GC model (Beining et al 2017)

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Accession:231818
A companion modeldb entry (NEURON only) to modeldb accession number 231862.
Reference:
1 . Beining M, Mongiat LA, Schwarzacher SW, Cuntz H, Jedlicka P (2017) T2N as a new tool for robust electrophysiological modeling demonstrated for mature and adult-born dentate granule cells eLife
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Dentate gyrus;
Cell Type(s): Dentate gyrus granule GLU cell;
Channel(s): I A; I Calcium; I h; I K; I K,Ca; I K,leak; I Na,t; I M; Kir2 leak;
Gap Junctions:
Receptor(s):
Gene(s): Cav1.2 CACNA1C; Cav1.3 CACNA1D; Cav2.2 CACNA1B; Cav3.2 CACNA1H; HCN1; Nav1.2 SCN2A; Nav1.6 SCN8A; Kir2.1 KCNJ2; Kv1.1 KCNA1; Kv1.4 KCNA4; Kv2.1 KCNB1; Kv3.3 KCNC3; Kv3.4 KCNC4; Kv4.2 KCND2; KCa1.1 KCNMA1; KCa2.2 KCNN2;
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Methods; Neurogenesis; Conductance distributions;
Implementer(s): Beining, Marcel [beining at fias.uni-frankfurt.de];
Search NeuronDB for information about:  Dentate gyrus granule GLU cell; I Na,t; I A; I K; I K,leak; I M; I h; I K,Ca; I Calcium; Kir2 leak;
/*
	GC model environment for NEURON, accompanying the e-Life publication Beining et al (2017): "XXXXXXXXXXXXXXXX"
	This script is to provide some functionalities of the model directly in NEURON without the need of Matlab and TREES toolbox.

	Please cite as
	XXXXXXXXXXXXXXXXXXXXXXXX
	
	Bug reports to
	marcel.beining@gmail.com
*/

// ***** Initialize Variables *****
strdef tmpstr, tmpstr2, caname // temporary string object
objref f, g
objref nil,cvode,strf,tvec,cell,cellList,pp,ppList,con,conList,nilcon,nilconList,playt,playtList,play,playList,thissec,thisseg,thisval,maxRa,maxcm 
 cellList = new List() // comprises all instances of cell templates, also artificial cells
 ppList = new List() // comprises all Point Processes of any cell
 conList = new List() // comprises all NetCon objects
 playtList = new List() //comprises all time vectors for play objects
 playList = new List() //comprises all vectors played into an object
 nilconList = new List() //comprises all NULL object NetCons
 cvode = new CVode() //the Cvode object
 thissec = new Vector() //for reading range variables
 thisseg = new Vector() //for reading range variables
 thisval = new Vector() //for reading range variables
thismorph = -1
thisbiophys =  -1
thisexp =  -1
accuracy = 0
cv = 1
singlemorph = 0
objref whichmorphology, whichbiophys, whichexp, pwmgraph
whichmorphology = new Vector(5) 
whichbiophys = new Vector(4)
whichexp = new Vector(2)
pwmgraph = new Vector(4)
pwmgraph.fill(-1)

// ***** Load standard libraries *****
io = load_file("nrngui.hoc")
io = nrn_load_dll("lib_mech/nrnmech.dll")
io = xopen("lib_genroutines/fixnseg.hoc")
io = xopen("lib_genroutines/genroutines.hoc")
io = xopen("lib_genroutines/pasroutines.hoc")




// ***** Procedures *****
proc close_windows() {
	for p = 0,pwmgraph.size()-1 {
		if (pwmgraph.x(p) !=-1) {
			PWManager[0].close(pwmgraph.x(p)-1)
			pwmgraph.x(p) = -1
			}
	}
	if (pwmrctrl !=-1) {
		PWManager[0].close(pwmrctrl-1)
		}
	if (pwmexppanel !=-1) {
		PWManager[0].close(pwmexppanel-1)
		}
	graphList[0].remove_all//(gind-1)
}

proc load_morphology() {
	if ($1 && thismorph >= 0) {
		if (whichmorphology.x(thismorph)==0) {  // do not allow unchecking
			whichmorphology.x(thismorph) = 1  // recheck mark
			return
		}else{
			whichmorphology.x(thismorph) = 0  // delete old check mark
			}
	}
	
	cellList.remove_all()  // destroy cell objects
	
	if ($1) {
		if (PWManager[0].is_mapped(pwmbiophys-1) ){   // biophysics might have been defined... remove! But only if load_morphology was not called from load_biophys
			whichbiophys.x(thisbiophys) = 0   // delete old check mark
			thisbiophys = -1   // reinit biophys
		}else{	PWManager[0].map(pwmbiophys-1)}
	}
	
