GIMME

GIMME(model, expressionRxns, threshold, obj_frac)

Use the GIMME algorithm (Becker and Palsson, 2008) to extract a context specific model using data. GIMME minimizes usage of low-expression reactions while keeping the objective (e.g., biomass) above a certain value. Note that this algorithm does not favor the inclusion of reactions not related to the objective.

USAGE:

tissueModel = GIMME(model, expressionRxns, threshold)

INPUTS:

model: input model (COBRA model structure) expressionRxns: expression data, corresponding to model.rxns (see

mapGeneToRxn.m)

threshold: expression threshold, reactions below this are

minimized

OPTIONAL INPUT:

obj_frac: minimum fraction of the objective(s) of model

(default value - 0.9)

OUTPUTS:

tissueModel: extracted model

Becker and Palsson (2008). Context-specific metabolic networks are consistent with experiments. PLoS Comput. Biol. 4, e1000082.