protocol for ecEcoli, and GECKO light protocol for Human-GEM

SysBioChalmers / GECKO

Toolbox for including enzyme constraints on a genome-scale model.

http://sysbiochalmers.github.io/GECKO/

MIT License

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protocol for ecEcoli, and GECKO light protocol for Human-GEM #314

Closed edkerk closed 1 year ago

edkerk commented 1 year ago

Description of the new feature:

[ ] Somewhat similar to the file in tutorials_yeast-GEM, a protocol.m should be written that details the reconstruction process of a GECKO light model. It could include comments only for the GECKO light specific commands and peculiarities, comments that are true for all of GECKO can be found in the tutorials_yeast-GEM example.

~- [ ] Minimal protocol.m for EcEcoli (full GECKO), based on stage 1-3 in the yeast-GEM tutorial. This protocol.m would only have comments for E. coli specific matters.~

Yu-sysbio commented 1 year ago

I am glad to make an E. coli protocol but the revision now does not mention any addition of E. coli. Is this E. coli protocol high priority? @edkerk

edkerk commented 1 year ago

No, let's scrap the E. coli protocol. The tutorials have also been renamed so not to directly mention the species (i.e. full_ecModel and light_ecModel), so it wouldn't make sense to include this.

Meanwhile, this would be useful to transition the ecModels to GECKO3, but this is outside the current revision, and the Issue should probably be raised in that repo instead.

mihai-sysbio commented 1 year ago

I believe PR #319 resolved this issue by setting up a tutorial for a full GECKO for yeast-GEM and a light GECKO for Human-GEM, so I'll go ahead and close it. Please reopen if needed.