SBML Software Matrix
This matrix provides an at-a-glance summary of software known to us to provide some degree of support for reading, writing, or otherwise working with SBML. The columns' meanings are explained below. For a list of longer descriptions grouped into themes, please see our SBML Software Summary page.
| Capabilities | Frameworks | API | Dep. | Platforms | SBML | Availabil. | ||||||||||||||
| acslXtreme | • | W | • | $ | $ | |||||||||||||||
| ALC | • | • | • | • | • | L, W, M, B | • | • | F | F | ||||||||||
| Asmparts | • | • | • | L, W | • | • | • | F | F | |||||||||||
| Antimony | • | • | C, C++ | L, W, M | • | • | • | F | F | |||||||||||
| AutoSBW | • | • | SBW | SBW | L, W, M | • | • | • | F | F | ||||||||||
| AVIS | • | various | L | • | • | F | F | |||||||||||||
| BALSA | • | Sigtran | ||||||||||||||||||
| BASIS | • | • | • | • | • | WS | B | • | • | • | F | F | ||||||||
| BetaWB | • | • | • | • | • | L, W, M | • | F | F | |||||||||||
| BiGG | • | B | • | F | ||||||||||||||||
| BiNoM | • | • | • | • | L, W, M | • | • | • | F | F | ||||||||||
| BiNoM Cytoscape Plugin | • | • | • | • | Cytoscape | L, W, M | • | • | • | F | F | |||||||||
| BIOCHAM | • | • | • | L, W, M | • | • | F | F | ||||||||||||
| BioCharon | • | • | • | • | • | CHARON | ||||||||||||||
| Biological Networks | • | • | • | L, W, M | • | • | F | $ | ||||||||||||
| BioCyc | • | • | F | $ | ||||||||||||||||
| BioGrid | ||||||||||||||||||||
| BioMet Toolbox | • | • | W | • | F | F | ||||||||||||||
| BioModels Database | • | • | • | WS | B | • | • | • | F | F | ||||||||||
| BioModels Importer | • | SBW | SBW | L, W, M | • | • | F | F | ||||||||||||
| BioNessie | • | • | • | • | • | • | L, W, M | • | • | F | F | |||||||||
| BioNetGen | • | • | • | • | • | • | L, W, M | • | • | F | F | |||||||||
| BioPathwise | • | • | • | • | • | • | • | • | • | Java, MatLab | L, W, M,B | • | $ | $ | ||||||
| BioRica | • | • | • | • | • | • | • | • | L,M | • | F | F | ||||||||
| Bio Sketch Pad | • | BioCharon | F | F | ||||||||||||||||
| BioSens | • | • | BSP | L, W | • | F | F | |||||||||||||
| BioSPICE Dashboard | • | • | • | • | • | • | • | L, W, M | ||||||||||||
| BioSpreadsheet | • | BSP | • | • | ||||||||||||||||
| BioTapestry | • | • | • | L, W, M | • | • | F | F | ||||||||||||
| BioUML | • | • | • | • | • | L, W, M | • | • | F | F | ||||||||||
| braincirc | • | • | • | • | • | • | • | • | L | • | • | F | F | |||||||
| BSTLab | MATLAB | • | F | F | ||||||||||||||||
| ByoDyn | • | • | • | • | • | • | • | • | • | • | Python,WS | L, M, B | • | • | F | F | ||||
| CADLIVE | • | • | • | • | .NET | W | • | • | F | F | ||||||||||
| Cain | • | • | • | • | • | • | C++ | L, W, M | • | • | • | F | F | |||||||
| CARMEN | • | • | Perl | L, W, M | • | • | • | F | F | |||||||||||
| CellDesigner | • | • | • | • | • | • | • | • | Java | L, W, M | • | • | • | F | F | |||||
| Cellerator | • | • | • | MMA | L, W, M | • | • | F | $ | |||||||||||
| Cell Illustrator | • | • | • | L, W, M | • | $ | $ | |||||||||||||
