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, Natschl├Ąger 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 ;
//moddir coba cuba cubadv
// Previous line is a directive to mos2nrn,
// which is called when this file is executed from a browser.
// It ensures compilation of mod files in coba, cuba, and cubadv.

// This variable controls reporting of results.
// mosinit==1 if the user executes mosinit.hoc, 
//   0 if the user executes any of the celltype/init.hoc files directly.
// If mosinit==1, the selected simulation runs in a "demo" mode,
//   periodically printing reports to the xterm, and updating a raster plot.
// If mosinit==0, the simulation runs in "industrial" mode, omitting periodic reports,
//   but writing final performance and spike time data to output files

mosinvl = 100
proc launch() {
	if ($2) {

// Create a panel that offers a menu of different kinds of simulations
{intrin = 1 netsim = 0}
xcheckbox("intrinsic cell behavior", &intrin, "intrin=1  netsim=0")
xcheckbox("network simulation", &netsim, "intrin=0 netsim=1")
xbutton("CobaHH", "mosinvl = 10 launch(\"cobahh\", intrin)")
xbutton("Coba", "mosinvl = 10 launch(\"coba\", intrin)")
xbutton("Cuba", "launch(\"cuba\", intrin)")
xbutton("CubaDV", "launch(\"cubadv\", intrin)")