SBML Software Summary

This page lists software known to us to provide some degree of support for reading, writing, or otherwise working with SBML. For an at-a-glance matrix summarizing key features of these software packages, please see our SBML Software Matrix page. Please use the survey form to notify us about additions and suggestions.

Simulators: Discrete stochastic

Note that several of the ODE/DAE-based simulators also include some form of stochastic simulation capability, and vice-versa.

• BioNetGen - Rule based language for generating models. Includes ODE and SSA simulators. Open source. Download requires email based registration. Requires Perl. Optional GUI uses JRE. SBML export. (Linux/Mac/Win)
• COPASI - ODE & Stochastic Simulator, model builder. SBML Import (L1/L2), Export (L2). Free Non Commercial License; Commercial License available. (Linux/Mac/Win).
• Cyto-Sim - Stochastic simulator based on automata theory (P system). Free download. JVM Based.
• Dizzy - Chemical kinetics simulator. SBML Import/Export (L1 Subset). Includes Gillespie, Gibson-Bruck and Tau Leap stochastic and ODE/RK5 deterministic methods. LGPL, open source, Free download. (Linux/Mac/Windows).
• ESS - Exact Stochastic Simulator. Part of the UTK/ORNL Bio-SPICE tool set which includes the BioSpreadsheet SBML model editor. Requires BioSpice Dashboard. Free download. Includes Source code.
• Gillespie2 from the BASIS Project. Source code.
• GNA Genetic Network Analyzer. Simulation and visualization of models (Acad/NP).
• iBioSim iBioSim is a tool that supports learning of genetic circuit models, efficient abstraction-based analysis of these models, and the design of synthetic genetic circuits. iBioSim includes project management features and a graphical user interface that facilitates the development and maintenance of genetic circuit models as well as both experimental and simulation data records. Models in iBioSim can be created using either an SBML editor or a Genetic Circuit Model (GCM) editor. (Linux/Mac/Windows)
• MODESTO - Merged ODE and Stochastic Simulator. Source code only. Linux. (MPL 1.1)
• Moleculizer - Command line stochastic simulator. Open source. (Linux) (GPL)
• PNK - Petri Net Simulator (JRE/SBW required) (GPL).
• SmartCell - Stochastic Simulator (Linux/Mac/Win) (Acad/NP).
• StochKit - C++ library that provides various SSA, tau-leaping and adaptive step size algorithms. Source code only. (Linux) (Acad/NP).
• StochSim Stochastic simulations with some multistate species. Open Source. (Linux/Mac/Win) (source plus binaries; PERL GUI) (GPL).
• STOCKS - SSA, Gibson-Bruck, and Tau-Leaping algorithms. Command line based tool. (source code, Linux/Windows) (GPL).
• SynBioSS - a suite of software tools for the modeling and simulation of synthetic gene constructs. SynBioSS utilizes the registry of standard biological parts, a database of kinetic parameters, and both graphical and command-line interfaces to multiscale (stochastic-discrete, stochastic-continuous and continuous-deterministic simulation) algorithms. A user can enter a sequence of BioBricks to synthesize a new gene network, obtain a set of biochemical reactions and model the dynamic behavior.
• Trelis Monte Carlo Simulator. Open Source (Windows) (LGPL).

