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

Hucka, Michael and Bergmann, Frank T. and Hoops, Stefan and Keating, Sarah M. and Sahle, Sven and Schaff, James C. and Smith, Lucian P. and Wilkinson, Darren J. (2010) The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. The Systems Biology Markup Language (SBML): Language Specification, L3 V1 Core. . http://resolver.caltech.edu/CaltechAUTHORS:20141028-175133969

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Abstract

This document defines Version 1 of the Systems Biology Markup Language (SBML) Level 3 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, the eXtensible Markup Language (Bray et al., 2004). This document contains many examples of SBML models written in XML. Formal schemas describing the syntax of SBML, as well as other materials and software, are available from the SBML project web site, http://sbml.org/. The SBML project is not an attempt to define a universal language for representing quantitative models. The rapidly evolving views of biological function, coupled with the vigorous rates at which new computational techniques and individual tools are being developed today, are incompatible with a one-size-fits-all idea of a universal language. A more realistic alternative is to acknowledge the diversity of approaches and methods being explored by different software tool developers, and seek a common intermediate format—a lingua franca—enabling communication of the most essential aspects of the models. The definition of the model description language presented here does not specify how programs should communicate or read/write SBML. We assume that for a simulation program to communicate a model encoded in SBML, the program will have to translate its internal data structures to and from SBML, use a suitable transmission medium and protocol, etc., but these issues are outside the scope of this document.


Item Type:Report or Paper (Documentation)
Related URLs:
URLURL TypeDescription
http://sbml.org/Special/specifications/sbml-level-3/version-1/core/sbml-level-3-version-1-core.pdfOrganizationThis document on sbml.org website.
ORCID:
AuthorORCID
Hucka, Michael0000-0001-9105-5960
Contact Email Address:mhucka@caltech.edu
Additional Information: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 Suite 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).
Funders:
Funding AgencyGrant Number
National Institute of General Medical SciencesGM070923
National Institute of General Medical SciencesGM077671
National Human Genome Research Institute UNSPECIFIED
International Joint Research Program of NEDO (Japan)UNSPECIFIED
JST ERATO-SORST Program (Japan)UNSPECIFIED
Japanese Ministry of AgricultureUNSPECIFIED
Japanese Ministry of Education, Culture, Sports, Science and TechnologyUNSPECIFIED
BBSRC e-Science Initiative (UK)UNSPECIFIED
DARPA IPTO Bio-Computation Program UNSPECIFIED
Army Research Office (ARO) Institute for Collaborative Biotechnologies UNSPECIFIED
Air Force Office of Scientific ResearchUNSPECIFIED
Record Number:CaltechAUTHORS:20141028-175133969
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20141028-175133969
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:50974
Collection:CaltechAUTHORS
Deposited By: Linda Taddeo
Deposited On:03 Nov 2014 23:55
Last Modified:21 Dec 2016 23:01

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