history.md

History

yeast 9.0.2:

• Fixes:
  • Curation based on auxotrophy predictions. (closes #371)
  • Correct UniProt ID for YCR024C. (closes #372)

yeast 9.0.1:

• 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:

• 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:

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

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:

• Features:
  • 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).

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).

yeast 8.4.0:

• Features:
  • New functions mapKEGGID.m and mapMNXMID.m for adding ids in model. Used them to add missing KEGG and MetaNetX ids for both metabolites and reactions (PR #220).
  • Solves #197: Added missing MetaNetX ids using KEGG ids and ChEBI ids (PR #220).
  • Added BiGG ids for all matched metabolites/reactions using MetaNetX + manual curation, together with lists containing new BiGG ids for the unmatched ones (PR #188).
  • New functions read_yeast_model and write_yeast_model for easier usage in python (PR #224).
  • Solves #172: Model can now be loaded with BiGG ids as main ids, for better compliance with cobrapy (PR #224).
• Fixes:
  • Solves #102: Every component of the model is now preserved when the model is opened with cobrapy, including gene names (PR #216).
  • Manual curation of MetaNetX, KEGG and ChEBI ids for metabolites/reactions (PRs #188 and #220).
  • Solves #187: Removed some duplicate reactions in the model (PR #188).
  • Mass/charge balanced most unbalanced reactions in model using checkSmatrixMNX.m, bringing the number down to 17 reactions (PR #222).
• Others:
  • Configured repo to ensure that files always use LF as EOL character (PR #221).
  • Gene SBO terms are now recorded, after update in COBRA toolbox (PR #188).

yeast 8.3.5:

• Fixes:
  • Closes #129: Removed non-S288C genes (PR #211).
  • Closes #198: Fixes function for converting model to anaerobic (PR #199).
• Tests:
  • Added growth tests for carbon & nitrogen limitation (#199).
  • Added test for computing gene essentiality (PR #200).
• Documentation/Others:
  • Clarified with README's the purpose of each script/data folder (#209).
  • Closes #206: Updated citation guidelines (PR #210).
  • Updated contribution guidelines + issue/PR templates (PR #210).
  • Created folders with deprecated scripts (PR #209).

yeast 8.3.4:

• Features:
  • Fixes #171: Added 101 GPR rules to transport rxns according to TCDB database (PR #178).
  • Added 18 met formulas from manual search (PR #155).
  • Performed gap-filling for connecting 29 dead-end mets, by adding 28 transport rxns (PR #185). Added documentation to the gap-filling functions in PR #195.
• Fixes:
  • Corrected typo in gene ID (PR #186).

yeast 8.3.3:

• Features:
  • Fixes #107: Two new pseudoreactions (cofactor pseudoreaction and ion pseudoreaction) added to the model as extra requirements to the biomass pseudoreaction (PRs #174 & #183).
• Fixes:
  • addSBOterms.m adapted to identify new pseudoreactions (PR #180).
  • Removed non-compliant symbol from a reaction name to avoid parsing errors (PR #179).
• Documentation:
  • Model keywords modified to comply with the sysbio rulebook (PR #173).
  • Added citation guidelines (PR #181).

yeast 8.3.2:

• Features:
  • Fixes #154: MetaNetX IDs added from the yeast7.6 MetaNetX model & from existing ChEBI and KEGG IDs in the model (PR #167).
  • Introduced contributing guidelines + code of conduct (PR #175).
• Fixes:
  • Fixes #161: Added as rxnNotes and metNotes the corresponding PR number (#112, #142, #149 or #156) in which each rxn and met was introduced (PR #170).
  • Fixes #169: Compartment error for r_4238 (PR #170).
  • Corrected confidence score of rxns from PR #142 (PR #170).

yeast 8.3.1:

• Features:
  • Added 21 reactions & 14 metabolites based on metabolomics data (PR #156).
  • Added metadata to the excel version of the model (PR #163).
  • Added ComplementaryData/physiology with biological data of yeast (PR #159).
• Fixes/Others:
  • Fixed bug that underestimated the biomass content (PR #159).
  • Fitted GAM to chemostat data (PR #159).

yeast 8.3.0:

• Features:
  • Added 225 new reactions and 148 new metabolites, based on growth data from a Biolog substrate usage experiment on carbon, nitrogen, sulfur and phosphorus substrates (PR #149).
• Fixes/Others:
  • Removed verbose details from README.md (PR #150).
  • Updated RAVEN, which added extra annotation to the .yml file (PR #151).
  • Minor changes to saveYeastModel.m (PR #152).
  • Model is now stored simulating minimal media conditions (PR #157).

yeast 8.2.0:

• Features:
  • Fixes #38: Added 183 new reactions, 277 new metabolites and 163 new genes based on the latest genome annotation in SGD, uniprot, KEGG, Biocyc & Reactome (PR #142).
• Fixes:
  • grRules deleted from pseudoreactions, removing with this 49 genes (PR #145).
• Chores:
  • Updated COBRA, which changed the number of decimals in some stoichiometric coefficients in .txt (PR #143)

yeast 8.1.3:

