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
                            
begintemplate GranuleSpine
public head, neck, all
create head, neck
objref all
proc init() {
	all = new SectionList()
	head all.append()
	neck all.append()
	connect head(0), neck(1)
	neck { L = 2  diam = .2 }
	head { L = 1  diam = 1 }
	memb()
}
proc memb() {
	forsec all {
		insert pas 
		insert kamt gbar_kamt=0.008 ek=-90
		insert nax gbar_nax=0.02 sh_nax=15 ena=60
		Ra = 80
		cm = 1
		g_pas = 1/30000
		e_pas = -65
		ek = -90
	}
}
endtemplate GranuleSpine

begintemplate Granule

public soma, priden, priden2, external_syn
public prilist
public position, x, y, z
objref external_syn

//create soma, priden2[3], priden
create soma, priden2[1], priden

objref prilist

proc init() {
	npri = 1
	create priden2[npri]
	prilist = new SectionList()
	priden prilist.append()
	for i=0, npri-1 priden2[i] { prilist.append() }
topol()
geometry()
segments()
memb()
	x = y = z = 0 // only change via position
}


proc topol() {local i
	connect priden(0), soma(1)
	for i=0, npri-1 {connect priden2[i](0), priden(.8)}
}

proc segments() {local i
	soma.nseg= 1
	forsec "priden" nseg = 10
}

proc geometry() {local i
	basic_shape()
	soma { L = 8  diam = 8}
	priden {L=150 diam=.5}
	for i=0, npri-1 {priden2[i] {L=100 diam=.4}}
//	define_shape()
}
	
proc basic_shape() {local i
  soma {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(0, 1, 0, 1)}
  priden {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(0, 1, 0, 1)}
  for i=0,npri-1 {
	priden2[i] {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(i/npri, 1, 0, 1)}
  }
}

proc memb() {
	forall {
		insert pas 
		insert kamt gbar_kamt=0.008 ek=-90
		insert nax gbar_nax=0.02 sh_nax=15 ena=60
		Ra = 80
		cm = 1
		g_pas = 1/30000
		e_pas = -65
		ek = -90
	}

	soma {
		gbar_nax=0.04
       		insert kdrmt gbar_kdrmt=0.006
		gbar_kamt = 0.004
		cm = 4
		g_pas = cm/30000
	}

	forsec prilist {
		cm = 4
		g_pas = cm/30000
	}
	 soma {
                external_syn = new Exp2Syn(.5)
                external_syn.e=0
                external_syn.tau1 = 5
                external_syn.tau2 = 50  
            }
	
}

proc position() { local i
  soma for i = 0, n3d()-1 {
    pt3dchange(i, $1-x+x3d(i), $2-y+y3d(i), $3-z+z3d(i), diam3d(i))
  }
  x = $1  y = $2  z = $3
}

endtemplate Granule

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