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;
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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
                            
// show the stimulus
load_file("start.hoc")

// fake mitral with a synodor to allow OBStim to work
begintemplate FakeMitral
public soma, synodor, external_syn
create soma
objref synodor, external_syn
proc init() {
	soma synodor = new Exp2Syn(.2)
	soma external_syn = new Exp2Syn(.2)
	synodor.e = 0
	synodor.tau1 = 20
	synodor.tau2 = 200
}
endtemplate FakeMitral


proc showstim() {local i, mgid, act  localobj nc, cell, nil, st, exist, smag
	exist = new Vector()
	smag = new Vector()
	stim_list_.remove_all()
	mt_noise_stim_list_.remove_all()
	gc_noise_stim_list_.remove_all()
	create_stim()

	for i = 0,  stim_list_.count-1 if (stim_list_.o(i).ww) {
		exist.append(i)
		smag.append(stim_list_.o(i).ww)
	}

	printf("mitral gids with odor stimuli\n")
	for i=1, 4 {
		printf("magnitude %d\n", i)
		exist.c.index(exist, smag.c.indvwhere("==", i)).printf
	}

	mgid = exist.x[0]
	pc.set_gid2node(mgid, 0)
	cell = new FakeMitral()
	cell.soma nc = new NetCon(&v(.5), nil)
	pc.cell(mgid, nc)
	create_stim()
	st = stim_list_.o(mgid)
	act = cvode_active()
	cvode_active(1)
	run()
	printf("odor event times\n")
	st.spktime.printf
	cvode_active(act)
	clear()
}

showstim()

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