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The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints

Olivier, Brett G. ; Bergmann, Frank T.

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
Constraint-based modeling is a well established modelling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size, genome scale models are typically analysed using constraint-based optimization techniques. One widely used method is Flux Balance Analysis (FBA) which, for example, requires a modelling description to include: the definition of a stoichiometric matrix, an objective function and bounds on the values that fluxes can obtain at steady state. 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 modelling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing. The FBC package establishes a base level for the unambiguous exchange of genome-scale, constraint-based models, that can be built upon by the community to meet future needs (e. g. by extending it to cover dynamic FBC models).


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Olivier, Brett G. ; Bergmann, Frank T.  (2015)  The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 12(2): Special Issue: Standards in Systems Biology, 2015

Online-Journal: http://journal.imbio.de
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2015/5373



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