Simulators: Continuous deterministic

• BIOCHAM - Programming environment with GUI, simulator, and rule-based modeling language. SBML import & export.
• BioNetGen - Rule based language for generating models. Includes ODE and SSA simulators. Open source. Download requires email based registration. Requires Perl. Optional GUI uses JRE. SBML export. (Linux/Mac/Win)
• BioTapestry - Graphical model development and simulation tool for genetic regulatory networks based on JRE. Uses Java Web Start. Free download. SBML export.
• braincirc - Braincirc is an open source model development and simulation environment developed primarily for linux platforms, originally developed to simulate brain circulation (Linux).
• ByoDyn - ODE/DAE/delays; parameter optimization; sensitivity analysis. Terminal based. Free Download vis SF (GPL, includes source). Requires Python, SciPy, f2py, libSBML 2.3.4++, PORT, Gnuplot. Optional Octave (required for DAE's), Open Modelica (required for DAEs with events), Open MPI, Scientific Python. SBML import. (Linux/Mac)
• CellDesigner - Graphical model development and simulation tool for all types of SBML models. Includes SBGN notation. SBML import & export.
• Cell Illustrator - Graphical model editor; Petri-net based algorithm; SBML Import. Commercial. (Linux/Mac/Win).
• Cellware - Block diagram model editor & simulator. SBML import. Free download (Academic/Non-Profit) (Linux/Mac/Win).
• COPASI - ODE & Stochastic Simulator, model builder. SBML Import (L1/L2), Export (L2). Free Non Commercial License; Commercial License available. (Linux/Mac/Win).
• DBSolve - Spreadsheet editor and simulator. Free. Requires registration/email verification. License TBD ...
• E-Cell - (Linux RPM/Win). Requires Python, Numpy, GSL, Boost. Command line, scripting, and GUI. Supports ODE/DAE and Gibson-Bruck SSA models. GUI requires Gnome, gnome-python2, and pygtk. GPL with exceptions. SBML import via SBML2EML converter. Limited SBML export via ecellj converter.
• Genetdes - Network optimization using Simulated Annealing. SBML Import/Export. Free download, requires email license (CCL- AN). (Linux)
• Gepasi - Forerunner of COPASI. ODE simulations, metabolic analysis. SBML L1 Inport/Export. (Windows or Linux under Wine). Limited license.
• iBioSim iBioSim is a tool that supports learning of genetic circuit models, efficient abstraction-based analysis of these models, and the design of synthetic genetic circuits. iBioSim includes project management features and a graphical user interface that facilitates the development and maintenance of genetic circuit models as well as both experimental and simulation data records. Models in iBioSim can be created using either an SBML editor or a Genetic Circuit Model (GCM) editor. (Linux/Mac/Windows)
• Jarnac - SBW tool for metabolic analysis, includes dynamic simulation. Simulation engine for JDesigner. BSD License.
• JSim - JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim's primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim's model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also imports the SBML and CellML model archival formats.
• Kinsolver - browser based simulation tool. Must install a java front end and compile the C/Fortran backend. Source code available. Does not appear to be currently supported (last updated 2006).
• Narrator - Graphical model design and simulation. Java-based, platform independent. Open source/free download (LGPL).
• Oscill8 - Bifurcation and Simulation. Windows Binary. (BSD).
• PathwayLab - Simulation, Visualization, MCA; Mathematica and Matlab integration; model creation. (Windows) (Commercial).
• Pathway Solver - ODE based simulation. Commercial. (formerly runSMBL)
• PET - PET is a graphical user interface (GUI) for discovering rate constants, of molecular network models, that fit experimental data. It is designed for use by theoretical biologists to build regulatory network models and compare the models to experimental results. (Linux/Win).
• PhysioLab Modeler - Whole organism modeling environment. Commercial.
• SBML-SAT SBML-SAT implements algorithms for simulation, steady state analysis, robustness analysis and local and global sensitivity analysis for SBML models. This software tool extends current capabilities through its execution of global sensitivity analyses using multi-parametric sensitivity analysis, partial rank correlation coefficient, SOBOL’s method, and weighted average of local sensitivity analyses in addition to its ability to handle systems with discontinuous events and intuitive graphical user interface.
• SBML-PET - Parameter Estimation tool (Linux/Win)
• SIMBA Wastewater simulation. SBML Support unspecified. Commercial(?).
• SimPheny - Simulation, visualization, model management
• SBTOOLBOX2 - Model development and simulation (ODE & Stochastic); SBML Import (L1/L2), Export (L2); parameter estimation; analysis tools; Metabolic control analysis. Requires MatLab (Linux/Win/Mac) (GPL).
• SynBioSS - a suite of software tools for the modeling and simulation of synthetic gene constructs. SynBioSS utilizes the registry of standard biological parts, a database of kinetic parameters, and both graphical and command-line interfaces to multiscale (stochastic-discrete, stochastic-continuous and continuous-deterministic simulation) algorithms. A user can enter a sequence of BioBricks to synthesize a new gene network, obtain a set of biochemical reactions and model the dynamic behavior.
• VCell - VCell is a complete model building, editing and simulation environment. Includes spatial modeling capabilites, deterministic, stochastic, and hybrid algorithms. Parameter sensitivity analysis and parameter optimization. Desktop application and web-based environment. Bio- and math-based interfaces. Database and model sharing/publishing. Free, registration required. Open source, source code available upon request. (Linux/Mac/Win/Web)
• WebCell - Online simulator, model builder, metabolic controal analysis. Includes database of bimodels and JWS models. Registration required.
• xCellerator - Mathematica based ODE simulator. SBML inport/export uses MathSBML. Requires Mathematica. Free download (LGPL). (Linux/Mac/Win).
• Xholon - Model development environment, tool set, simulation. (Linux/Win) Open Source (LGPL).
• XPPAUT - ODE solver, analysis tool. Open Source. Free download. (Linux/Mac/Win)

