Table 1.

List of simulation tools and model repositories.

Tool/Repository	Website	References
SIMULATION TOOL
Brian	http://brian2.readthedocs.io/en/stable/index.html	Goodman and Brette, 2008
Copasi	http://copasi.org/	Hoops et al., 2006
Cortex3D	https://www.ini.uzh.ch/~amw/seco/cx3d/	Zubler and Douglas, 2009
Dizzy	http://magnet.systemsbiology.net/software/Dizzy/	Ramsey et al., 2005
GENESIS/ Kinetikit	http://genesis-sim.org/, https://www.ncbs.res.in/faculty/bhalla-kinetikit	Wilson et al., 1989; Bower and Beeman, 1998; Bhalla and Iyengar, 1999; Bhalla, 2001, 2002
Gepasi	http://www.gepasi.org/	Mendes, 1993, 1997; Mendes and Kell, 1998
Jarnac/JDesigner	http://jdesigner.sourceforge.net/	Sauro, 2000, 2001
Narrator	https://omictools.com/narrator-tool	Mandel et al., 2007
NEST	http://www.nest-simulator.org/	Eppler et al., 2015
NETMORPH	http://www.netmorph.org/Home, http://www.scholarpedia.org/article/NETMORPH	Koene et al., 2009
NEURON	https://www.neuron.yale.edu/neuron/	Carnevale and Hines, 2006
PyNN	http://neuralensemble.org/PyNN/	Davison et al., 2009
SimTool	Request from the author	Aho, 2003
Systems Biology Toolbox	http://www.sbtoolbox.org/	Schmidt and Jirstrand, 2006
XPPAUT	http://www.math.pitt.edu/~bard/xpp/xpp.html	Ermentrout, 2002
MODEL REPOSITORY
DOQCS	http://doqcs.ncbs.res.in/	Sivakumaran et al., 2003
DRYAD	http://datadryad.org/
ModelDB	http://senselab.med.yale.edu/modeldb/	Migliore et al., 2003; Hines et al., 2004

This table lists the names of the simulation tools and model repositories as well as their websites and references.