MathSBML: a Package for Manipulating SBML-based Biological Models

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2004 Apr 17

PMID 15087311

Citations 20

Authors

Bruce E Shapiro

Michael Hucka

Andrew Finney

John Doyle

Affiliations

Soon will be listed here.

Abstract

Unlabelled: 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 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

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MathIOmica: An Integrative Platform for Dynamic Omics.

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Quantitative Systems Pharmacology: A Framework for Context.

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