Networks of spiking neurons: a review of tools and strategies (Brette et al. 2007)

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This package provides a series of codes that simulate networks of spiking neurons (excitatory and inhibitory, integrate-and-fire or Hodgkin-Huxley type, current-based or conductance-based synapses; some of them are event-based). The same networks are implemented in different simulators (NEURON, GENESIS, NEST, NCS, CSIM, XPP, SPLIT, MVAspike; there is also a couple of implementations in SciLab and C++). The codes included in this package are benchmark simulations; see the associated review paper (Brette et al. 2007). The main goal is to provide a series of benchmark simulations of networks of spiking neurons, and demonstrate how these are implemented in the different simulators overviewed in the paper. See also details in the enclosed file Appendix2.pdf, which describes these different benchmarks. Some of these benchmarks were based on the Vogels-Abbott model (Vogels TP and Abbott LF 2005).
1 . Vogels TP, Abbott LF (2005) Signal propagation and logic gating in networks of integrate-and-fire neurons. J Neurosci 25:10786-95 [PubMed]
2 . Brette R, Rudolph M, Carnevale T, Hines M, Beeman D, Bower JM, Diesmann M, Morrison A, Goodman PH, Harris FC, Zirpe M, Natschläger T, Pecevski D, Ermentrout B, Djurfeldt M, Lansner A, Rochel O, Vieville T, Muller E, Davison AP, El Boustani S, Destexhe A (2007) Simulation of networks of spiking neurons: a review of tools and strategies. J Comput Neurosci 23:349-98 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s): Abstract integrate-and-fire leaky neuron;
Gap Junctions:
Simulation Environment: NEURON; GENESIS; NEST; C or C++ program; XPP; CSIM; NCS; SPLIT; MVASpike; SciLab; Brian; PyNN; Python;
Model Concept(s): Activity Patterns; Methods;
Implementer(s): Carnevale, Ted [Ted.Carnevale at]; Hines, Michael [Michael.Hines at]; Davison, Andrew [Andrew.Davison at]; Destexhe, Alain [Destexhe at]; Ermentrout, Bard []; Brette R; Bower, James; Beeman, Dave; Diesmann M; Morrison A ; Goodman PH; Harris Jr, FC; Zirpe M ; Natschlager T ; Pecevski D ; Djurfeldt M; Lansner, Anders [ala at]; Rochel O ; Vieville T ; Muller E ; El Boustani, Sami [elboustani at]; Rudolph M ;
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ù	ø	°	e	!	Û•gf\[ÕœuTed Carnevalecoba model changed to corimplemetation of the coba model (see coba/cobacell.hoc).NEURON implemetation of the coba model (see coba/cobacell.hoc).20110805 Ted Carnevale corrected the synaptic time constants for the REVISIONSCambridge: Cambridge University Press, 2006).and chapters 5, 6, and 9-13 of The NEURON Book (Carnevale and Hines, Reference ( and usage of hoc and NMODL are detailed in the Programmer's aid those who wish to pursue the implementational strategy more closely.  Comments have been inserted into the source code at selected points to cuba, and cubadv.specific code has been factored into directores called coba, cobahh, cells, and how these cells are affected by synaptic inputs.  Cell-The models differ with respect to the properties of their constituent directory.shared across the models; it too has been placed in the common results and gathers and reports performance information, is also common.  The "instrumentation code," which displays simulation code that sets this up has been factored into a directory called All four benchmark models have the same network structure, so the PROGRAM IMPLEMENTATION NOTESunder MPI.individual single processor machines, or on parallel cluster machines The network simulations are ready to run, without modification, on Performance information is appended to the perf.dat file.    nrngui ../common/spkplt.hocThe latter will produce an out.dat file which can be viewed with    nrngui init.hocand to run the network simulation use    nrngui intrinsic.hocthe intrinsic cell properties, use(after linking the model specific mod file). In that case, to view Alternatively, each model can be run from within its subdirectory     nrngui mosinit.hoc    nrnivmodl coba cuba cubadvin the directory containing the mosinit.hoc file runTo manually run from the mosinit.hoc file under Linux or Mac OS X,Autolaunching requires version 5.9.30 or higher.a review of tools and strategies.Simulation of networks of spiking neurons: of the NEURON benchmark models for Brette et al (2006) DESCRIPTION AND USAGE NOTES