Model and simulation files for the paper "Synaptic clusters function as odor
operators in the olfactory bulb", by Michele Migliore,
Francesco Cavarretta, Addolorata Marasco, Eleonora Tulumello, Michael
L. Hines, and Gordon M. Shepherd, PNAS in press (2015)

A full HD version movie of Fig.2 can be downloaded from:
To run a simulation or visualize the results, the first step
is to create the gid dictionary by executing

nrniv -python

It generates the file g37.dic, that must be placed
in the simulation working directory.

-- simulation--
The simulation requires NEURON 7.3 or above with python.

After compilation of the mod files the simulation can be run with a
script and a command line that depends on the parallel computer
system.  For an IBM BlueGene/Q, such as the FERMI system at CINECA
(Bologna, Italy), the command line is

runjob --ranks-per-node 16 --exe powerpc64/special --args -mpi --args 
-python --args

Using 1024 processes the simulation takes less than 30 minutes.
The final weight and spike time files need to be compacted with

./ g37e1i002

It generates two output files, g37e1i002.weight.dat and g37e1i002.spk
that are used by the visualization tool.
-- visualization --

The visualization requires the Mayavi installed.  To
visualize a version of Fig.1E of the paper including granule cells:

mayavi2 -dict g37.dic -weights g37e1i002.weight.dat -gweight -hist g37e1i002.spk

Questions and comments should be sent to