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BulbSurf.py
BulbSurf.py
 
 
ThreshDetect.mod
ThreshDetect.mod
 
 
all2all.py
all2all.py
 
 
ampanmda.mod
ampanmda.mod
 
 
balance.py
balance.py
 
 
bindict.py
bindict.py
 
 
colors.py
colors.py
 
 
common.py
common.py
 
 
complexity.py
complexity.py
 
 
custom_params.py
custom_params.py
 
 
customsim.py
customsim.py
 
 
destroy_model.py
destroy_model.py
 
 
determine_connections.py
determine_connections.py
 
 
distribute.py
distribute.py
 
 
distrt.mod
distrt.mod
 
 
fi.mod
fi.mod
 
 
fig7.py
fig7.py
 
 
fixnseg.hoc
fixnseg.hoc
 
 
getmitral.py
getmitral.py
 
 
gidfunc.py
gidfunc.py
 
 
glom.py
glom.py
 
 
granule.hoc
granule.hoc
 
 
granules.py
granules.py
 
 
input-odors.txt
input-odors.txt
 
 
kamt.mod
kamt.mod
 
 
kdrmt.mod
kdrmt.mod
 
 
loadbalutil.py
loadbalutil.py
 
 
lpt.py
lpt.py
 
 
mayasyn.py
mayasyn.py
 
 
mgrs.py
mgrs.py
 
 
misc.py
misc.py
 
 
mitral.hoc
mitral.hoc
 
 
mitral_dend_density.py
mitral_dend_density.py
 
 
mkmitral.py
mkmitral.py
 
 
modeldata.py
modeldata.py
 
 
multisplit_distrib.py
multisplit_distrib.py
 
 
naxn.mod
naxn.mod
 
 
net_mitral_centric.py
net_mitral_centric.py
 
 
odordisp.py
odordisp.py
 
 
odors.py
odors.py
 
 
odorstim.py
odorstim.py
 
 
params.py
params.py
 
 
parrun.py
parrun.py
 
 
readme.html
readme.html
 
 
realgloms.txt
realgloms.txt
 
 
runsim.py
runsim.py
 
 
split.py
split.py
 
 
util.py
util.py
 
 
weightsave.py
weightsave.py
 
 

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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>

About

3D model of the olfactory bulb (Migliore et al. 2014)

modeldb.science/151681

Topics

neuron-simulator olfactory-bulb-main-mitral-glu-cell-olfactory-bulb pattern-recognition-activity-patterns-bursting-tem

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