Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
Workflow of automatic update of enzyme-constrained models. Taken from the original publication: https://doi.org/10.1038/s41467-022-31421-1Abstract
This is the sequel of the GECKO paper that I developed in my PhD, for integration of proteomics data in GEMs. In this new paper, Iván, an extremely talented former colleague, took over the lead of the code development and elevated the GECKO tool to new heights. The main achievements were to make the tool compatible with any GEM reconstruction, and to develop a workflow where as GEMs get upgraded and curated, the enzyme-constrained counterparts (ecModels) get automatically updated, using a container called ecModels (see figure). This was implemented for 5 species: Saccharomyces cerevisiae, Yarrowia lipolytica, Kluyveromyces marxianus, Escherichia coli and Homo sapiens. GECKO this way becomes an even more versatile tool for studying the interplay between enzymes and metabolic reactions within cells.
