The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core

  • 1 California Institute of Technology, Pasadena, CA, USA
  • 2 Applied Bioinformatics Group, Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Sand 14, Office # C320, 72076 Tübingen, Germany
  • 3 Biocomplexity Institute of Virginia Tech, Blacksburg, Va 24061, USA
  • 4 European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom of Great Britain and Northern Ireland
  • 5 Babraham Institute, Cambridge, Cambridgeshire, United Kingdom of Great Britain and Northern Ireland
  • 6 University of Utah, Salt Lake City, UT, USA
  • 7 Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
  • 8 University of Heidelberg, Heidelberg, Germany
  • 9 University of Connecticut, Storrs, CT, USA
  • 10 University of Washington, Seattle, WA, USA
  • 11 University of Rostock, Rostock, Germany
  • 12 Newcastle University, Newcastle, United Kingdom of Great Britain and Northern Ireland

Abstract

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

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Journal + Issues

The Journal of Integrative Bioinformatics is an international journal dedicated to methods and tools of computer science and electronic infrastructure applied to biotechnology. The journal covers mainly but not exclusively data/method integration, modeling, simulation and visualization in combination with applications of theoretical/computational tools and any other approach supporting an integrative view of complex biological systems.

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