0 votes

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

Michael Hucka¹, Andrew M. Finney², Stefan Hoops³, Sarah M. Keating⁴ & Nicolas Le Novere⁵

Correspondence: (Login to view email address)

1. California Institute of Technology, USA
2. Oxford Computer Consultants Ltd, UK
3. Virginia Bioinformatics Institute, USA
4. University of Hertfordshire, UK
5. EMBL European Bioinformatics Institute, UK

PDF (2.4 MB)

Document Type:

Manuscript

Date:

Received 26 October 2007 08:21 UTC; Posted 05 November 2007

Subjects:

Bioinformatics

Tags:

• systems biology
• Systems Biology Markup Language
• SBML

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 specification presents 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/.

Discussion

Votes:

0 votes

(Login to vote)

Comments:

0 comments

(Login to post a comment)

Share:

(Login to share with a colleague)

Additional information

License:

This document is licensed to the public under the Creative Commons Attribution 2.5 License

How to cite this document:

Hucka, Michael, Finney, Andrew, Hoops, Stefan, Keating, Sarah, and Le Novere, Nicolas. Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2007.58.2> (2007)

Version info:

Other versions of this document in Nature Precedings

Version number	Document title	Date
v1	Posted 18 June 2007

Other versions of this document elsewhere on the web

None known.

Submit a new version link