A Caltech Library Service

MathSBML: a package for manipulating SBML-based biological models

Shapiro, Bruce E. and Hucka, Michael and Finney, Andrew and Doyle, John (2004) MathSBML: a package for manipulating SBML-based biological models. Bioinformatics, 20 (16). pp. 2829-2831. ISSN 1367-4803. PMCID PMC1409765.

PDF - Published Version
See Usage Policy.

[img] PDF - Accepted Version
See Usage Policy.


Use this Persistent URL to link to this item:


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 and Supplementary information: Extensive online documentation is available at Additional examples are provided at

Item Type:Article
Related URLs:
URLURL TypeDescription CentralArticle
Hucka, Michael0000-0001-9105-5960
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.
Funding AgencyGrant Number
JST/ERATO Kitano Symbiotic Systems ProjectUNSPECIFIED
PubMed Central ID:PMC1409765
Record Number:CaltechAUTHORS:20111004-150808819
Persistent URL:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:26314
Deposited By: Tony Diaz
Deposited On:06 Oct 2011 15:21
Last Modified:21 Dec 2016 23:57

Repository Staff Only: item control page