SBML models and MathSBML

Bruce E. Shapiro, Andrew Finney, Michael Hucka, Benjamin Bornstein, Akira Funahashi, Akiya Jouraku, Sarah M. Keating, Nicolas Le Novère, Joanne Matthews, Maria J. Schilstra

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)

Abstract

MathSBML is an open-source, freely downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a tool-neutral, computer-readable format for representing models of biochemical reaction networks, and it is 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, which is 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 Math- SBML, a number of other tools that support SBML model examination and manipulation are provided on the http://sbml.org Web site, including libSBML, which is 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
PublisherHumana Press
Pages395-421
Number of pages27
ISBN (Print)9781588297068
DOIs
Publication statusPublished - 2007
Externally publishedYes

Fingerprint

Markup languages
Systems Biology
Language
Computational Biology
Cell signaling
Bioinformatics
Metabolic Networks and Pathways
Application programming interfaces (API)
XML
Internet
MATLAB
Libraries
Publications
Websites
Reading

Keywords

  • BioModels
  • libSBML
  • MathSBML
  • SBML
  • systems biology
  • XML

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Shapiro, B. E., Finney, A., Hucka, M., Bornstein, B., Funahashi, A., Jouraku, A., ... Schilstra, M. J. (2007). SBML models and MathSBML. In Introduction to Systems Biology (pp. 395-421). Humana Press. https://doi.org/10.1007/978-1-59745-531-2_20

SBML models and MathSBML. / Shapiro, Bruce E.; Finney, Andrew; Hucka, Michael; Bornstein, Benjamin; Funahashi, Akira; Jouraku, Akiya; Keating, Sarah M.; Le Novère, Nicolas; Matthews, Joanne; Schilstra, Maria J.

Introduction to Systems Biology. Humana Press, 2007. p. 395-421.

Research output: Chapter in Book/Report/Conference proceedingChapter

Shapiro, BE, Finney, A, Hucka, M, Bornstein, B, Funahashi, A, Jouraku, A, Keating, SM, Le Novère, N, Matthews, J & Schilstra, MJ 2007, SBML models and MathSBML. in Introduction to Systems Biology. Humana Press, pp. 395-421. https://doi.org/10.1007/978-1-59745-531-2_20
Shapiro BE, Finney A, Hucka M, Bornstein B, Funahashi A, Jouraku A et al. SBML models and MathSBML. In Introduction to Systems Biology. Humana Press. 2007. p. 395-421 https://doi.org/10.1007/978-1-59745-531-2_20
Shapiro, Bruce E. ; Finney, Andrew ; Hucka, Michael ; Bornstein, Benjamin ; Funahashi, Akira ; Jouraku, Akiya ; Keating, Sarah M. ; Le Novère, Nicolas ; Matthews, Joanne ; Schilstra, Maria J. / SBML models and MathSBML. Introduction to Systems Biology. Humana Press, 2007. pp. 395-421
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