MathSBML

Bruce E. Shapiro
Biological Network Modeling Center
The Beckman Institute, Division of Biology
California Institute of Technology
Pasadena, CA, 91125-7400, USA
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What is MathSBML?

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.

Download and Installation

To download the package, including complete documentation, please visit the MathSBML area at SourceForge.net.

For detailed installation instructions Click Here.

The current release of MathSBML is version 2.7.1, released on 7 December, 2007. There may be additional incremental releases in the CVS repository at SourceForge. Changes in both incremental (CVS) and major (bundled) file releases are summarized in the release notes, which may be viewed here.

Summary of Functions Provided by MathSBML

  1. SBMLRead is the primary function provided by MathSBML. It can, at the user's option:

    Click here to learn more about SBMLRead.

  2. SBMLNDSolve provides an wrapper for NDSolve. It can:

    An experienced Mathematica user can also solve the model returned by SBMLRead directly using NDSolve or any other Mathematica function.

    Click here to learn more about SBMLNDSolve

  3. SBMLPlot can be used to plot the solution. It

    An experienced Mathematica user can also graph the output of SBMLNDSolve using Plot directly.

    Click here to learn more about SBMLPlot.

  4. SBMLWrite will translate an SBML model into a different format. The following formats are currently supported: Fortran, HML, BerkeleyMadonna, XPP.

    Click here to learn more about SBMLWrite.

  5. SBMLCopy is intended to make a machine-generated SBML file more human-readable. It can:

    Click here to learn more about SBMLCopy.

  6. A Model Builder containing a suite of functions that can be used to build a model manually. Functionality includes: The model builder only supports SBML Level 2 (both versions 1 and 2).
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We Encourage Feedback

Our purpose is to support the biological community in general and SBML users in particular. If there is a feature you would like to see added to or modified in MathSBML, or to provide us with any suggestions or user feedback at all, please contact us. We look forward to your suggestions. To make a suggestion or report a bug, please click here.

For additional inquiries, contact bshapiro at caltech dot edu.


Support for MathSBML was provided by generous grants from thee Japan Science and Technology Agency under the ERATO Kitano Symbiotic Systems Project; The National Institutes of Health (USA); the National Science Foundation (USA); the DARPA IPTO Bio-Computation Program (USA), the Army Research Office's Institute for Collaborative Biotechnologies (USA), and the Beckman Institute at Caltech. Additional support has been provided by the California Institute of Technology (USA) and the University of Hertfordshire(UK).
This page was last revised 29 Nov 2007