MBA

MBA(model, medium_set, high_set, tol)

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.