Simulators: Spatial

• MesoRD - Reaction/Diffusion simulator. Stochastic and Deterministic simulations. Free download (GPL). (Linux/Mac/Win)
• SmartCell - Stochastic Reaction/Diffusion Simulator (Linux/Mac/Win) (Acad/NP).
• VCell -VCell is a complete model building, editing and simulation environment. Includes spatial modeling capabilites, deterministic, stochastic, and hybrid algorithms. Parameter sensitivity analysis and parameter optimization. Desktop application and web-based environment. Bio- and math-based interfaces. Database and model sharing/publishing. Free, registration required. Open source, source code available upon request. (Linux/Mac/Win/Web).

Simulation and Programming Environments

• acslextreme is a commercial modeling environment that uses a script language called CSL. Has SBML import. Windows only.

• For Mathematica
  • MathSBML - SBML import/export and simulation within Mathematica.
  • PathwayLab - Stand alone simulation; Visualization; MCA; Mathematica and Matlab integration; model creation. (Windows) (Commercial).
  • xCellerator - requires MathSBML for SBML input/export.

• For MATLAB
  • SBTOOLBOX² from Henning Schmidt. Requires SBML Toolbox.
  • SBMLToolbox from the SBML Team.
  • SimBiology from The MathWorks includes both stochastic and deterministic simulation suport and a GUI model builder.
  • BioSens - ODE Simulation & Sensitivity analysis for BioSpice Dashboard Dashboard. Requires dashboard, Matlab, XPP, Cygwin, libSBML, DASPK, Tapenade. Requires Biospice dashboard, Matlab, XPP, Cygwin, libSBML, DASPK, Tapenade. Free download (License unspecified). (Windows)
  • BSTLAB - GMA and S-Systems based toolbox for Biochemical Systems Theory.
  • CellNetAnalyzer (formerly FluxAnalyzer) - CellNetAnalyzer (CNA) is a MATLAB toolbox providing a comprehensive and user-friendly environment for structural analysis of biochemical networks. CNA supports mass-flow (metabolic, stoichiometric) and signal-flow (signaling, regulatory) networks and provides various algorithms for functional network analysis such as FBA, flux analysis, elementary modes (mass-flow netw.) or signaling paths, feedback loops, global interdependencies, logical I/O analysis, intervention sets (signal-flow netw.).
  • Metatool - A tool for metabolic pathway analysis with the main focus in elementary modes calculation. Enzyme subsets and conservation relations are also determined.
  • PathwayLab - Stand alone simulation; Visualization; MCA; Mathematica and Matlab integration; model creation. (Windows) (Commercial).
  • PottersWheel - ODE based Simulation, model fitting, visualization, clustering, model design. (Free download; Optimization toolbox recommended).
  • RMBNToolbox - Toolbox for generating random notebooks (GPL).
• For Octave (Some MATLAB tools may also work in Octave)
  • Simpathica - ODE based simulation. Part of BioSpice.
• For Python and SciPy
  • ByoDyn - ODE/DAE/delays; parameter optimization; sensitivity analysis. Terminal based. Free Download vis SF (GPL, includes source). Requires Python, SciPy, f2py, libSBML 2.3.4++, PORT, Gnuplot. Optional Octave (required for DAE's), Open Modelica (required for DAEs with events), Open MPI, Scientific Python. SBML import. (Linux/Mac)
  • Netbuilder' - Tool for specification and simulation of models of well-stirred (bio)chemical reaction systems, with options facilitating modelling of complex control interactions. Petri-net (to user) and matrix (to simulation engine) model representation. Supports DAE, stochastic, deterministic, and full hybrid simulation.
  • pysbml for Python - library for interfacing with SBML in Python. Uses SciPy.
  • PySCeS requires SciPy; includes ODE solve, MCA, bifurcation tools, parametric scanning. SBML import/export. Open source (GPL).
  • semanticSBML - Package that facilitates model merging (GPL).
  • SloppyCell - Simulation Package (ODE and SSA). Uses NumPy, SciPy, matplotlib. Open Source
• For R
  • RSBML - SBML interface library for R (GPL). (available from CRAN).
  • SBMLR - SBML interface library for R.
  • RANGE - Random network generator. Noise added by R-script. Source code in C, yacc, lex. (GPL).

