Squid axon (Hodgkin, Huxley 1952) (NEURON)

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Accession:5426
The classic HH model of squid axon membrane implemented in NEURON. Hodgkin, A.L., Huxley, A.F. (1952)
Reference:
1 . HODGKIN AL, HUXLEY AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117:500-44 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Axon;
Brain Region(s)/Organism:
Cell Type(s): Squid axon; Hodgkin-Huxley neuron;
Channel(s): I Na,t; I K;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potentials; Invertebrate;
Implementer(s): Hines, Michael [Michael.Hines at Yale.edu];
Search NeuronDB for information about:  I Na,t; I K;
objref f, list, list,  mat, sf, g, transform, pt, scalemat, offset
f = new File()
sf = new StringFunctions()
f.chooser("r", "Read idraw file", "*.id")
strdef line, tstr
transform = new Matrix(3, 2)

proc rd() {
	list = new List()
	if (!f.chooser) { return }
	f.ropen()
	while(!f.eof) {
		f.gets(line)
		parse(line)
	}
	f.close()
}

proc parse() {
	if( sf.head(line, "Begin %I Line", tstr) != -1 ) {
		parseLine()
	}
	if( sf.head(line, "Begin %I MLine", tstr) != -1 ) {
		parseMLine()
	}
}

proc gettransform() {
//	transform.scanf(f, 3, 2) // available aftger version 5.2
	before52(transform)
	f.gets(line)
	scalemat = transform.bcopy(0, 0, 2, 2)
	offset = transform.getrow(2)
}

proc dotransform() {local i
	pt = new Vector(2)
	for i=0, mat.nrow-1 {
		pt = mat.getrow(i)
		scalemat.mulv(pt, pt)
		pt.add(offset)
		mat.setrow(i, pt)
	}
}

proc parseLine() {
	for i=1, 8 { f.gets(line) }
	gettransform()
	mat = new Matrix(2, 2)
//	mat.scanf(f, mat.nrow, mat.ncol) // available after version 5.2
	before52(mat)			// implement above using Vector
	dotransform() // transform mat	
	list.append(mat)
}

objref tmpvec
tmpvec = new Vector()
proc before52() {local i
	for i=0, $o1.nrow-1 {
		tmpvec.scanf(f, $o1.ncol)		
		$o1.setrow(i, tmpvec)
	}
}

		

proc parseMLine() {local i,  n
	for i=1, 8 { f.gets(line) }
	gettransform()
	n = f.scanvar()
	mat = new Matrix(n, 2)
//	mat.scanf(f, mat.nrow, mat.ncol) //availabel after version 5.2
	before52(mat)
	dotransform() // transform mat	
	list.append(mat)
}

rd()

		
proc gr() { local i, c
	g = new Graph()
	for i = 0, list.count - 1 {
		mat = list.object(i)
		c = 1
		if (mat.nrow == 2) {
			c = 2
		}
		mat.getcol(1).line(g, mat.getcol(0), c, 1)
	}
	g.exec_menu("View = plot")
}

gr()

xpanel("tools")

xscale=1
yscale=1
yorg = 0
xorg = 0

xvalue("x real size", "xscale", 1)
xbutton("xorg and xscale line (grab line first)", "setscale(1)")
xvalue("y real size", "yscale", 1)
xbutton("yscale line", "setscale(0)")
xbutton("yorigin line", "yorg = hoc_obj_[0].x[0]")
xbutton("Polyline", "doit()")
xpanel()

proc setscale() {local org, sclfac
	org = hoc_obj_[$1].x[0]
	sclfac = hoc_obj_[$1].x[1] - org
	if ($1 == 1) {
		xsclfac = xscale/sclfac
		xorg = org
	}else{
		ysclfac = yscale/sclfac
	}
}

strdef tstr
load_file("vecwrap.hoc", "VecWrap")
makeVecWrap()

proc doit() {
	hoc_obj_.sub(yorg).mul(ysclfac)
	hoc_obj_[1].sub(xorg).mul(xsclfac)
	if(string_dialog("Label", tstr)) {
		hoc_obj_.label(tstr)
		VecWrap[0].input(hoc_obj_[1], hoc_obj_[0])
	}
}

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