Gimme

GIMME(model, expressionRxns, threshold, obj_frac)[source]

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.