Model and simulation files for the paper

Parallel odor processing by mitral and middle tufted cells in the olfactory bulb

by Francesco Cavarretta, Shawn D. Burton, Kei M. Igarashi, Michael L. Hines, 
Gordon M. Shepherd, Michele Migliore,
Nature Scientific Reports (2018)


The model is organized in two directories that are named sim and vis.
They contain the simulation and the visualization software tools, respectively.

simulation

The simulation requires NEURON 7.5 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, the command line is

mpirun nrniv -mpi -python bulb3dtest.py

The final connectivity, synaptic weight, and spike time files need to be compacted with

./catfiles.sh bulb3dtest

It thus generates three output files, bulb3dtest.dic, bulb3dtest.weight.dat, and bulb3dtest.spk2
that are used by the visualization tool.
    

visualization

The visualization requires the Enthought.com Mayavi installed. 

To initialize the visualization software tool, one must generate the mitral and middle tufted cell morphology archive
by running the following command

nrniv cellwriter.py

This python module is located in sim. This command needs to be executed only once.

To visualize the simulated data (likewise in Figure 1C), run the visualization software tools located in vis:

mayavi2 bulbgui.py -prefix bulb3dtest

Questions and comments should be sent to francescocavarretta@hotmail.it.