Capabilities Frameworks API Dep. Platforms SBML Availabil.
     
ABC-SysBio Python F F
acslXtreme
ALC F F
AMICI MATLAB symbolic toolbox F F
AMIGO MATLAB MATLAB F
Antimony C, C++, Python F F
APMonitor MATLAB, Octave, Python Web Browser, Python, Octave, or MATLAB F F
Arcadia
Asmparts F F
Athena SBW, .NET F F
AutoSBW SBW SBW F F
AVIS F F
BALSA Sigtran
BASIS Web Services F F
BenTen F F
BetaWB F F
Bifurcation Discovery Tool SBW F F
BiGG F
BiNoM F F
BiNoM Cytoscape Plugin Cytoscape F F
Bio Sketch Pad BioCharon F F
BioBayes F F
BIOCHAM F F
BioCharon CHARON
BioCyc F
BioGRID
Biological Networks F
BioMet Toolbox F F
BioModels Database web services F F
BioModels Importer SBW, .NET F F
BioNessie F F
BioNetGen F F
BioPARKIN C++, Python F F
BioPathwise Java, MATLAB
BioPAX2SBML F F
BioRica F F
BioSens BioSPICE Dashboard F F
BioSPICE Dashboard Java F F
BioSpreadsheet BioSPICE Dashboard
BioSyS Java F F
BioTapestry F F
BioUML F F
BiVeS JAVA F F
BoolNet R F F
braincirc F F
BRENDA F
BSTLab MATLAB F F
ByoDyn Python, Web Services F F
CADLIVE C F F
Cain C++ F F
CARMEN Perl, CellDesigner F F
CBMPy Python, web services Python F F
Cell Collective coming in October, 2014 F
Cell Illustrator
CellDesigner Java F F
Cellerator Mathematica F
CellMC F F
CellML2SBML F F
CellNetAnalyzer MATLAB MATLAB F
CellNOpt R R (Python and Cytoscape are optional) F F
CellOrganizer Matlab Matlab F
Cellware F
CLEML F F
CL-SBML Common Lisp F F
COBRA MATLAB F F
CompuCell3D Python, C++ N/A F F
ConsensusPathDB F F
COPASI C++, Perl, R, Java, Octave, SBW, Python F F
CRdata R, REST, Web Services F F
CycSim Java, Web Services F
CySBML Java Cytoscape F F
Cytoscape Java F F
Cyto-Sim F F
DBSolve F F
DEDiscover Not really F F
Dizzy F F
DOTcvpSB MATLAB MATLAB F
D-VASim F F
E-CELL F F
ecellJ F F
EPE Java F F
EPISIM F F
ESS BioSPICE Dashboard F F
Facile F F
FAME F F
FASIMU Biological Network Analyzer, Cytoscape F F
FBASBW SBW SBW F F
FERN Java F F
FlexFlux GLPK or CPLEX F F
FluxBalance SBW SBW F F
Fluxor BioSPICE Dashboard F F
framed Python Python F F
GeNeDA F F
Genetdes F
Genetic Network Analyzer Java F
Gepasi F F
Gillespie2 C++, Python F F
GINsim Java, Python and Javascript engine F F
GNAT MATLAB MATLAB F
GNU MCSim F F
GRENDEL F F
HSMB BioCharon
HybridSBML BioCharon
iBioSim F F
IBRENA SBMLToolbox
Insilico Discovery
insilicoIDE Python F F
iPathways F F
iPathways+ F F
JACOBIAN F
Jacobian Viewer SBW SBW F F
Jarnac SBW SBW F F
JarnacLite SBW, .NET F F
JDesigner SBW SBW F F
JigCell F F
jNeuroML Java F F
JSBML Java F F
JSim Java, C, Fortran F F
JWS Online F F
Karyote* F F
KEGGconverter F
KEGGtranslator Java F F
KiMoSys F
Kineticon F F
Kinsolver Linux, Java Servlets F F
libAnnotationSBML Java F F
libRoadRunner C, C++, Python, Julia None F F
libSBML C, C++, .NET, Java, Python, Perl, Octave, Ruby, MATLAB, R F F
libSBMLSim C, C++, C#, Java, Python, Perl, Ruby F F
libStruct C, C++, .NET F F
MASS Toolbox Mathematica F F
MatCont MATLAB MATLAB F F
MathSBML MMA Mathematica F F
Medicel
MEMOSys F F
meneco Python, pyasp F
MesoRD F F
Meta-All Oracle F F
Metaboflux R, Python F F
MetaCrop F F
MetaFluxNet F
MetaNetX Internet connection F F
Metannogen network sockets F F
Metatool MATLAB, Octave MATLAB, Octave F
MetExplore F F
Metingear F F
MetNetMaker Microsoft Access 2007+ F F
MIRIAM Resources Web Services F F
MMT2
modelMaGe COPASI COPASI, python netoworkx package F F
ModeRator networkx, pylevenshtein, xlrd, matplotlib F F
Modesto F F
Moleculizer F F
MonaLisa F
Monod F F
Moose Python Users can operate Moose via GUI without any knowledge of Python. However advanced users can interact with Moose via the Python APIs F F
Morpheus F F
MoSeC F F
MuVal (Multi-valued logic) CellNetAnalyzer
Narrator F F
nemo F F
NetBuilder' F F
NetPath SPARQL F F
NetPro
Odefy MATLAB, Octave MATLAB, Octave F F
Omix Java
ONDEX Java, Web Services F F
optflux Java F F
Oscill8 F F
PANTHER Pathway F F
PathArt
PathSBML plugin for PathVisio F F
Pathway Access CellDesigner CellDesigner F F
Pathway Analyser F F
Pathway Builder BioSPICE Dashboard F F
Pathway Solver Pathway Studio F
Pathway Tools F
PathwayLab Microsoft Visio
PATIKAweb F
PaVESy
PAYAO CellDesigner F F
PET F F
PhysioLab Modeler
PINT F F
PK-Sim / MoBi MATLAB, R F
PNK SBW F F
PottersWheel MATLAB MATLAB F
precursor Python, pyasp F
PRISM F F
ProcessDB No. No.