| CellMC | • | L,M | • | • | F | F | ||||||||||||||
| CellML2SBML | • | L, W | • | • | F | F | ||||||||||||||
| CellNetAnalyzer | • | • | • | MATLAB | MATLAB | L, W, M | • | • | F | $ | ||||||||||
| Cellware | • | • | • | L, W, M | • | • | F | $ | ||||||||||||
| CL-SBML | • | • | LISP | LISP | L | • | • | F | F | |||||||||||
| CLEML | • | L, W | • | • | F | F | ||||||||||||||
| COBRA | • | • | • | • | MATLAB | L, W, M | • | • | • | F | F | |||||||||
| CompuCell3D | • | • | • | • | Python, C++ | L, W, M | • | F | F | |||||||||||
| ConsensusPathDB | • | B | • | • | • | F | F | |||||||||||||
| COPASI | • | • | • | • | • | • | C++, Java, Python,SBW | L, W, M | • | • | • | F | $ | |||||||
| Cyto-Sim | • | • | • | L, W, M | F | F | ||||||||||||||
| Cytoscape | • | • | Java | L, W, M | • | • | F | F | ||||||||||||
| CycSim | • | • | • | • | • | Java, WS | B | • | • | F | $ | |||||||||
| DBSolve | • | • | • | • | • | • | F | F | ||||||||||||
| Dizzy | • | • | • | L, W, M | • | • | • | F | F | |||||||||||
| DOTcvpSB | • | • | • | • | MatLab | MatLab | L, W, M | • | F | $ | ||||||||||
| E-CELL | • | • | • | • | L, W | • | • | F | F | |||||||||||
| ecellJ | • | • | F | F | ||||||||||||||||
| EPE | • | • | • | Java | L, W, M | • | F | F | ||||||||||||
| ESS | • | • | BSP | • | F | F | ||||||||||||||
| FBASW | • | • | SBW | SBW | L, W, M | • | • | F | F | |||||||||||
| FERN | • | • | • | • | • | Java | L, W, M | • | • | • | F | F | ||||||||
| Fluxor | • | BSP | L | • | F | F | ||||||||||||||
| Genetdes | • | • | • | L | • | • | • | F | $ | |||||||||||
| Gepasi | • | • | • | • | • | L, W | • | • | F | F | ||||||||||
| Gillespie2 | • | • | C++, Python | L, W, M | • | F | F | |||||||||||||
| GNA | • | • | • | • | • | • | • | L, W, M | • | • | F | $ | ||||||||
| GNU McSim | • | • | • | • | • | • | L, W, M | • | • | F | F | |||||||||
| GRENDEL | • | • | • | • | • | L | • | • | F | F | ||||||||||
| HSMB | • | BioCharon | • | • | ||||||||||||||||
| HybridSBML | • | • | BioCharon | |||||||||||||||||
| iBioSim | • | • | • | • | • | • | • | • | L, W, M | • | • | F | F | |||||||
| Insilico Discovery | • | • | • | • | • | • | • | L, W, M | • | • | $ | $ | ||||||||
| JACOBIAN | • | • | • | F | $ | |||||||||||||||
| Jacobian Viewer | • | • | SBW | SBW | L, W, M | • | • | F | F | |||||||||||
| Jarnac | • | • | • | • | • | • | SBW | SBW | W | • | • | • | F | F | ||||||
| JDesigner | • | • | • | • | SBW | SBW | W | • | • | • | F | F | ||||||||
| JigCell | • | • | XPP | L,M | • | • | F | F | ||||||||||||
| JSim | • | • | • | • | • | • | • | • | • | • | Java, C | L, W, M | • | • | F | F | ||||
| JWS Online | • | • | • | • | • | • | • | • | • | B | • | • | F | F | ||||||
| Karyote* | • | B | F | F | ||||||||||||||||
| KeggConverter | • | L, W, B | • | • | F | F | ||||||||||||||
| KEGG2SBML | • | L, W, M | • | • | F | $ | ||||||||||||||
| Kineticon | • | B | • | F | F | |||||||||||||||
| Kinsolver* | • | • | B | • | • | |||||||||||||||
| libSBML | (many) | L, W, M | • | • | • | F | F | |||||||||||||
