MathSBML: a package for manipulating SBML-based biological models | Zendy

Bruce E. Shapiro | Zendy; Michael Hucka | Zendy; Andrew Finney | Zendy; John C. Doyle | Zendy

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MathSBML: a package for manipulating SBML-based biological models

Author(s) -

Bruce E. Shapiro,

Michael Hucka,

Andrew Finney,

John C. Doyle

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bth271

Subject(s) - sbml , computer science , r package , programming language , software package , software , markup language , theoretical computer science , operating system , xml

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.

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