ProMoT F F
PROTON Java, CORBA FastObjects F F
pybrn Python Python F F
PyDSTool Python F F
PyLESS F F
PySB Python BioNetGen F F
PySCeS Python, web services Python F F
RANGE R F F
RAVEN MATLAB, MOSEK F
Reactome F F
ReMatch F F
RMBNToolbox MATLAB F F
roadRunner SBW, .NET F F
RSBML R R F F
SABIO-RK Web Services F
Saint F F
SBFC Java, Web Services F F
SBML Harvester F F
SBML Layout .NET, SBW, Web Services F F
SBML Reaction Finder F F
SBML Translators SBW SBW F F
SBML2APM MATLAB, Python SBFC, JSBML F F
SBML2BioPax SBFC, BioPax F F
SBML2LaTeX Java, Web Services F F
SBML2NEURON NEURON F F
SBML2Octave Octave, MATLAB, SBFC F F
SBML2SMW Semantic, MediaWiki, CellDesigner F F
SBML2TikZ F F
SBML2XPP SBFC F F
SBMLEditor F F
SBML-PET-MPI F F
SBMLR
SBML-SAT MATLAB F F
SBML-shorthand Python F F
SBMLSim BioCharon, MATLAB F F
SBMLsqueezer Java, Web Services F F
sbmltidy F F
SBMLToolbox MATLAB, Octave MATLAB, Octave F F
SbmlViewer
SBMM assistant F
SBO Web Services F F
SBSI F F
SBtab python, MATLAB F F
SBToolbox2 MATLAB MATLAB, SBMLToolbox F F
sbtranslate F F
SBW C, C++, .NET, Java, Python, Web Services F F
SBW: Auto Layout SBW, .NET F F
sbw: javasim Java SBW F F
sbw: stochastic simulator SBW F F
SCIpath
SED-ML Web Tools F F
semanticSBML F F
SensA Python F F
SensSB MATLAB MATLAB F
SGMP F F
Sigmoid* F F
SIGNALIGN
SignaLink F
SigPath F F
SigTran
SIMBA MATLAB
SimBiology MATLAB MATLAB
SIMMUNE C++, Python F
Simpathica Octave F F
SimPheny*
SImpleSBML No Python F F
Simulate3D SBW, .NET F F
Simulation Tool .NET, SBW F F
SimWiz F F
SloppyCell Python Python F F
SmartCell F
Snoopy F F
SOSlib C SUNDIALS, optionally: XMgrace, GraphViz F F
SPDBS F F
SRS
STEPS Python F F
StochKit C++ F
StochPy Python Python F F
StochSim F F
STOCKS F F
SurreyFBA F F
SyBiL F F
SYCAMORE F F
SynBioSS F F
Systems Biology Simulation Core Library Java Java Virtual Machine F F
Systrip F F
TERANODE Suite
Tide Python F F
TinkerCell C, C++, Python, Octave F F
Trelis F F
UTKornTools BioSPICE Dashboard F F
VANTED Java F F
Virtual Cell Restful API, not yet publicly advertised none (java is bundled now) F F
Virtual Parts Repository Java F F
WebCell F F
WinSCAMP F F
Wolfram SystemModeler Mathematica
xCellerator Mathematica F F
Xholon F F
XPPAUT F F
This matrix was generated on 2017-05-07 (total number of tools: 290)