MathSBML

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:
   • Read an SBML model into Mathematica;
   • Translate rules and reactions in the model into differential and algebraic equations;
   • Optionally generate an interpretive, human-readable listing of the model;
   • Optionally call SBMLNDSolve (see below);
   • Optionally call SBMLPlot (see below) immediately after returning from SBMLNDSolve;
   • Return a Mathematica data structure, encoding the model, that is compatible with standard Mathematica functions such as NDSolve.

   Click here to learn more about SBMLRead.

2. SBMLNDSolve provides an wrapper for NDSolve. It can:
   • Solve the system of differential equations encapsulated in the data structure returned by SBMLRead;
   • Solve a system of differential/algebraic equations encapsulated in the data structure returned by SBMLRead, if the user has Mathematica version 5;
   • Optionally call SBMLPlot to plot the solution as a function of time;
   • Return a list of Mathematica-Standard Interpolating Functions of the same form as those returned by NDSolve.

   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
   • Provides a simple interface to Plot for graphing the SBMLNDSolve.
   • Displays graphs of solution variables as a function of time;
   • Plots on linear and logarithmic scales.

   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:
   • Read an SBML file;
   • Write the original model to a new file;
   • Format the output using Mathematica's XML-indentation capability.

   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:
   • Add or remove individual objects in a model (e.g., reactions, species, etc.). All SBML objects are currently supported.
   • Modify (edit) individual objects in a model.
   • Export a model as an SBML text file.
   • Generate SBML text for individual SBML objects, e.g., <species../>.
   • Import a model.
   • Export the model for SBMLNDSolve.
   The model builder only supports SBML Level 2 (both versions 1 and 2).

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.