	if (PWManager[0].is_mapped(pwmexp-1)){
		ppList.remove_all()  // destroy point process objects
		PWManager[0].hide(pwmexp-1)
		if (thisexp >= 0){
			whichexp.x(thisexp) = 0   // delete old check mark
			close_windows()
			thisexp = -1   // reinit exp
		}
	}	
	thismorph = whichmorphology.indwhere("==", 1)   // find (new) check mark now
	
	if (thismorph == 0) {
		xopen("init_cells_SH07MouseGC.hoc")
	}
	if (thismorph == 1) {
		xopen("init_cells_SynMouseGC.hoc")
	}
	if (thismorph == 2) {
		xopen("init_cells_BeiningRatGC.hoc")
	}
	if (thismorph == 3) {
		xopen("init_cells_SynRatGC.hoc")
	}
	if (thismorph == 4) {
		xopen("init_cells_ClaiborneRatGC.hoc")
	}
	

}


proc load_biophys() {
	if ($1 && thisbiophys >= 0){
		if (whichbiophys.x(thisbiophys) ==0) {  // do not allow unchecking
			whichbiophys.x(thisbiophys) = 1  // recheck mark
			return
		}else{
			whichbiophys.x(thisbiophys) = 0   // delete old check mark
		}
	}
	thisbiophys = whichbiophys.indwhere("==", 1)  // find new check mark
	
	// as there is no "uninsert all" function, the cells have to be reloaded to get rid of the inserted mechanisms. This is how I do it
	load_morphology(0)  // clear and reload morphologies, thereby do not delete biophys windows
	
	if (thisbiophys == 0) {
		xopen("init_mech_MatureMouseGC.hoc")
		v_init = -92.100000
		caname = "cai"
	}
	if (thisbiophys == 1) {
		xopen("init_mech_YoungMouseGC.hoc")
		v_init = -92.100000
		caname = "cai"
	}
	if (thisbiophys == 2) {
		xopen("init_mech_MatureRatGC.hoc")
		v_init = -92.100000
		caname = "cai"
	}
	if (thisbiophys == 3) {
		xopen("init_mech_AH99_MatureRatGC.hoc")
		v_init = -70.000000
		caname = "caim_Caold"
	}
	if (thisbiophys >= 0) {
		PWManager[0].map(pwmexp-1)
	}
}


proc load_exp() {
	if (thisexp >= 0){
		if (whichexp.x(thisexp) ==0) {  // do not allow unchecking
			whichexp.x(thisexp) = 1  // recheck mark
			return
		}else{
			whichexp.x(thisexp) = 0   // delete old check mark
			close_windows()
			}
	}
	thisexp = whichexp.indwhere("==", 1)  // find new check mark

	if (thisexp == 0) {
		io = xopen("init_exp_curr.hoc")
		print "Current injection experiment loaded"
	}
	if (thisexp == 1) {
		io = xopen("init_exp_bAP.hoc")
		print "bAP experiment loaded"
	}
}

proc setcvode() {
	cvode.active(cv)
}

// ***** Some settings *****
celsius = 24
prerun = 400
tstart = 0
tstop = 200
dt = 0.05
setcvode()

io = xpanel("Load Morphologies")
io = xlabel("Load Morphologies")
io = xstatebutton("Load only single morphology",&singlemorph,"load_biophys(0)")
io = xstatebutton("SH07 mouse GCs",&whichmorphology.x(0),"load_morphology(1)")
io = xstatebutton("Synthetic mouse GCs",&whichmorphology.x(1),"load_morphology(1)")
io = xstatebutton("Beining rat GCs",&whichmorphology.x(2),"load_morphology(1)")
io = xstatebutton("Synthetic rat GCs",&whichmorphology.x(3),"load_morphology(1)")
io = xstatebutton("Claiborne rat GCs",&whichmorphology.x(4),"load_morphology(1)")
io = xpanel(0,150)
pwmmorph = PWManager[0].count

io = xpanel("Load Biophysics")
io = xlabel("Load Biophysics")
io = xstatebutton("mature mouse GC",&whichbiophys.x(0),"load_biophys(1)")
io = xstatebutton("young mouse GC",&whichbiophys.x(1),"load_biophys(1)")
io = xstatebutton("mature rat GC",&whichbiophys.x(2),"load_biophys(1)")
io = xstatebutton("mature rat GC (Aradi&Holmes99)",&whichbiophys.x(3),"load_biophys(1)")
io = xpanel(0,450)
pwmbiophys = PWManager[0].count
io = PWManager[0].hide(pwmbiophys-1)

io = xpanel("Load Experiment")
io = xlabel("Load Experiment")
io = xstatebutton("Current injection",&whichexp.x(0),"load_exp()")
io = xstatebutton("bAP",&whichexp.x(1),"load_exp()")
io = xpanel(0,700)
pwmexp = PWManager[0].count
io = PWManager[0].hide(pwmexp-1)