Olfactory bulb cluster formation (Migliore et al. 2010)

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Accession:127995
Functional roles of distributed synaptic clusters in the mitral-granule cell network of the olfactory bulb.
Reference:
1 . Migliore M, Hines M, McTavish TS, Shepherd GM (2010) Functional roles of distributed synaptic clusters in the mitral-granule cell network of the olfactory bulb Frontiers in Integrative Neuroscience 4:122 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Olfactory bulb;
Cell Type(s): Olfactory bulb main mitral cell; Olfactory bulb main interneuron granule MC cell;
Channel(s): I Na,t; I K;
Gap Junctions:
Receptor(s): AMPA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation; Short-term Synaptic Plasticity; 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 cell; Olfactory bulb main interneuron granule MC cell; AMPA; I Na,t; I K;
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migliore2010
README
ampanmda.mod
fi.mod
kamt.mod *
kdrmt.mod *
naxn.mod *
ThreshDetect.mod *
.hg_archival.txt
6.2.3.2203.spk
allsynhinton.hoc *
clear.hoc *
connect.hoc
granule.hoc
iterator.hoc
lptiter.hoc
mgrs.hoc
mitral.hoc
mosinit.hoc
net-5mt-100-900.hoc
odors.txt
parinit.hoc
pattern.hoc
perfrun.hoc
show.hoc
somesyn.hoc *
start.hoc
start.ses *
stim-odors-AB-seq.hoc
weight_movie.hoc *
weight-forfig3-bulb1.dat
weightsave.hoc
                            
An example of a parallel run is
  mpiexec -n 12 nrniv -mpi parinit.hoc
which takes about an hour and
creates a weight-forfig3-bulb1.dat file and an out12.dat file
(the number of processors is used to construct the spike output file name).
The former contains the synapse weights at time 59900.
The latter contains the spike time, gid pairs for granule and mitral soma
and all the reciprocal synapse spike detectors (two per synapse).
When a simulation is carried out using more than one processor, the out.dat
file should be sorted with (taking the above example)
sort -k 1n,1n -k 2n,2n out12.dat > out.spk

To explore the results of a simulation run, use
  nrngui start.hoc

Quantitative identity of the spike output and weight files can only be
obtained if one uses NEURON -- Release 6.2.3 (2203) 2008-08-28
http://www.neuron.yale.edu/ftp/neuron/versions/v6.2/ More recent
versions of NEURON will give very similar results but not quantitatively
identical due to differences in the delivery event times when events do
not occur on time step boundaries for the fixed step method. 
(Note that pattern.hoc has been modified to read the 6.2.3.2203.spk
instead of an out.spk file)

The mosinit.hoc file runs start.hoc and shows a hinton plot of the weights at
time 59900.

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