University of Hertfordshire

By the same authors

SBML models and MathSBML

Research output: Chapter in Book/Report/Conference proceedingChapter

Documents

  • B.E. Shapiro
  • A. Finney
  • M. Hucka
  • B. Bornstein
  • A. Funahashi
  • A. Jouraku
  • S. Keating
  • N. Le Novere
  • J. Matthews
  • M. Schilstra
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Original languageEnglish
Title of host publicationIntroduction to Systems Biology
EditorsS. Choi
PublisherHuman Press / Springer
Pages395-421
ISBN (Print)978 1 58829 706 8
Publication statusPublished - 2007

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.

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