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Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

Michael Hucka¹, Stefan Hoops², Sarah M. Keating¹, Nicolas Le Novère³, Sven Sahle⁴ & Darren Wilkinson⁵

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1. California Institute of Technology, USA
2. Virginia Bioinformatics Institute, USA
3. EMBL European Bioinformatics Institute, UK
4. University of Heidelberg, DE
5. Newcastle University, UK

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Document Type:

Manuscript

Date:

Received 24 December 2008 09:21 UTC; Posted 24 December 2008

Subjects:

Bioinformatics

Tags:

• Systems
• biology
• SBML
• modeling

Abstract:

With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models. The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.

Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene regulation etc., SBML can also be used to encode any kinetic model. SBML offers mechanisms to describe biological components by means of compartments and reacting species, as well as their dynamic behaviour, using reactions, events and arbitrary mathematical rules. SBML also offers all the housekeeping structures needed to ensure an unambiguous understanding of quantitative descriptions.

This is Release 1 of the specification for SBML Level 2 Version 4, describing the structures of the language and the rules used to build a valid model. SBML XML Schema and other related documents and software are also available from the SBML project web site, http://sbml.org/.

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This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Hucka, Michael, Hoops, Stefan, Keating, Sarah, Le Novère, Nicolas, Sahle, Sven, and Wilkinson, Darren. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2008.2715.1> (2008)

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