yeast 9.0.0

• Fixes:
  • Correct unbalanced reactions r_4196 (closes #358), r_4240, r_4722. (PR #360)
  • Correct metFormula of various dolichol-related metabolites. (PR #360)
  • increaseVersion uses YAML-model as input, to ensure it contains the deltaG annotations. (PR #360)

yeast 8.7.1

• Features:
  • UniProt annotations for all genes. (PR #349)
• Fixes:
  • Failing GitHub Action workflows. (PR #350)
  • Correct 'enxyme' in r_1024 reaction name. (PR #355)
  • Make .standard-GEM.md hidden. (PR #357)

yeast 8.7.0

• Features:
  • Add reactions based on KEGG and MetaCyc annotations. (PR #304)
  • Add metDeltaG and rxnDeltaG fields. (PR #330)
  • Add metSmiles field. (PR #344)
• Fixes:
  • Fructose transporter r_1134 as facilitated diffusion, not symport. (closes #332)
  • Remove genes from spontaneous half-reactions (r_0029 and r_0030) of 3-isopropylmalate dehydrogenase. (closes #331)

yeast 8.6.3

• Feature:
  • New reactions and metabolites related to volatile esters & polyphosphates. (PR #337)

yeast 8.6.2

• Fixes:
  • Correct ATP synthase mitochondrial complex gene associations (PR #323).

yeast 8.6.1

• Fixes:
  • Manual curation of gene associations of transport reactions, based on various databases. (PR #306, closes #160)
  • Correct annotation of gene associations of enzyme complex, based on Complex Portal, Uniprot and SGD. (PR #305)
  • Curate 19 new GPR and consolidate curations between model releases. (PR #313)
• Features:
  • Assignment of single subSystem per reactions. (PR #307, closes #11)
• Refactor:
  • Reduce software dependencies of modelTests. (PR #305, closes #309)

yeast 8.6.0

• Fixes:
  • Closes #265: Make r_0446 (formate-tetrahydrofolate ligase) irreversible, to prevent non-zero flux through TCA cycle (PR #290).
• Features:
  • Add pathways responsible for the formation of hydrogen sulfide as well as other volatile sulfur compounds during fermentation (PR #300).
  • Closes #302: Simplify model curation with curateRxnsGenesMets function (PR #300).
  • Remove COBRA Toolbox and MATLAB-git dependencies for the MATLAB-based curation pipeline (PR #303).
  • Closes #308: Distribute yeast-GEM.mat in RAVEN's format, to include grRules and metComps fields (PR #301).
• Refactor:
  • Change format of yeast-GEM.txt file to include metabolite names and compartments, instead of metabolite identifiers, to simplify diff-ing (metabolite identifiers are already trackable in the yml-file) (PR #312).

yeast 8.5.0

• Features:
  • Set up memote as GitHub Action for pull requests (PR #162)
  • Moved old subSystems to reaction annotations (in rxnMiriams or rxnKEGGpathways) (PR #253)
• Fixes:
  • Combine glycolysis + gluconeogenesis as single KEGG pathway annotations (PR #251).
  • Closes #252: Correct grRule of r_4590 (PR #255).
  • Closes #254: Corrects name of s_1218 (PR #255).
  • saveYeastModel.m now correctly handles Unicode characters (PR #255).
  • Closes #238: Correct indentation of yeastGEM.yml (PR #236 and #255).
• Chore:
  • Update dependencies in *requirements.txt (PR #256).
  • Minor changes in model file formatting due to updates in COBRA+RAVEN toolboxes (PR #253).
• Refactor:
  • Closes #232: Follow standard-GEM specifications (PR #257).
  • Closes #258: Rename git branches master and devel to main and develop (PR #261).

yeast 8.4.2

• Features:
  • saveYeastModel.m now checks if the model can grow and, based on the allowNoGrowth flag, returns either warnings or errors if not (PR #244).
  • Added several fatty acid ester producing reactions to the model, for improved simulation of alcoholic fermentation conditions (PRs #190 and #248).
• Fixes:
  • Closes #242: Fixed a bug that prevented the model from growing (PR #243).
  • Corrected directionality of 23 reactions and removed a generic reaction (PR #228).

NOTE: This release is made with the main version of COBRA; however, as they have dropped tagged releases for the time being, /ModelFiles/dependencies.txt points to a specific commit from their master branch.

yeast 8.4.1

• Features:
  • Switched to pip-tools for managing python dependencies, distinguishing between user requirements /requirements/requirements.txt and developer requirements /requirements/dev-requirements.txt (PR #235).
• Fixes:
  • Closes #201: Changed generic protein name to avoid confusion (PR #237).
  • Closes #205: Finished correcting reactions' stoichiometry based on KEGG data (PR #237).
  • Closes #215: Corrected wrong gene rule in reaction (PR #237).
  • Closes #225: Moved MNX rxn ids from notes to the proper annotation field (PR #226).
• Documentation:
  • Closes #223: Clarified releasing steps, including authorship criteria for Zenodo releases, in contributing guidelines (PR #233).
  • Closes #227: Removed authorships/dates from all scripts, as it is redundant information (PR #230).
  • Added admin guidelines for managing python dependencies (PR #235).
  • Included links for model visualization in README file (PR #240).

NOTE: This release is (still) made with the development version of COBRA toolbox, as their latest release is not able to preserve BiGG ids.