GEM reconstruction protocol: Hansenula polymorpha

This protocol is 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. It is the published pipeline, in order, and states the choices made.

It is the counterpart to the user guide. Each numbered guide page covers one operation; this protocol covers a whole reconstruction in order.

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

Protocol steps

Page	Content
Introduction	what is being built, and from what
Materials and installation	software, databases and input files
Importing template models	the S. cerevisiae and R. toruloides models the draft is built from
Draft from homology	BLAST and getModelFromHomology; see also Reconstruction from homology
Biomass composition	measuring and assembling the biomass equation
Curation of lipid reactions	SLIME formalism for the lipid reactions
Gap-filling	making the draft able to produce biomass; see also Gap-filling
Saving to GitHub and simulating	writing the model out and checking it grows
Manual curation	fixing gene associations and adding methanol metabolism

Related

• Legacy tutorials, five shorter exercises from the original RAVEN paper.

• Reconstruction from homology, the same technique at small scale, in both languages, with every example executed.