| libAnnotationSBML | • | Java | L, W, M | • | • | • | F | F | ||||||||||||
| libStruct | • | • | (C/C++/C#) | LAPACK | L, W, M | • | • | F | F | |||||||||||
| MathSBML | • | • | • | • | • | MMA | MMA | L, W, M | • | • | • | F | F | |||||||
| Medicel | • | • | $ | $ | ||||||||||||||||
| MesoRD | • | • | • | • | L, W, M | • | • | F | F | |||||||||||
| Meta-All | • | • | Oracle | L, W, M | • | F | F | |||||||||||||
| Metatool | • | • | MATLAB, Octave | MATLAB or Octave | L, W, M | • | F | $ | ||||||||||||
| MetaFluxNet | • | • | • | .NET | W | F | $ | |||||||||||||
| MetExplore | • | • | • | W | • | F | F | |||||||||||||
| MetNetMaker | • | • | • | MS Access | W | • | • | F | F | |||||||||||
| MIRIAM Resources | • | • | WS | B | • | F | F | |||||||||||||
| MMT2 | • | • | • | • | L | • | ||||||||||||||
| modelMaGe | • | • | • | • | • | • | • | • | WS | Python, COPASI | L, W, M | • | • | • | F | F | ||||
| Modesto | • | • | • | L | • | F | F | |||||||||||||
| Moleculizer | • | • | L | • | F | F | ||||||||||||||
| Monod | • | • | L,M | • | F | F | ||||||||||||||
| MOOSE | • | • | • | • | • | • | • | • | C++, Python | Python, Genesis | L, W, M, S | • | • | • | F | F | ||||
| Narrator | • | • | • | L, W, M | • | • | • | F | F | |||||||||||
| NetBuilder' | • | • | • | • | • | • | Python | L, W, M | • | • | F | F | ||||||||
| NetPath | • | SPARQL | B | • | • | F | F | |||||||||||||
| NetPro | • | $ | $ | |||||||||||||||||
| OptFlux | • | • | • | L, W | L, W, M | • | • | F | F | |||||||||||
| Oscill8 | • | • | • | W | • | F | F | |||||||||||||
| PANTHER Pathway | • | L, W, M | • | F | F | |||||||||||||||
| PathArt | • | • | $ | $ | ||||||||||||||||
| Pathway Analyser | • | L | • | • | F | F | ||||||||||||||
| PathwayLab | • | • | • | • | MATLAB, MMA | Visio | W | • | $ | $ | ||||||||||
| Pathway Tools | • | • | • | F | $ | |||||||||||||||
| Pathway Builder | • | BSP | L, W, M | • | • | F | F | |||||||||||||
| PATIKAweb | • | • | B | • | • | F | $ | |||||||||||||
| PaVESy | • | • | L, W, M | |||||||||||||||||
| PAYAO | • | • | W | • | • | |||||||||||||||
| PET | • | • | • | • | • | Perl | L, W | • | F | F | ||||||||||
| PhysioLab Modeler | • | • | • | • | ||||||||||||||||
| PK-Sim | • | • | • | • | • | • | • | R, MatLab | L, W | • | F | $ | ||||||||
| PNK | • | • | • | SBW | L, W, M | • | • | • | F | F | ||||||||||
| PottersWheel | • | • | • | • | • | • | • | • | MATLAB | MATLAB | L, W, M | • | • | F | $ | |||||
| PRISM | • | • | • | L, W, M | • | F | F | |||||||||||||
| ProcessDB | • | • | ? | ? | ||||||||||||||||
| ProMoT | • | • | • | • | • | • | • | L, W | • | • | • | F | F | |||||||
| PROTON | • | • | • | • | • | • | • | • | Java, CORBA | J2SDK, FastObjects | L, W, M (Client), W (Server) | • | • | F | F | |||||
| pysbml | • | • | Python | Python | L | • | • | • | F | F | ||||||||||
| PySCeS | • | • | • | • | • | • | Python | Python | L, W, M | • | • | • | F | F | ||||||
| RANGE | • | • | R | L | • | • | F | F | ||||||||||||
| Reactome | • | B | • | F | F | |||||||||||||||
| ReMatch | • | • | • | B | • | • | F | F | ||||||||||||
