Mba

MBA(model, medium_set, high_set, tol)[source]

Uses the MBA algorithm (Jerby et al., 2010) to extract a context specific model using data. MBA algorithm defines high-confidence reactions to ensure activity in the extracted model. Medium confidence reactions are only kept when a certain parsimony trade-off is met. In random order, the algorithm prunes other reactions and removes them if not required to support high- or medium- confidence reactions.

USAGE

tissueModel = MBA (model, medium_set, high_set)

INPUTS

  • model – input model (COBRA model structure)

  • medium_set – list of reactions with medium confidence

  • high_set – list of reactions with high confidence

OPTIONAL INPUTS

tol – minimum flux threshold for “expressed” reactions (default 1e-8)

OUTPUT

tissueModel – extracted model

Jerby et al. (201)). Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol. Syst. Biol. 6, 401.