DESCRIPTION AND USAGE NOTES
of the NEURON benchmark models for Brette et al (2006)
Simulation of networks of spiking neurons:
a review of tools and strategies.
Autolaunching requires version 5.9.30 or higher.
To manually run from the mosinit.hoc file under Linux or Mac OS X,
in the directory containing the mosinit.hoc file run
nrnivmodl coba cuba cubadv
Alternatively, each model can be run from within its subdirectory
(after linking the model specific mod file). In that case, to view
the intrinsic cell properties, use
and to run the network simulation use
The latter will produce an out.dat file which can be viewed with
Performance information is appended to the perf.dat file.
The network simulations are ready to run, without modification, on
individual single processor machines, or on parallel cluster machines
PROGRAM IMPLEMENTATION NOTES
All four benchmark models have the same network structure, so the
code that sets this up has been factored into a directory called
common. The "instrumentation code," which displays simulation
results and gathers and reports performance information, is also
shared across the models; it too has been placed in the common
The models differ with respect to the properties of their constituent
cells, and how these cells are affected by synaptic inputs. Cell-
specific code has been factored into directores called coba, cobahh,
cuba, and cubadv.
Comments have been inserted into the source code at selected points to
aid those who wish to pursue the implementational strategy more closely.
Syntax and usage of hoc and NMODL are detailed in the Programmer's
and chapters 5, 6, and 9-13 of The NEURON Book (Carnevale and Hines,
Cambridge: Cambridge University Press, 2006).
20110805 Ted Carnevale corrected the synaptic time constants for the
NEURON implemetation of the coba model (see coba/cobacell.hoc).