| RMBNToolbox | • | • | MATLAB | L, W, M | • | F | F | |||||||||||||
| roadRunner | • | • | • | • | • | • | SBW | L, W, M | • | • | F | F | ||||||||
| RSBML | • | • | R | R | L, W, M | • | • | F | F | |||||||||||
| Pathway Solver | • | • | • | • | Pathway Studio | • | F | $ | ||||||||||||
| SABIO-RK | • | B | • | F | $ | |||||||||||||||
| SAINT | • | • | B | • | • | • | F | F | ||||||||||||
| SBML ODE Solver | • | • | C | L, W, M | • | • | • | F | F | |||||||||||
| SBML-PET | • | • | • | L, W | • | • | F | F | ||||||||||||
| SBML2LaTeX | • | • | • | • | • | WS | L, W, M, B | • | • | F | F | |||||||||
| SBMLeditor | • | L, W, M | • | • | • | F | F | |||||||||||||
| SBMLR | • | • | R | R | L, W, M | • | • | • | F | F | ||||||||||
| SBML-SAT | • | • | • | • | MATLAB | L, W, M | • | F | F | |||||||||||
| SBMLSim | • | • | • | BioCharon | F | F | ||||||||||||||
| SBMLsqueezer | • | • | • | Java | CellDesigner | L, W, M | • | • | • | F | F | |||||||||
| sbmltidy | • | tidy | L, W, M | • | • | • | F | F | ||||||||||||
| SBMLToolbox | • | • | • | • | MATLAB | MATLAB | L, W | • | • | • | F | F | ||||||||
| SBML Translators | • | • | SBW | SBW | L, W, M | • | • | F | F | |||||||||||
| SBMM assistant | • | • | B | • | ||||||||||||||||
| SBO | • | WS | B | • | • | F | F | |||||||||||||
| SBSI | • | • | • | • | L, W, M | • | • | • | F | F | ||||||||||
| SBToolbox2 | • | • | • | • | • | MATLAB | MATLAB, SBML Toolbox | L, W, M | • | • | • | F | F | |||||||
| SBW | • | • | • | • | • | • | • | L, W, M | • | • | • | F | F | |||||||
| sbw: auto layout | • | • | SBW | L, W, M | • | • | • | F | F | |||||||||||
| sbw: bifurcation discovery | • | • | SBW | L, W, M | • | • | • | F | F | |||||||||||
| sbw: javasim | • | • | • | • | • | SBW, JDK | L, W, M | • | • | • | F | F | ||||||||
| sbw: stochastic simulator | • | • | • | SBW | L, W, M | • | • | • | F | F | ||||||||||
| SCIpath | • | • | L, W, M | • | • | |||||||||||||||
| semanticSBML | • | • | Python | L, W, M | • | • | • | F | F | |||||||||||
| Sigmoid* | • | • | • | • | L, W, M | • | • | F | F | |||||||||||
| SIGNALIGN | • | • | B | • | ||||||||||||||||
| SigPath | • | • | L | • | F | F | ||||||||||||||
| SigTran | ||||||||||||||||||||
| SIMBA | • | MATLAB | W | $ | $ | |||||||||||||||
| SimBiology | • | • | • | MATLAB | L, W, M | • | • | $ | $ | |||||||||||
| Simpathica | • | • | • | Octave | L, W | • | F | F | ||||||||||||
| SimPheny* | • | • | • | $ | $ | |||||||||||||||
| Simulate3D | • | • | • | • | • | SBW, .NET | W | • | • | $ | $ | |||||||||
| SimWiz | • | L, W | • | • | F | F | ||||||||||||||
| SloppyCell | • | • | • | • | Python | L, W, M | • | • | • | F | F | |||||||||
| SmartCell | • | • | • | L, W, M | • | • | F | $ | ||||||||||||
| SRS Pathway Editor | • | L | $ | $ | ||||||||||||||||
| StochSim | • | • | L, W, M | • | • | • | F | F | ||||||||||||
| StochKit | • | • | C++ | L | • | • | F | $ | ||||||||||||
| STOCKS | • | • | • | L, W | • | F | F | |||||||||||||
| Sycamore | • | • | • | • | • | • | B | • | • | F | F | |||||||||