Flux / Metabolic Analysis

• CellNetAnalyzer (formerly FluxAnalyzer) - CellNetAnalyzer (CNA) is a MATLAB toolbox providing a comprehensive and user-friendly environment for structural analysis of biochemical networks. CNA supports mass-flow (metabolic, stoichiometric) and signal-flow (signaling, regulatory) networks and provides various algorithms for functional network analysis such as FBA, flux analysis, elementary modes (mass-flow netw.) or signaling paths, feedback loops, global interdependencies, logical I/O analysis, intervention sets (signal-flow netw.).
• Fluxor - Flux analysis. Free, part of BioSpice tool set. Linux.
• Jarnac - SBW tool for metabolic analysis. Based on SCAMP. Includes dynamic simulation. BSD License.
• MetaFluxNet - Model creator, manager, flux and metabolic pathway analysis and visualization. Free academic version with limited functionality. Windows only (req. .NET). User must send hard-copy of signed license by mail before s/w can be downloaded.
• Pathway Analyser - Flux analysis. Free download, open source (Linux).
• MMT2 - Metabolic modeling, model fitting, automated high-performance code generation. (Linux only).
• SBTOOLBOX2 - MCA: Steady state control coefficients and elasticities; Structural analaysis: conservation relation analysis; model development; simulation; SBML Import/Export; parameter estimation; analysis tools. Requires MatLab (Linux/Win/Mac) (GPL).
• WebCell - Online MCA, Visualization, and dynamic simulation.
• WinSCAMP - Windows Binary for SCAMP. Metabolic analysis, ODE solver. Binary download only. Source code on request.

Modeling Frameworks for Biology

• Bio-Spice - Large collection of tools, integrated via a "Dashboard." Free download (BSD), various platforms.
• SBW - Systems Biology Workbench. A framework for connecting and running various applications written in different languages or on different systems, and a collection of available modules for model development, analysis, and simulation. Free/Open Source. (BSD)
• Teranode - Suite of tools for model management, design, and simulation. (Linux/Mac/Windows) Commercial (30-day trial available).

SBML and Modeling libraries

• libSBML for C, C++, Java, Lisp, Python, Perl, Matlab, Octave, and Ruby. Free Download (LGPL). (Linux/Mac/Win).
• cl-sbml Common Lisp library for SBML. Uses libSBML. License unspecified. Source Code (Lisp). Free Download via CVS.
• SBML ODE Solver - C-based simulation library and API for SBML. Uses Sundials. Source Code (Linux/Max/Win) (LGPL).

