SysBioChalmers / panYeast-GEM

Reconstruction of a pan-genome metabolic model for S. cerevisiae - the pan model and scripts to make strain-specific models.

Creative Commons Attribution 4.0 International

0 stars 1 forks source link

convert yeast-GEM to pan-submodel #1

Open edkerk opened 6 years ago

edkerk commented 6 years ago

A large part of the panYeast-GEM will be derived from yeast-GEM. For now, prepare Matlab scripts that can do this conversion. In the future, this should ideally be dealt with through continuous integration with e.g. Jenkins.

[ ] initiate Matlab script that loads yeast-GEM model and will do the conversion
[ ] replace S288c genes in yeast-GEM with their corresponding panIDs
[ ] check whether grRules still make sense, particularly concerning the same panID occuring multiple times due to isoenzymes

edkerk commented 6 years ago

7 now provides the table to replace S288c genes with their panIDs. Keep in mind:

'Or' relation should be used if one panID(nonORF) and another panID(ORF from s288c genome) are belong to the 'ortholog' relation.

Example: YML056C exists as panID 5975-YML056C but also annotated as ortholog for panID 1729-snap_masked-BBH_6-7041. Any grRule with YML056C in yeast-GEM should then be replaced with 5975-YML056C OR 1729-snap_masked-BBH_6-7041.