title: The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.
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).
authors.forename: Brett G
authors.initials: BG
authors.lastname: Olivier
authors.forename: Frank T
authors.initials: FT
authors.lastname: Bergmann
mesh_terms: D000818:Animals; D064229:Biological Ontologies; D003196:Computer Graphics / Q000592:standards; D066264:Datasets as Topic / Q000592:standards; D004282:Documentation / Q000592:standards; D006801:Humans; D016247:Information Storage and Retrieval / Q000592:standards; D038622:Internationality; D064688:Metabolic Flux Analysis / Q000592:standards*; D008954:Models, Biological; D011381:Programming Languages; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D049490:Systems Biology / Q000592:standards*
chemical_list: D020543:Proteome