Model Management, Data Integration, and Analysis

• BioPathwise - integrated data management, pathway visualization, annotation, analysis and simulation. SBML import. Commercial. (Windows)
• Medicel - commercial data integration framework.
• Pathway Tools extracts and integrates information from pathway/genome databases (see [http:biocyc.org/ BioCyc]); metabolic analysis; gene code prediction; operon prediction; gene expression analysis. Optional support: Oracle or MySQL, Browser, BLAST, Marvin Msketch, JME/OpenBabel. SBML support via BioCyc. Free academic; fee for commercial. License application must be reviewed by SRIC before download. SRI unique license. (Linux/Windows/Solaris/Mac).
• PATIKA - Pathway database integration; pathway visualization and analysis. Online tool only. (Acad/NP)
• ProcessDB - Model design and management. Commercial.
• PROTON - Integrated modeling environment. Reconstructs biochemical systems from molecular databases in an automated and user-centric way. Fuses information from distributed databases and the reconstruction of systems is interactively controlled by the user. The approach is based on different layers which allow the integrative modelling of biochemical systems at multiple levels. ODE based modeling and simulation. (Free Download. Optional Server, Windows; Client: Linus/Windows/Mac).
• SCIPath - microarray data management. (Linux/Windows).
• SIGNALIGN - online pathway alignment service.
• SigPath Bioinformatic database and pathway management (GPL).
• SRS - Data integration for bioinformatics. Commercial.

Model Development Tools

• BALSA  : Front end for Sigtran (inactive?)
• BioCharon includes a suite of tools for developing models for use with CHARON. It includes the graphical BioSketchPad for desigining models, a hybrid SBML/C++ language model builder, and a metabolic analyzer.
• BiologicalNetworks pathway model development supports SBML Import/Export (only supports simple mass action kinetics); visualization; data management; network/metabolic analysis; clustering. No simulation engine. Free academic download (Java web start, Windows/Linux/Mac).
• BioNetGen - Rule based language for generating models. Includes ODE and SSA simulators. Open source. Download requires email based registration. Requires Perl. Optional GUI uses JRE. (Linux/Mac/Win)
• Bio Sketch Pad - graphical model design tool, front end for BioCharon
• BioSpreadsheet - SBML model editor. Part of the UTK/ORNL Bio-SPICE tool set which includes the Exact Stochastic Simulator (ESS). Requires BioSpice Dashboard. Free download. Includes Source code.
• BioTapestry - Graphical model development and simulation tool for genetic regulatory networks based on JRE. Uses Java Web Start. Free download. SBML export.
• CADLIVE - Graphical Model Design Tool. Includes an ODE simulator. SBML L2 Import/Export. Windows Only. Free Download.
• Cell Illustrator - Graphical model editor; Petri-net based simulation algorithm; SBML Import. Commercial. (Linux/Mac/Win).
• Cystoscape - Graphical model design and layout. SBML L2 Import. Free download (LGPL) (Linux/Mac/Win).
• Edinburgh Pathway Editor (EPE) - Edinburgh Pathway Editor is a biological pathway drawing/editing application. Currently it can draw diagrams using SBGN PD Level 1, Cytoscape and Metabolic notations. It can export SBML Level 2 v3 and BioPAX Level 3 from the metabolic notation and BioPAX export for SBGN will be coming soon. It is completely customisable and can be configured to support a wide variety of graphical notations. In addition it has an extensible architecture that allows addition exporters to be added. The ability to import SBML models will come soon.
• HSMB - Hybrid SBML Model Builder for BioCharon.
• JDesigner - Graphical model design tool. Typically uses Jarnac as a simulation engine via SBW. Free/Open Source (LGPL).
• JigCell - Model development tool and run manager. Depends on XPP/XPPAUT, JRE. Part of Bio-Spice Tool Kit. Free Download (Biospice/DARPA license) (Linux/Mac/Windows). Inlcudes SBML L2 Parser. Not updated since 2004. Some pages are dead.
• Karyote - Online model development tool based on online database of parts. Claims to have some sort of simulator and SBML support. Level unclear. Documentation absent.
• MONOD "Modeler's Notebook and Data Store" model annotation manager. (Linux/Mac OS) Open Source, Must build from source (LGPL).
• Pathway Builder - Graphical model design. Part of Bio-Spice. (BioSpice BSD License)
• PathwayLab - Deterministic simulation; Visualization; MCA; Mathematica and Matlab integration; model creation. (Windows) (Commercial).
• ProMoT - ProMoT (for Process Modeling Tool) is software for the set-up and manipulation of models of complex technical or biological systems. Key features are the support of modular models, specialized libraries for different application areas and advanced graphical support. Dynamic models can contain DAE and discrete events for simulation in DIVA, Diana or Matlab. Logical/boolean models are exported to CellNetAnalyzer. (Linux).
• SBMLeditor - SBML Model editor. Free download (GPL). (Linux/Mac/Win).
• SBML Shorthand - python tools for converting SBML Shorthand to/from SBML
• Sycamore - Model design, integration with SABIO-RK, integration with simulation, and parameter estimation.

