The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Creators: Hucka, Michael; Bergmann, Frank T.; Hoops, Stefan; Keating, Sarah M.; Sahle, Sven; Schaff, James C.; Smith, Lucian P.; Wilkinson, Darren J.

Abstract

This is the final specification for Release 1 of SBML Level 3 Version 1 Core, an electronic model representation format for systems biology. 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. SBML is defined neutrally with respect to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML. This document contains many examples of SBML models written in XML.

Additional Information

© 2010 Nature Publishing Group. Creative Commons Attribution 3.0 License. Received 06 October 2010 05:59 UTC; Posted 06 October 2010. The development of SBML was originally funded by the Japan Science and Technology Agency (JST) under the ERATO Kitano Symbiotic Systems Project during the years 2000-2003. From 2003 to the present, funding for development of SBML and associated software such as libSBML and the SBML Test Suite5 has been provided chiefly by the National Institute of General Medical Sciences (USA) via grant numbers GM070923 and GM077671. Additional grant funding has in the past been provided by National Human Genome Research Institute (USA); the International Joint Research Program of NEDO (Japan); the JST ERATO-SORST Program (Japan); the Japanese Ministry of Agriculture; the Japanese Ministry of Education, Culture, Sports, Science and Technology; the BBSRC e-Science Initiative (UK); the DARPA IPTO Bio-Computation Program (USA); the Army Research Office's Institute for Collaborative Biotechnologies (USA); and the Air Force Office of Scientific Research (USA). Additional support has been or continues to be provided by the following institutions, either directly for activities related to SBML or indirectly by supporting the work of present and past SBML Editors: the Beckman Institute at the California Institute of Technology (USA), EML Research gGmbH (Germany), the University of Heidelberg (Germany), the European Molecular Biology Laboratory's European Bioinformatics Institute (UK), the Molecular Sciences Institute (USA), the University of Hertfordshire (UK), the University of Newcastle (UK), the Systems Biology Institute (Japan), and the Virginia Bioinformatics Institute (USA). The following individuals served as past SBML Editors and authors of SBML specifications. Their efforts helped shape what SBML is today: - Hamid Bolouri - Andrew M. Finney - Nicolas Le Novère - Herbert M. Sauro SBML was first conceived at the JST/ERATO-sponsored First Workshop on Software Platforms for Systems Biology, held in April, 2000, at the California Institute of Technology in Pasadena, California, USA. The participants collectively decided to begin developing a common XML-based declarative language for representing models. The development and evolution of the Systems Biology Markup Language has continued ever since. Many discussions are archived online in the mailing list/forums area of http://sbml.org; many more discussions took place during meetings and workshops (a list of which is also available at http://sbml.org). SBML Level 3 has benefitted from so many contributions, large and small, by so many people who constitute the international SBML Forum, that we regret it has become infeasible to list individuals by name. We thank everyone who has participated in SBML's development throughout the years, and we hope that this latest specification before you is a good step forward in SBML's continued evolution.

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