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Releases: SysBioChalmers/yeast-GEM

yeast 9.0.1

14 Aug 14:08
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  • Features:
    • Provide reference metabolite concentration from YMDB, which can be loaded with code/missingFields/addYMDBconcentrations.m. (PR #364)
  • Documentation:
    • Update citation and README.md. (PR #368)
  • Chore:
    • Use latest RAVEN (2.9.3) for import/export (resolved bug SysBioChalmers/RAVEN#529 results in higher accuracy in gene essentiality prediction).

yeast 9.0.0

04 Dec 08:52
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  • 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

17 Oct 20:42
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  • 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

21 Jul 17:32
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  • 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

07 Jul 23:18
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  • Feature:
    • New reactions and metabolites related to volatile esters & polyphosphates. (PR #337)

yeast 8.6.2

05 Sep 18:27
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  • Fixes:
    • Correct ATP synthase mitochondrial complex gene associations (PR #323).

yeast 8.6.1

05 Sep 13:42
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  • 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

18 May 01:28
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  • 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

02 Jul 17:10
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  • 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

23 Sep 08:30
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  • 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.