| SynBioSS | • | • | • | • | • | • | • | • | L, W, M | • | • | • | F | F | ||||||
| TERANODE Suite | • | • | • | L, W, M | • | • | $ | $ | ||||||||||||
| Tide | • | • | • | • | Python | L, W, M | • | • | F | F | ||||||||||
| TinkerCell | • | • | • | • | • | • | C, C++, Python | L, W, M | • | • | • | F | F | |||||||
| Trelis | • | • | W | • | F | F | ||||||||||||||
| UTKornTools | • | • | BSP | • | F | F | ||||||||||||||
| VANTED | • | L, W, M | • | • | F | F | ||||||||||||||
| Vcell | • | • | • | • | • | • | • | • | • | L, W, M | • | • | • | F | F | |||||
| WebCell | • | • | • | L, W, M | • | • | F | F | ||||||||||||
| WinSCAMP | • | • | • | W | • | F | F | |||||||||||||
| xCellerator | • | • | • | MMA | L, W, M | • | • | • | F | F | ||||||||||
| Xholon | • | • | • | L, W | • | F | F | |||||||||||||
| XPPAUT | • | • | • | L, W, M | • | • | F | F | ||||||||||||
| This matrix was generated on 2010-08-20 (total number of tools:188) | ||||||||||||||||||||
The columns of this table should be read in the following way:
- Capabilities summarizes the facilities that a package provides by itself (i.e., without invoking another package) for working with SBML: "Creation" = creating/editing models, "Simulation" = performing time-series simulation of models, "Analysis" = analyzing models (e.g., sensitivity analysis, flux-balance analysis, etc.), "Database" = providing a database of models, and "Utility" = providing other utility functions (e.g., translating SBML to/from other formats).
- Frameworks summarizes the modeling frameworks supported by a package, regardless of whether the package also supports simulation or analysis using those same frameworks: "ODE" = ordinary differential equations, "DAE" = differential-algebraic equations, "PDE" = partial differential equations, "Stochastic" = discrete stochastic simulation, "Events" = discrete events, "Logical" = logical (e.g., Boolean) models, and "Other" = frameworks not listed here.
- API indicates whether a package exposes an application programming interface to other software systems; entries in this column are the programming languages for which that API is provided. "WS" = web services.
- Dep. indicates dependencies on other software environments. "MMA" = Mathematica, "BSP" = Bio-SPICE.
- Platforms indicates the operating systems for under which the software runs. "L" = Linux, "W" = Windows, "M" = MacOS, "B" = web browser-based, "S" = Solaris.
- SBML indicates whether a package allows importing or exporting SBML, or both. (Level and Version of SBML are not indicated because it is impossible to determine this in all cases without exhaustive research.)
- Availabil. indicates the availability of the software. "Open source" indicates whether the source code is offered. "Academic use" indicates whether the software is free (F) or for-cost ($) to academic users. "Commericial use" indicates the same for nonacademic use.
Please use the survey form to notify us about additions and suggestions.
Authors
Bruce E. Shapiro and Michael Hucka.