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

 Download zip file   Auto-launch 
Help downloading and running models
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
                            
{load_file("default.hoc")}

//network size parameters
default_var("len", 5000)  //5000um, size of the linear domain, mitral positions range from 0 to len
default_var("Lsec", 1500) // mitral dendrite secden length
default_var("ngranule", 10000) // 10000 granual cell,distributed uniformly over the linear domain
default_var("nmitral", 500) //  500 mitral cell,distributed uniformly over the linear domain
default_var("ring", 1)  // 1 - wraparound of mitral cells lateral dendrites

// connection parameters
default_var("g2m_mean", 0.1)
default_var("g2m_var" , 0.05)
default_var("g2m_ranseed", 1)
default_var("g2m_priden_seed_offset", 1000) // 0 means all at 0.5

// Simulation vars
default_var("net_idx", 0)  // ID of a trained network from a particular odor
default_var("odor_idx", 0) // ID of odor to use for stimulation
default_var("odor_mix", 0) // Odor mixture flag
default_var("stop_time", 10000) // tstop

// plasticity
/*
default_var("ltdinvl", 1)
ltdinvl_AmpaNmda=ltdinvl
ltpinvl_AmpaNmda=ltdinvl
ltdinvl_FastInhib=ltdinvl
ltpinvl_FastInhib=ltdinvl
*/

default_var("global_exc_gmax", 0.5)
default_var("global_inh_gmax", .003)
default_var("global_fi_tau1", 1)
default_var("global_fi_tau2", 100)

// odor parameters
default_str("odorstr","o26")
default_var("owfactor", 1e-3)
default_var("global_wl", .08)
default_var("global_wh", .12)
default_var("global_stod", 2)
default_var("global_endod", 10000)
default_var("global_si", 1)

// administrative
default_var("checkpoint_interval", 2000) //interval for spike output
default_var("n_spkout_files", 16) // number of spkxxx.dat file to write
default_var("n_spkout_sort", 16) // number of ranks used to sort files

Loading data, please wait...