Part 2: manual curation

gempipe recon produced a draft pan-GSMM: before proceeding with the derivation of strain-specific GSMMs (gempipe derive), the draft pan-GSMM must be curated. Its manual curation consists of several tasks, such as:

• ensuring the stoichiometric consistency of the model.

• removing eventual erroneous energy-generating cycles (EGCs).

• adding missing reactions, finding unmodeled metabolic genes on the functional annotation table.

• adapting the biomass assembly reaction, for example removing strain-specific biomass precursors.

• and so on…

The Gempipe API includes handy functions to speed up the manual curation, like for example check_reactants, which indicates the blocked precursors of a reaction, or perform_gapfilling, which suggests reactions to include to enable the biosynthesis of a particular metabolite. Tutorials are available to show the usage of some of the Gempipe API functions:

• Tutorial: gap-filling

• Tutorial: sanity check

The provided API is not aimed to replace the community effort Memote, but just to provide a quick and convenient way to check the main sanity standards and perform gap-fillings before going on deriving strain-specific GSMMs with gempipe derive.

⏩ Warning! An additional command line program gempipe autopilot is provided, which internally calls gempipe recon and gempipe derive, linking them together performing an automated gap-filling on the draft pan-GSMM, as a (discouraged) alternative to the manual curation.