Mouse 1.1 - Githubissues

SysBioChalmers / Mouse-GEM

Genome-scale model for Mus musculus

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Mouse 1.1 #7

Closed haowang-bioinfo closed 3 years ago

haowang-bioinfo commented 3 years ago

Main improvements in this PR:

Style (PR #6):
- update .standard-GEM.md file according to the spec of standard-GEM ver 0.5
Features (commit b7a4c06598cb906ef92467f56d3b0861fdf45e65):
- include a gap-filling step for essential metabolic tasks
Features (commit 534aabf0cf52bf0b5dc4454c492fb796c69ac058):
- add ascorbate transport rxn to allow Vitamin C biosynthesis

mihai-sysbio commented 3 years ago

With the versioning in Human-GEM and Mouse-GEM being different, I'm wondering how to make it more obvious to the community what version of the Human-GEM is used. Perhaps the version could be added to the Readme in the line with "Model source".

haowang-bioinfo commented 3 years ago

Good question. The version dependency information is stored in the dependencies.txt file under model folder.

mihai-sysbio commented 3 years ago

Good question. The version dependency information is stored in the dependencies.txt file under model folder.

It looks like that file duplicates some of the dependencies listed in the Readme. According to the DRY principle, I find it better to have only one place to store this. And for ease of access, the Readme looks like a better place. But perhaps that dependencies.txt file is managed programatically?

haowang-bioinfo commented 3 years ago

It looks like that file duplicates some of the dependencies listed in the Readme. According to the DRY principle, I find it better to have only one place to store this. And for ease of access, the Readme looks like a better place. But perhaps that dependencies.txt file is managed programatically?

The dependencies.txt is the only place for version information. Yes, this file should be updated programatically.