GEM reconstruction protocol: Hansenula polymorpha#

A complete homology-based reconstruction of hanpo-GEM, followed from start to finish: it takes template models as input and produces a growing methylotrophic draft. This is the published pipeline, in order, with the judgement calls left visible.

It is the counterpart to the user guide. The numbered guide pages answer "how do I do this one thing"; this protocol answers "what does a whole reconstruction look like, and in what order".

Note

MATLAB only, and not executed here The protocol predates the dual-language guide and its steps are MATLAB. Its commands are also not run by the documentation build, unlike the numbered guide pages; several steps take hours and need data that is not shipped with this site.

The steps#


Introduction	what is being built, and from what
Materials and installation	software, databases and input files
Import template models	the S. cerevisiae and R. toruloides models the draft is built from
Draft from homology	BLAST and `getModelFromHomology`; see also 12. Reconstruction from homology
Biomass composition	measuring and assembling the biomass equation
Curation of lipid reactions	the part that never generalises
Gap-filling	closing the holes; see also 17. Gap-filling
Save and simulate	writing the model out and checking it grows
Manual curation	what no function does for you