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

2019-06-20Journal article Open access
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dc.contributor.authorHucka, Michael
dc.contributor.authorBergmann, Frank T.
dc.contributor.authorChaouiya, Claudine
dc.contributor.authorDräger, Andreas
dc.contributor.authorHoops, Stefan
dc.contributor.authorKeating, Sarah M.
dc.contributor.authorKönig, Matthias
dc.contributor.authorNovère, Nicolas Le
dc.contributor.authorMyers, Chris J.
dc.contributor.authorOlivier, Brett G.
dc.contributor.authorSahle, Sven
dc.contributor.authorSchaff, James C.
dc.contributor.authorSheriff, Rahuman
dc.contributor.authorSmith, Lucian P.
dc.contributor.authorWaltemath, Dagmar
dc.contributor.authorWilkinson, Darren J.
dc.contributor.authorZhang, Fengkai
dc.date.accessioned2020-03-11T12:19:51Z
dc.date.available2020-03-11T12:19:51Z
dc.date.issued2019-06-20
dc.description.abstractComputational 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/.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationHucka, M., Bergmann, F. T., Chaouiya, C., Dräger, A., Hoops, S., Keating, S. M., König, M., Novère, N. L., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Sheriff, R., Smith, L. P., Waltemath, D., Wilkinson, D. J., & Zhang, F. (2019). The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. Journal of integrative bioinformatics, 16(2), 20190021. https://doi.org/10.1515/jib-2019-0021pt_PT
dc.identifier.doi10.1515/jib-2019-0021pt_PT
dc.identifier.issn1613-4516
dc.identifier.urihttp://hdl.handle.net/10400.7/935
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherDe Gruyter Openpt_PT
dc.relation.publisherversionhttps://www.degruyter.com/view/j/jib.2019.16.issue-2/jib-2019-0021/jib-2019-0021.xmlpt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectSystems Biology Markup Language, Standards, Visualization, Representationpt_PT
dc.titleThe Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2pt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.conferencePlaceBerlin/Bostonpt_PT
oaire.citation.issue2pt_PT
oaire.citation.titleJournal of Integrative Bioinformaticspt_PT
oaire.citation.volume16pt_PT
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT

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