GEM reconstruction protocol: Hansenula polymorpha#
The protocol is a complete homology-based reconstruction of hanpo-GEM, from the template models as input to a draft that grows on methanol. It follows the published pipeline in order and states the choices that were made.
The protocol complements the user guide. Each page of the guide covers one operation, and the protocol covers a whole reconstruction in order.
The guide covers MATLAB and Python, and the protocol steps use MATLAB. The documentation build does not run its commands, unlike the guide pages. Several steps take hours and need data that this site does not ship.
Protocol steps#
Page |
Content |
|---|---|
what is built, and from what |
|
software, databases and input files |
|
the S. cerevisiae and R. toruloides models that the draft is built from |
|
BLAST and |
|
measuring and assembling the biomass equation |
|
the SLIME formalism for the lipid reactions |
|
making the draft able to produce biomass (Gap-filling) |
|
writing the model and checking that it grows |
|
correcting gene associations and adding methanol metabolism |