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Published November 1, 2004 | Accepted Version + Published
Journal Article Open

MathSBML: a package for manipulating SBML-based biological models


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). Math-SBML 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

Additional Information

© 2004 Oxford University Press. Received on December 22, 2003; revised on March 7, 2004; accepted on April 1, 2004. Advance Access publication April 15, 2004. Valuable suggestions during the development of MathSBML were provided by Ben Bornstein. The research described in this paper was carried out at the California Institute of Technology, and was supported by the JST/ERATO Kitano Symbiotic Systems Project and the US National Science Foundation.

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Published - SHAbioinf04.pdf

Accepted Version - nihms7156.pdf


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