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Large scale model of the olfactory bulb (Yu et al., 2013)
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: Yu Y, McTavish TS, Valenti C, Hines ML, Shepherd GM, Migliore M (2013) Sparse distributed representation of odors in a large-scale olfactory bulb circuit PLoS Comput. Biol. 9(3):e1003014
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type:  Network; Channel; Dendrite;
Brain Region(s)/Organism:  Olfactory bulb;
Cell Type(s):  Olfactory bulb mitral cell; Olfactory bulb granule 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;
Implementer(s):  Hines, Michael [Michael.Hines at Yale.edu]; Migliore, Michele [Michele.Migliore at Yale.edu];
Search NeuronDB for information about:  Olfactory bulb mitral cell; Olfactory bulb granule 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
default.hoc
allsynhinton.hoc
granule.hoc
hinton.hoc
init.hoc
iterator.hoc
clear.hoc
lptiter.hoc
mgrs.hoc
michele_movie.hoc
mitral.hoc
mosinit.hoc
connect.hoc
net.hoc
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
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
viewspikes.hoc
viewspikes1.hoc
weightsave.hoc
weight_movie.hoc
antest.ses
subset_control.ses
control.ses
start.ses
odors.txt
odors-forsim500-kensaku.txt
.hg_archival.txt
lindgren.job
                            
A full HD movie showing the network activity during learning 
of odor k3-3 (an aliphatic ketone) can be downloaded from:

http://senselab.med.yale.edu/modeldb/data/odor39-full-HD.avi

The start.hoc file is used to analyze results of a parallel run.

An example of a parallel run on the Lindgen computer
http://www.pdc.kth.se/resources/computers/lindgren
is specified in lindgren.job

A parallel run produces one or more sorted spikeoutput files
called "spkxxx.dat". These files are filtered by spkdat2bin.hoc
into a single binras.dat binary file for fast loading by start.hoc.

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