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Mouse 1.0 #4

Merged
merged 14 commits into from
Oct 24, 2020
Merged

Mouse 1.0 #4

merged 14 commits into from
Oct 24, 2020

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haowang-bioinfo
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@haowang-bioinfo haowang-bioinfo commented Oct 21, 2020 •
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Main improvements in this PR:

  • Features (PR feat: add model generation code #3):
    • add code masterScriptMouseGEM for the reconstruction of Mouse-GEM
  • Features (PR feat: add data #2):
    • upload data files
      • mouse-specific pathways in mouseSpecificRxns.tsv and mouseSpecificMets.tsv
      • ortholog pairs from Alliance of Genomes ver 3.1.1
      • MSigDB gene sets for mouse (ver 7.0)
  • Features (PR feat: update README #1):
    • update README according to the spec defined in standard-GEM ver 0.5

@mihai-sysbio
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mihai-sysbio commented Oct 21, 2020 •
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Just a side-note, the 2 README files in code and data are empty. Also, the docs/ folder should be deleted - I believe it was left over from an old version of standard-GEM. I would also like to take the opportunity to suggest using tags without v, as described here.

mihai-sysbio
mihai-sysbio reviewed Oct 21, 2020
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I was expecting to see a Mouse-GEM.yml on the devel branch. If possible, it would be cool also to see the script that takes all the input files and generates that yam - that would be really reproducible.

johan-gson
johan-gson approved these changes Oct 21, 2020
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I did not look into detail here

@haowang-bioinfo haowang-bioinfo merged commit b2085b8 into master Oct 24, 2020
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@mihai-sysbio mihai-sysbio mihai-sysbio left review comments

@JonathanRob JonathanRob JonathanRob approved these changes

@johan-gson johan-gson johan-gson approved these changes

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@haowang-bioinfo @mihai-sysbio @JonathanRob @johan-gson