pstbar_K_Pst= gK_Pstbar_opt
		// gSK_E2bar_SK_E2= gSK_E2bar_opt
		// gImbar_Im= gImbar_opt
		gIhbar_Ih= gIhbar_opt
	}

	/*
	forsec Axonal {
		insert SKv3_1
		insert K_Pst
		insert SK_E2
		insert CaDynamics_E2
		insert Im
		insert Ih

		decay_CaDynamics_E2= 460.0
		gamma_CaDynamics_E2= 0.000501
		gSKv3_1bar_SKv3_1= gSKv3_1bar_opt
		gK_Pstbar_K_Pst= gK_Pstbar_opt
		gSK_E2bar_SK_E2= gSK_E2bar_opt
		gImbar_Im= gImbar_opt
		gIhbar_Ih= gIhbar_opt
	}
	*/
}