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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan

4 Issues per year


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 12, Issue 2

Issues

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

Michael Hucka / Frank T. Bergmann / Andreas Dräger / Stefan Hoops / Sarah M. Keating
  • European Bioinformatics Institute, Cambridgeshire, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Nicolas Le Novère / Chris J. Myers / Brett G. Olivier / Sven Sahle / James C. Schaff / Lucian P. Smith
  • California Institute of Technology, Pasadena, United States of America
  • University of Washington, Seattle, United States of America
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Dagmar Waltemath
  • California Institute of Technology, Pasadena, United States of America
  • University of Rostock, Rostock, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Darren J. Wilkinson
  • California Institute of Technology, Pasadena, United States of America
  • Newcastle University, Newcastle, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2015-271

Summary

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. 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. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

About the article

Published Online: 2016-10-18

Published in Print: 2015-06-01


Citation Information: Journal of Integrative Bioinformatics, Volume 12, Issue 2, Pages 731–901, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2015-271.

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© 2015 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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