SBML models and MathSBML

B.E. Shapiro, A. Finney, M. Hucka, B. Bornstein, A. Funahashi, A. Jouraku, S. Keating, N. Le Novere, J. Matthews, M. Schilstra

    Research output: Chapter in Book/Report/Conference proceedingChapter

    2 Citations (Scopus)
    72 Downloads (Pure)

    Abstract

    MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation.
    Original languageEnglish
    Title of host publicationIntroduction to Systems Biology
    EditorsS. Choi
    PublisherSpringer Nature
    Pages395-421
    ISBN (Print)978 1 58829 706 8
    Publication statusPublished - 2007

    Keywords

    • Biomodels

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