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Bioinformatics Advance Access originally published online on April 15, 2004
Bioinformatics 2004 20(16):2829-2831; doi:10.1093/bioinformatics/bth271
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Bioinformatics vol. 20 issue 16 © Oxford University Press 2004; all rights reserved.

Applications Note

MathSBML: a package for manipulating SBML-based biological models

Bruce E. Shapiro 1,*, Michael Hucka 2, Andrew Finney 3 and John Doyle 2

1 Jet Propulsion Laboratory, California Institute of Technology, Mail Stop 126-347, 4800 Oak Grove Drive, Pasadena, CA 91109, USA, 2 Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA and 3 Science and Technology Research Center, University of Hertfordshire, Hatfield, UK

Received on December 22, 2003; revised on March 7, 2004; accepted on April 1, 2004
Advance Access Publication April 15, 2004

Summary: MathSBML is a Mathematica package designed for manipulating Systems Biology Markup Language (SBML) models. It converts SBML models into Mathematica data structures and provides a platform for manipulating and evaluating these models. Once a model is read by MathSBML, it is fully compatible with standard Mathematica functions such as NDSolve (a differential-algebraic equations solver). MathSBML also provides an application programming interface for viewing, manipulating, running numerical simulations; exporting SBML models; and converting SBML models in to other formats, such as XPP, HTML and FORTRAN. By accessing the full breadth of Mathematica functionality, MathSBML is fully extensible to SBML models of any size or complexity.

Availability: Open Source (LGPL) at http://www.sbml.org and http://www.sf.net/projects/sbml.

Supplementary information: Extensive online documentation is available at http://www.sbml.org/mathsbml.html. Additional examples are provided at http://www.sbml.org/software/mathsbml/bioinformatics-application-note

Contact: bshapiro{at}caltech.edu

* To whom correspondence should be addressed.


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