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:
- adding reactions from external multi-organism databases such as KEGG or MetaCyc to the model,
- allowing for reactions to also operate in their reverse directions, and
- adding transport reactions (both intra and extracellular in the case of multi-compartment models).
The code is freely available for academic users. Before downloading our software, we ask for your name and institution so we may better design future versions of our software. Every consideration has been made during the design, writing, and posting of this code to ensure the program works properly.