Free Release of GEMrefine MATLAB Application

In Silico Fermentation is pleased to announce the release of GEMrefine, a free MATLAB application that enables manual refinement and analysis of draft genome-scale metabolic reconstructions (GEMs) within a GUI environment. The main app allows the tabularization and search of all model, reactions and genes along with their relevant properties. Existing reactions and metabolites can be edited, while new metabolites and genes can be automatically added through the manual addition of new reactions. For draft models generated with the ModelSEED and KBase platforms or other pipelines such as gapseq that utilize ModelSEED nomenclature, new reactions and metabolites can be added directly from a tabularized version of the ModelSEED biochemistry database.

An integrated companion app allows detailed structural and functional analysis of the refined reconstruction. To identify pathway gaps, the user can display all blocked reactions as well as all dead-end and blocked metabolites. Pathway function can be checked by calculating the maximal flux between any two metabolites. Nutrient uptake bounds can be modified before performing flux balance analysis (FBA) and flux variability analysis (FVA) to calculate and plot the growth rate, nutrient uptake fluxes, and product secretion fluxes. The modified model can be saved at any point during the refinement process.

More information about GEMrefine and the freely downloadable application are available here.