GapFind automatically identifies metabolites that cannot be produced/consumed in a metabolic network. Specifically, the GapFind optimization formulation pinpoints metabolites that have no production/consumption routes (root no production/consumption metabolites) in the metabolic model AND the metabolites downstream/upstream of these metabolites that cannot carry any flux.

Using the list of gaps identified by GapFind, GapFill attempts to correct them by augmenting the metabolic model. GapFill is an optimization procedure that proceeds to fill these gaps by making the minimal number of modifications to the metabolic model using one or more of the following strategies:

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