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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 / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

Michael HuckaORCID iD: https://orcid.org/0000-0001-9105-5960 / Frank T. BergmannORCID iD: https://orcid.org/0000-0001-5553-4702 / Claudine ChaouiyaORCID iD: https://orcid.org/0000-0003-2350-0756 / Andreas DrägerORCID iD: https://orcid.org/0000-0002-1240-5553
  • Department of Computer Science, University of Tübingen, Tübingen, Germany
  • Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
  • German Center for Infection Research (DZIF), Tübingen, Germany
  • orcid.org/0000-0002-1240-5553
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Stefan HoopsORCID iD: https://orcid.org/0000-0001-8503-8371 / Sarah M. KeatingORCID iD: https://orcid.org/0000-0002-3356-3542 / Matthias KönigORCID iD: https://orcid.org/0000-0003-1725-179X / Nicolas Le NovèreORCID iD: https://orcid.org/0000-0002-6309-7327 / Chris J. MyersORCID iD: https://orcid.org/0000-0002-8762-8444 / Brett G. OlivierORCID iD: https://orcid.org/0000-0002-5293-5321 / Sven Sahle / James C. SchaffORCID iD: https://orcid.org/0000-0003-3286-7736 / Rahuman SheriffORCID iD: https://orcid.org/0000-0003-0705-9809 / Lucian P. SmithORCID iD: https://orcid.org/0000-0001-7002-6386 / Dagmar WaltemathORCID iD: https://orcid.org/0000-0002-5886-5563 / Darren J. WilkinsonORCID iD: https://orcid.org/0000-0003-0736-802X / Fengkai ZhangORCID iD: https://orcid.org/0000-0001-7112-9328
Published Online: 2019-06-20 | DOI: https://doi.org/10.1515/jib-2019-0021

Abstract

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. 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 Release 2 of Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. Release 2 corrects some errors and clarifies some ambiguities discovered in Release 1. 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 website at http://sbml.org/.

Keywords: Systems Biology Markup Language; Standards; Visualization; Representation

About the article

Received: 2019-03-30

Accepted: 2019-05-20

Published Online: 2019-06-20


Citation Information: Journal of Integrative Bioinformatics, 20190021, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2019-0021.

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© 2019, Michael Hucka et al., published by Walter de Gruyter GmbH, Berlin/Boston. This work is licensed under the Creative Commons Attribution 4.0 Public License. BY 4.0

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