SBMLToolbox

Version 3.0.0 released 26 January 2008
Sarah M. Keating

SBMLToolbox is built on top of libSBML and provides a set of basic functions allowing SBML models to be used in MATLAB. SBMLToolbox provides functions for reading, writing, and validating SBML models; viewing model structures in a simple GUI; converting models into a symbolic form suitable for use with MATLAB's Symbolic Math Toolbox; and simulate models using MATLAB's ordinary differential equation solvers.

SBMLToolbox works by translating SBML models to/from a MATLAB structure called MATLAB_SBML. It provides facilities for manipulating this and its substructures within MATLAB, as well as functions for saving and loading MATLAB_SBML structures to/from MATLAB data files.

The toolbox is not intended to be a complete Systems Biology toolbox for MATLAB, but rather a platform facilitating getting SBML in and out of MATLAB and serving as a starting point from which users can develop their own functionality.

Please cite the paper if you use SBMLToolbox

Article citations are crucial to our academic careers. If you use SBMLToolbox and you publish papers about work that was performed using SBMLToolbox, we ask that you please cite the SBMLToolbox paper:

Keating, S. M., Bornstein, B. J., Finney, A., and Hucka M. (2006) SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics, 22(10):1275–1277.

Compatibility note

A number of third-party MATLAB toolboxes use SBMLToolbox. Beware that they may have restrictions on the version of SBMLToolbox with which they are compatible. For example, some are only compatible with version 2.0.2, not the current version 3 of SBMLToolbox. Please make sure to check the third-party software's documentation to determine which version of SBMLToolbox it needs.