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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 15, Issue 1

Issues

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core

Michael HuckaORCID iD: http://orcid.org/0000-0001-5553-4702 / Frank T. BergmannORCID iD: https://orcid.org/0000-0001-5553-4702 / Andreas DrägerORCID iD: https://orcid.org/0000-0002-1240-5553 / Stefan Hoops / Sarah M. KeatingORCID iD: https://orcid.org/0000-0002-3356-3542 / 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: http://orcid.org/0000-0002-5293-5321 / Sven Sahle / James C. Schaff / Lucian P. SmithORCID iD: http://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
Published Online: 2018-03-09 | DOI: https://doi.org/10.1515/jib-2017-0081

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 Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

Keywords: SBML; modeling; computational biology; systems biology; standards

About the article

Received: 2017-12-19

Accepted: 2018-02-02

Published Online: 2018-03-09


Citation Information: Journal of Integrative Bioinformatics, Volume 15, Issue 1, 20170081, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2017-0081.

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©2018 Michael Hucka et al., published by De Gruyter, Berlin/Boston. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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