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Bioinformatics Advance Access published online on April 15, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth271
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received December 22, 2003
Revised March 7, 2004
Accepted March 1, 2004

Applications note

MathSBML: a package for manipulating SBML-based biological models

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

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

* To whom correspondence should be addressed. E-mail: bshapiro{at}caltech.edu.


  Abstract

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 to other formats such as XPP, HTML, 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.


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