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:

To run a simulation or visualize the results, the following files need
to be placed in the same directory of the main code:


They can be downloaded from:

-- 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

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 Mayavi installed.  To
visualize a version of Fig.7C of the paper including granule cells:


Questions and comments should be sent to