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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 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

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Volume 12, Issue 2


SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3

Lucian P. Smith / Michael Hucka
  • Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, United States of America
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Stefan Hoops / Andrew Finney / Martin Ginkel / Chris J. Myers
  • Electrical and Computer Engineering, University of Utah, Salt Lake City, United States of America
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/ Ion Moraru
  • University of Connecticut Health Center, University of Connecticut, Farmington, United States of America
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/ Wolfram Liebermeister
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2015-268


Constructing a model in a hierarchical fashion is a natural approach to managing model complexity, and offers additional opportunities such as the potential to re-use model components. The SBML Level 3 Version 1 Core specification does not directly provide a mechanism for defining hierarchical models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Hierarchical Model Composition package for SBML Level 3 adds the necessary features to SBML to support hierarchical modeling. The package enables a modeler to include submodels within an enclosing SBML model, delete unneeded or redundant elements of that submodel, replace elements of that submodel with element of the containing model, and replace elements of the containing model with elements of the submodel. In addition, the package defines an optional “port” construct, allowing a model to be defined with suggested interfaces between hierarchical components; modelers can chose to use these interfaces, but they are not required to do so and can still interact directly with model elements if they so chose. Finally, the SBML Hierarchical Model Composition package is defined in such a way that a hierarchical model can be “flattened” to an equivalent, non-hierarchical version that uses only plain SBML constructs, thus enabling software tools that do not yet support hierarchy to nevertheless work with SBML hierarchical models.

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 603–659, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2015-268.

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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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