BioNetGen 2.1.5
Cain 1.5
CellDesigner 4.1 (including plugin SBMLsqueezer 1.3)
COPASI 4.5.30 with java and python bindings
Cytoscape 2.8.1 (including plugin BiNoM 1)
Edinburgh Pathway Editor 3.0.0
Ekee 2.0.2
ISATools 1.3
JSim 1.6.98
libSBML 3.4.1 (with java, python, matlab bindings)
libSBML 4.1.0 (with java, python, matlab bindings, in /opt/lib/)
modelMage 1.0beta
OpenAlea/VPlants/Alinea 0.9
Protege 4.1-beta.213
RuleBuilder 1.51
SBML2LaTeX 0.9.8
SBML-PET-MPI 1.1 (also in a singlecore version)
SBMLeditor 1.3.4
SystemsBiologyWorkbench 2.8.1
SQuad 2
semanticSBML 1.0.11
STSE 20110222svn
Taverna Workbench 2.2.0
vanted 1.9
vcell 4.8beta
vmd 1.8.7
TiDE 1.2.1
Xppaut 6.0