A portal site for systems biology.

http://www.sbml.org/software/libsbml

Version 3.1.1 released 25 February 2008

MathSBML is an open-source package for working with SBML models in Mathematica. It provides facilities for reading SBML models, converting them to systems of ordinary differential equations for simulation and plotting in Mathematica, and translating the models to other formats. It supports both Level 1 and Level 2 SBML.

http://www.sbml.org/mathsbml.html

Convert KEGG files into SBML

http://www.sbml.org/kegg2sbml.html

Convert CellML files into SBML

http://sbml.org/software/cellml2sbml/

Convert BioCyc files into SBML
http://genome.dfci.harvard.edu/%7Ezucker/BPHYS/biocyc-open/

http://biocomp.ece.utk.edu/tools.html

The toolbox, BSTLab, implements functions common to BST-based studies and is designed to integrate easily into the widely used Matlab environment, automate many common tasks, and allow expansion and customization by the user. The toolbox also includes functions needed to reformulate and transport models from SBML, the emerging Systems Biology Markup Language.
https://bioinformatics.musc.edu/bstlab/

CL-SBML is a Common Lisp SBML Library

http://common-lisp.net/project/cl-sbml/

The software system ecellJ is a package for manipulating rule files for the ecell system which is used to simulate biological reaction networks. ecellJ was created by Jörg R. Weimar during a reserach stay at the Institute for Advanced Biosciences, Keio University, Japan.

http://www.jweimar.de/ecellJ

The Systems Biology Toolbox for MATLAB offers systems biologists an open and extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological systems.
http://www.fcc.chalmers.se/%7Ehenning/SBtoolbox/

Monod -- the Modeler's Notebook and Datastore.

Monod is a web-based environment supporting collaborative work by scientists studying complex biological systems.

http://monod.molsci.org/

http://bioinformatics.ai.sri.com/ptools/

SBMLeditor provides the ability to use the annotation framework based on RDF and dublin core dc:creator and dc:relation elements. Some functions provided by libSBML are available if the library is setup properly on the system.
http://www.ebi.ac.uk/compneur-srv/SBMLeditor.html

An interface program between SBML and R. R is a free software environment for statistical computing and graphics.
http://epbi-radivot.cwru.edu/

The SBMLToolbox, linking to LIBSBML, provides a set of functions that allow an SBML model to be imported into MATLAB and stored as a structure within the MATLAB environment.
http://sbml.org/software/sbmltoolbox

http://sys-bio.org/sbwWiki/doku.php?id=sysbio:sbw