Rat 1.8.0

• Features:
  • update Human-GEM template to ver 1.18.0

Rat 1.7.0

• Features:
  • update ortholog pairs from Alliance of Genomes to ver 6.0.0 (commit c7eb59b)
  • update Human-GEM template to ver 1.17.0

Rat 1.6.0

• Fixes (commit 3251232):
  • modify met ids to avoid potential conflict with Human-GEM
• Features:
  • update Human-GEM template to ver 1.16.0

Rat 1.5.0

• Fixes (commit 565a306):
  • change reaction IDs conflicting to recent changes to Human-GEM
• Features:
  • update ortholog pairs from Alliance of Genomes to ver 5.4.0 (commit f250eaf)
  • update Human-GEM template to ver 1.15.0
• Style (commit 565a306):
  • add gene names to new field geneShortNames

Rat 1.4.0

• Fixes (PR 460):
  • fix: correct MAM03882 annotation, as reported in Mouse-GEM #21
• Fixes (PR 429):
  • feat: add Acod1(Irg1) gene and associated reaction, as discussed in Mouse-GEM #20
• Features:
  • update ortholog pairs from Alliance of Genomes to ver 5.3.0 (commit f5f7845)
  • update Human-GEM template to ver 1.14.0
• Style (commit cee1e29):
  • change human-rat ortholog file from json to tsv, as discussed in Mouse-GEM #15

Rat 1.3.1

• remove additional annotation information from .mat and .yml model files (PR #9)
  • resolves SysBioChalmers/Mouse-GEM#16
• Sync model with latest version of Human-GEM (now v1.12.0)
  • done automatically by running masterScriptRatGEM script

Rat 1.3.0

• Fixes/Features (commit e212ed3 , PR 382):
  • add annotation information to model with updated annotateGEM function, before exporting
  • change compartment abbreviation from p to x, to sync with changes made in Human-GEM PR 341
  • update ortholog pairs from Alliance of Genomes to ver 5.1.1
• Style (PR #7):
  • add .gitattributes to ensure consistent LF (\n) line endings
  • add citation
  • rename branches: master --> main, devel --> develop

Rat 1.2.0

• Features (commit c71e121):
  • update GEM generating script by using function updateAnimalGEM and providing annotation files in tsv format
• Style (commit e78e04a):
  • apply MA format met/rxn identifiers in alignment with Human-GME v1.8
• Style (commit e7f5e34):
  • add metsNoComp column to ratSpecificMets.tsv

Rat 1.1.0

• Style (commit a01ebbd):
  • update .standard-GEM.md file according to the spec of standard-GEM ver 0.5
• Features (commit 2d6ed9b):
  • include a gap-filling step for essential metabolic tasks
• Features (commit db4e941):
  • add ascorbate transport rxn to allow Vitamin C biosynthesis

Rat 1.0.0

• Features (PR #3):
  • add code masterScriptRatGEM for the reconstruction of Rat-GEM
• Features (PR #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 #1):
  • update README according to the spec defined in standard-GEM ver 0.5