SBML Level 3 Package: Flux Balance Constraints version 2
- Creators
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Olivier, Brett G.
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Bergmann, Frank T.
Abstract
Constraint-based modeling is a well established modeling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size and complexity such steady-state flux models are, typically, analyzed using constraint-based optimization techniques, for example, flux balance analysis (FBA). The Flux balance constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modeling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing. Version two expands on the original release by adding official support for encoding gene-protein associations and their associated elements. In addition to providing the elements necessary to unambiguously encode existing constraint-based models, the FBC Package provides an open platform facilitating the continued, cross-community development of an interoperable, constraint-based model encoding format.
Additional Information
©2018 Brett G. Olivier et al., published by De Gruyter. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. Received: 2017-12-21; Accepted: 2018-02-08; Published Online: 2018-03-09. We would like to thank all the people who contributed in various ways to the development of both the original proposal and this specification. For financial/travel/technical support and highly productions discussions we thank especially (in alphabetical order): Michael Hucka (CalTech, USA), Ursula Kummer (Heidelberg University, Germany), Herbert Sauro (University of Washington, USA) and Bas Teusink (VU University Amsterdam, The Netherlands). A special word of thanks goes to Sarah M. Keating for her invaluable work with the libSBML and SBML Toolbox implementations and critical reading of this document. We also would like to thank (in alphabetical order) Andreas Dräger, Ali Ebrahim, Ronan Fleming, Ben Heavner, Daniel Hyduke, Nicolas Le Novère, Chris Myers, Nicolas Rodriguez, Kieran Smallbone, Lucian Smith, Neil Swainston, Alex Thomas, other members of the FBC Package Working Group, the libSBML and JSBML development teams and all others who contributed to discussions on various occasions. If you feel you should be mentioned in this section please contact the authors and ask to be included.Attached Files
Published - SBML_Level_3_Package_Flux_Balance_Constraints_version_2.pdf
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Additional details
- Eprint ID
- 86112
- Resolver ID
- CaltechAUTHORS:20180430-094555195
- Created
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2018-04-30Created from EPrint's datestamp field
- Updated
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2021-11-15Created from EPrint's last_modified field