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<html><body><pre>
Model files for the paper
"Distributed organization of a brain microcircuit analysed by
three-dimensional modeling: the olfactory bulb" by Migliore M,
Cavarretta F, Hines ML, Shepherd, GM Frontiers in Computational
Neuroscience (2014), doi: 10.3389/fncom.2014.00050
A full HD version of movie 1 of the paper can be downloaded from:
<a href="http://senselab.med.yale.edu/modeldb/data/151681/movie1.mp4">http://senselab.med.yale.edu/modeldb/data/151681/movie1.mp4</a>
To run a simulation or visualize the results, the following files need
to be placed in the same directory of the main code:
fig7.weight.dat
c10.dic
mitral.dump
They can be downloaded from:
<a href="http://senselab.med.yale.edu/modeldb/data/151681/bulb3d-files.zip">http://senselab.med.yale.edu/modeldb/data/151681/bulb3d-files.zip</a>
-- simulation--
The simulation requires NEURON 7.3 with python.
After compilation of the mod files the simulation can be run with a
script and a command line that depends on your parallel computer
system. For an IBM BlueGene/Q, such as the FERMI system at CINECA
(Bologna, Italy), the command line was
runjob --ranks-per-node 16 --exe powerpc64/special --args -mpi --args
-python --args customsim.py
Using 2048 processes the simulation takes about 10 hours.
The final weight files need to be compacted with
cat fig7.weight.dat.* > fig7.weight.dat
-- visualization --
The visualization requires the Enthought.com Mayavi installed. To
visualize a version of Fig.7C of the paper including granule cells:
mayavi2 mayasyn.py
Questions and comments should be sent to francesco.cavarretta@unimi.it
</pre></body></html>