Rat 1.0

[haowang-bioinfo]

Main improvements in this PR:

• Features (PR feat: add model generation code #3):
  • add code masterScriptRatGEM for the reconstruction of Rat-GEM
• Features (PR feat: add ortholog data and rat-specific reactions and metabolites #2):
  • upload data files
    • rat-specific pathways in ratSpecificRxns.tsv and ratSpecificMets.tsv
    • ortholog pairs from Alliance of Genomes ver 3.1.1
• Features (PR feat: update readme #1):
  • update README according to the spec defined in standard-GEM ver 0.5

[johan-gson]

I did not look into details here

[JonathanRob]

Looks good. Only minor comment: the README now references the contribution guidelines (CONTRIBUTING.md), but they're currently empty. Might be good to update this soon.

[mihai-sysbio]

@JonathanRob this file was provided empty by standard-GEM. The instructions in .standard-GEM.md in the File tree section cover this compulsory requirement, together with a few others, such as the presence of the yml file on branch devel.