Large scale model of the olfactory bulb (Yu et al., 2013)

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Accession:144570
The readme file currently contains links to the results for all the 72 odors investigated in the paper, and the movie showing the network activity during learning of odor k3-3 (an aliphatic ketone).
Reference:
1 . Yu Y, McTavish TS, Hines ML, Shepherd GM, Valenti C, Migliore M (2013) Sparse distributed representation of odors in a large-scale olfactory bulb circuit. PLoS Comput Biol 9:e1003014 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Channel/Receptor; Dendrite;
Brain Region(s)/Organism: Olfactory bulb;
Cell Type(s): Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron granule MC GABA cell;
Channel(s): I Na,t; I A; I K;
Gap Junctions:
Receptor(s): NMDA; Glutamate; Gaba;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Pattern Recognition; Activity Patterns; Bursting; Temporal Pattern Generation; Oscillations; Synchronization; Active Dendrites; Detailed Neuronal Models; Synaptic Plasticity; Action Potentials; Synaptic Integration; Unsupervised Learning; Olfaction;
Implementer(s): Hines, Michael [Michael.Hines at Yale.edu]; Migliore, Michele [Michele.Migliore at Yale.edu];
Search NeuronDB for information about:  Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron granule MC GABA cell; NMDA; Glutamate; Gaba; I Na,t; I A; I K; Gaba; Glutamate;
/
YuEtAl2012
readme.html
ampanmda.mod
fi.mod
kamt.mod *
kdrmt.mod *
naxn.mod *
ThreshDetect.mod *
.hg_archival.txt
allsynhinton.hoc *
antest.ses *
clear.hoc *
connect.hoc
control.ses
default.hoc
granule.hoc *
hinton.hoc
init.hoc *
iterator.hoc *
lindgren.job
lptiter.hoc
mgrs.hoc
michele_movie.hoc
mitral.hoc
mosinit.hoc *
net.hoc
odors.txt
odors-forsim500-kensaku.txt
param.hoc
parinit.hoc
pattern.hoc
perfrun.hoc
record.hoc
show.hoc
showstim.hoc
showw.hoc
somesyn.hoc *
spike2file.hoc
spkdat2bin.hoc
split.hoc
start.hoc
start.ses *
stim-AB-rnd-500mt.hoc
stim-o11o12.hoc
stim-o14.hoc
stim-o26.hoc
stim-o26d1-mnoise5hz-gnoise-5s.hoc
stim-o5high-o6low.hoc
stim-odors-AB-seq.hoc
stim-pair.hoc
stim-seq-rnd.hoc
subset.hoc
subset_control.ses *
viewspikes.hoc
viewspikes1.hoc
weight_movie.hoc *
weightsave.hoc
                            
// The spike viewer colors spikes using the theme of red if
// a spike is potentiating, blue if depressing, and black if unchanged.
//Spikes are shown for a selected mitral cell at each granule position.
// The lower graph is a zoom view of the indicated postion in the
// full raster upper graph

begintemplate SpikeViewer1
external ngranule, nmitral, ncell
external gid2mg
objref tpat, idpat, vb, g, gz, this
objref dtpat, mat[2], xsel, ysel, csel
proc init() {
	mdetect = 1
	zv_width = 1000
	tpat = $o1 // pattern_tvec
	idpat = $o2 // pattern_idvec
	color_spikes()
	xmitral = int(nmitral/2)
	xsel = tpat.c.resize(0)
	ysel = tpat.c.resize(0)
	csel = tpat.c.resize(0)
	build()
}

proc build() {
	vb = new VBox()
	vb.ref(this)
	vb.save("")
	vb.intercept(1)
	xpanel("",1)
	xmenu("Z View Width")
	xbutton("200", "zvw(200)")
	xbutton("500", "zvw(500)")
	xbutton("1000", "zvw(1000)")
	xmenu()
	xcheckbox("M detect", &mdetect, "x_change()")
	xpvalue("Mitral gid", &xmitral, 1, "x_change()")
	xpanel()
	g = new Graph()
	g.menu_tool("zoomed view", "zview")
	g.size(0, 1000*int(tpat.x[tpat.size-1]/1000 + .5), 0, ngranule)
	g.view(0,0,zv_width,ngranule,0,0,300,200)
	vb.intercept(0)
	vb.map("Spike Viewer", 200, 200, 500, 600)
	g.exec_menu("zoomed view")
	x_change()
}

proc zvw() {local x
	zv_width = $1
	x = g.view_info(1, 5)
	g.view_size(1, x, x+zv_width, -10, ngranule+10)
}
proc zview() {local i
	i = g.view_info()
	if (i == 0) {
		g.view_size(1, $2-zv_width/2, $2+zv_width/2, -10, ngranule+10)
	}else{
		translate($1, $2, $3)
	}
}

i=0
x=0
width=0
proc translate() {local x0,y0
        if ($1 == 2) {
                i = g.view_info()
                x = g.view_info(i, 5)
                xrel=g.view_info(i, 11, $2)
                width=g.view_info(i,1)
        }
        if ($1 == 1) {
                x1 = g.view_info(i, 11, $2)
                x0 = x - width*(x1 - xrel)
                g.view_size(i, x0, x0 + width, -10, ngranule+10)
        }
}


proc x_change() {local i, c, f, gid, m, g, is_m2g
	if (xmitral < 0) {
		xmitral = 0
	}else if (xmitral > nmitral-1) {
		xmitral = nmitral-1
	}else{
		xmitral = int(xmitral)
	}
	xsel.resize(0)
	ysel.resize(0)
	csel.resize(0)
	for i=0, tpat.size-1 {
		gid = idpat.x[i]
		f = 0
		if (gid > ncell){
			gid2mg(gid, &m, &g, &is_m2g)
			if (m == xmitral && is_m2g != mdetect) {
				f = 1
				xsel.append(tpat.x[i])
				ysel.append(g)
			}
		}
		if (f) {
			dt = dtpat.x[i]
			if (dt < ltpinvl_AmpaNmda) {
				c = 2
			}else if (dt > ltdinvl_AmpaNmda) {
				c = 1
			}else{
				c = 3
			}
			csel.append(c)
		}
	}
	gplt()
}
proc color_spikes() {local i, gid, m, g, is_m2g
	dtpat = tpat.c
	mat[0] = new Matrix(nmitral+1, ngranule+1)
	for m=0, nmitral for g = 0, ngranule { mat[0].x[m][g] = -1000 }
	mat[1] = mat[0].c
	for i=0, tpat.size-1 {
		gid = idpat.x[i]
		if (gid < nmitral) {
			m = gid + 1  g = 0  is_m2g = 0
		}else if (gid < nmitral + ngranule) {
			m = 0  g = gid - nmitral + 1
		}else{
			gid2mg(gid, &m, &g, &is_m2g)
			m += 1
			g += 1
		}
		
		dtpat.x[i] = tpat.x[i] - mat[is_m2g].x[m][g]
		mat[is_m2g].x[m][g] = tpat.x[i]
	}
}
proc gplt() {local i
	g.erase()
	for i=0, xsel.size-1 {
		g.mark(xsel.x[i], ysel.x[i], "|", 2, csel.x[i], 1)
	}
}
endtemplate SpikeViewer1

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