Model Visualization Tools

Please note that most of the model simulation, development, and analysis tools listed elsewhere on this page include some form of visualization, so they are not re-listed in this section.

• PaVESy - Pathway Visualization Editing System. Java based. (Linux/Mac/Win). Free download.
• SBML Layout Viewer will automatically generate an SBML Layout and render the image from an SBML file. Web based.
• SimWiz Visualizes simulation outputs from tools such as Copasi and STODE. (Linux/Win) (European Media License)
• VANTED - "Visualization and Analysis of Networks containing Experimental Data" - analysis and visualization of graph heirarchies. Requires JRE. Java web start. Includes all other dependencies. Various free licenses for dependencies.

Model Repositories, Test Suites, and Databases

• Stochastic Test Suite from BASIS
• Biomodels Database is a curated database of published quantitative models that may be downloaded in SBML. Some models are also available in CellML, SciLab, XPP, and BioPAX format and most can be simulated via JWS Online.
• BioCyc - collection of pathway/genome databases. May be downloaded in SBML, BioPAX, or flat format. Free limited academic license (detailed). May be explored with Pathway Tools
• JWS Online - online database and simulator. Only models already in the database can be simulated. Models can not currently be downloaded.
• kineticon - online resource for kinetic data, reactions, enzymes, pathways. SBML L2V1 Export.
• Meta-All - Pathway database manager.
• NetPro - Molecular interaction database (commercial).
• PathArt - Pathway database collection. (Commercial)
• Panther Pathway - Pathway database (online resource).
• Reactome - Pathway database (online resource).
• SABIO-RK - Reaction and Kinetic data base (online resource). See also Sycamore.
• SIGMOID - Model database, explorer, visualization, Cellerator-based simulations as a web service.

SBML Conversion Tools

Many of other tools listed on this page include translators between SBML and their tool-unique language; this list is for tools that only do translation, independent of a specific tool.

• CellML2SBML
• ecellj - converts between ecell models and various other formats including SBML and open office spreadsheets.
• KEGG2SBML

SBML Extensions

• CLEML Carbon Labeling Experiment Markup Language. The libCLEML is freely downloadable (GPL). (Linux/Win).

Analysis and Utility Programs

• BiNoM - Biological Network Manager. Network design and manipulation. Visualization. Model conversion (CellDesigner, BioPAX); Structural Analysis; BioPAX Queries. Available as an independent library or Cytoscape plugin.
• SBMLsqueezer - Plug-in for CellDesigner 4.0 that generates rate equations for biochemical networks according to SBGN and the context of the reaction. Rate laws include generalized mass action; detailed enzyme kinetics (Michaelis-Menten) for up to two substrates or products; Hill equations; or the approximative convenience rate law. User defined settings specify which equation to apply for any type of reaction. Equations can be created using contextual menus. MathML is inserted directly into the SBML file.LaTeX or Text ODE Export.
• SBML-SAT SBML-SAT implements algorithms for simulation, steady state analysis, robustness analysis and local and global sensitivity analysis for SBML models. This software tool extends current capabilities through its execution of global sensitivity analyses using multi-parametric sensitivity analysis, partial rank correlation coefficient, SOBOL’s method, and weighted average of local sensitivity analyses in addition to its ability to handle systems with discontinuous events and intuitive graphical user interface.

Authors

Bruce E. Shapiro and Mike Hucka.