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

Hucka, Michael and Finney, Andrew and Le Novère, Nicolas (2006) Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. . (Unpublished) http://resolver.caltech.edu/CaltechAUTHORS:20130111-172633006

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Abstract

We present the Systems Biology Markup Language (SBML) SBML Level 2 Version 2, a model representation formalism for systems biology. SBML is oriented towards describing systems of biochemical reactions of the sort common in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others. SBML is defined in a neutral fashion with respect to programming languages and software encoding; however, it is primarily oriented towards allowing models to be encoded using XML, the eXtensible Markup Language (Bosak and Bray, 1999; Bray et al., 2000). This document contains many examples of SBML models written in XML, as well as the text of an XML Schema (Biron and Malhotra, 2000; Fallside, 2000; Thompson et al., 2000) that defines SBML Level 2 Version 2. A downloadable copy of the XML Schema and other related documents and software are also 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 of the scope of this document.


Item Type:Report or Paper (Documentation)
Related URLs:
URLURL TypeDescription
http://sbml.org/Documents/Specifications/SBML_Level_2/Version_2OtherUNSPECIFIED
ORCID:
AuthorORCID
Hucka, Michael0000-0001-9105-5960
Additional Information:This is the specification for SBML Level 2 Version 2.
Funders:
Funding AgencyGrant Number
NIHGM070923
National Human Genome Research Institute UNSPECIFIED
International Joint Research Program of NEDO (Japan)UNSPECIFIED
JST ERATO-SORST Program (Japan)UNSPECIFIED
Ministry of Agriculture (Japan)UNSPECIFIED
Ministry of Education, Culture, Sports, Science and Technology (MEXT)UNSPECIFIED
Biotechnology and Biological Sciences Research Council (BBSRC)UNSPECIFIED
Defense Advanced Research Projects Agency (DARPA)UNSPECIFIED
Air Force Office of Scientific Research (AFOSR)UNSPECIFIED
CaltechUNSPECIFIED
University of HertfordshireUNSPECIFIED
Molecular Sciences Institute UNSPECIFIED
Systems Biology Institute (Japan)UNSPECIFIED
Record Number:CaltechAUTHORS:20130111-172633006
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20130111-172633006
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:36339
Collection:CaltechAUTHORS
Deposited By: Linda Taddeo
Deposited On:14 Jan 2013 15:47
Last Modified:21 Dec 2016 23:44

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