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

J Integr Bioinform. 2015 Sep 4;12(2):269. doi: 10.2390/biecoll-jib-2015-269.

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).

Publication types

  • Guideline

MeSH terms

  • Animals
  • Biological Ontologies
  • Computer Graphics / standards
  • Datasets as Topic / standards
  • Documentation / standards
  • Guidelines as Topic / standards
  • Humans
  • Information Storage and Retrieval / standards
  • Internationality
  • Metabolic Flux Analysis / standards*
  • Models, Biological*
  • Programming Languages*
  • Proteome / metabolism*
  • Signal Transduction / physiology*
  • Systems Biology / standards*

Substances

  • Proteome