• Features:
  • Added SBO terms for all metabolites and reactions, based on an automatic script now part of saveYeastModel.m (PR #132).
  • increaseVersion.m now avoids conflicts between devel and master by erroring before releasing and guiding the admin to change first devel (PR #133).
  • Website now available in gh-pages branch: http://sysbiochalmers.github.io/yeast-GEM/
• Fixes:
  • Standardize naming of pseudo-metabolites "lipid backbone" & "lipid chain" (PR #130).
• Chores:
  • Updated COBRA, which swapped around the order of the bqbiol:is and bqbiol:isDescribedBy qualifiers in the .xml file (PR #131).

yeast 8.1.2:

• New features:
  • saveYeastModel.m now checks if the model is a valid SBML structure; if it isn't it will error (PR #126).
  • Date + model size in README.md updates automatically when saving the model (PR #123).
  • Added modelName and modelID; the latter which will now store the version number (PR #127).
• Fixes:
  • Fixes #60: New GPR relations for existing reactions were added according to new annotation from 5 different databases (PR #124).
  • Various fixes in README.md (PR #123).

yeast 8.1.1:

• Fixes:
  • Fixes #96: regardless if the model is saved with a windows or a MAC machine, the .xml file is now stored with the same scientific format.
  • Fixes #108: No CHEBI or KEGG ids are now shared by different metabolites. Also, updated the metabolites that were skipped in the previous manual curation (PR #74).
  • Remade function for defining confidence scores, which fixed 38 scores in rxnConfidenceScores (most of them from pseudoreactions).
  • loadYeastModel and saveYeastModel were improved to allow their use also when outside of the actual folder.

yeast 8.1.0:

• New features:
  • SLIME reactions added to the model using SLIMEr, to properly account for constraints on lipid metabolism (fixes #21):
    • SLIME rxns replace old ISA rxns for lumping lipids. They create 2 types of lipid pseudometabolites: backbones and acyl chains.
    • There are now 3 lipid pseudoreactions: 1 constrains backbones, 1 constrains acyl chains, 1 merges both.
• Fixes:
  • All metabolite formulas made compliant with SBML (fixes #19). Model is now a valid SBML object.
  • Biomass composition was rescaled to experimental data from Lahtvee et al. 2017, including protein and RNA content, trehalose and glycogen concentrations, lipid profile and FAME data. Biomass was fitted to add up to 1 g/gDW by rescaling total carbohydrate content (unmeasured).
• Refactoring:
  • Organized all files in ComplementaryData

yeast 8.0.2:

• New features:
  • Model can now be used with cobrapy by running loadYeastModel.py
  • loadYeastModel.m now adds the rxnGeneMat field to the model
• Refactoring:
  • Moved pmids of model from rxnNotes to rxnReferences (COBRA-compliant)
  • yeastGEM.yml and dependencies.txt are now updated by RAVEN (a few dependencies added)
  • Moved boundaryMets.txt and dependencies.txt to the ModelFiles folder
• Documentation:
  • Added badges and adapted README ro reflect new features

yeast 8.0.1:

• .yml format included for easier visualization of model changes
• Empty notes removed from model
• Issue and PR templates included
• README.md updated to comply with new repo's name

yeast 8.0.0:

First version of the yeast8 model, to separate it from previous versions:

• Manual curation project:
  • All metabolite information manually curated (names, charges, kegg IDs, chebi IDs)
  • Reaction gene rules updated with curation from the iSce926 model. 13 genes added in this process
• Format changes:
  • Folder ComplementaryData introduced
  • All data is stored in .tsv format now (can be navigated in Github)
  • Releases now come in .xlsx as well
• Other new features:
  • Added loadYeastModel.m
  • A much smarter increaseVersion.m
  • Lots of refactoring

yeast 7.8.3:

• curated tRNA's formulas
• started tracking COBRA and RAVEN versions
• dropped SBML toolbox as requirement
• reorganized complementaryScripts
• switched to a CC-BY-4.0 license

yeast 7.8.2:

• fixed subSystems bug: now they are saved as individual groups
• solved inter-OS issues
• remade license to follow GitHub format
• added history.md and made it a requirement to update when increasing version

yeast 7.8.1:

• started following dependencies
• started keeping track of the version in the repo (version.txt)
• included .gitignore
• dropped .mat storage for devel + feature branches (but kept it in master)

yeast 7.8.0:

• Added information:
  • metFormulas added for all lipids
  • rxnKEGGID added from old version
  • rxnNotes enriched with Pubmed ids (pmid) from old version
  • rxnConfidenceScores added based on automatic script (available in ComplementaryScripts)
• Format changes:
  • Biomass clustered by 5 main groups: protein, carbohydrate, lipid, RNA and DNA

yeast 7.7.0:

• Format changes:
  • FBCv2 compliant
  • Compatible with latest COBRA and RAVEN parsers
  • Created main structure of repository
• Added information:
  • geneNames added to genes based on KEGG data
  • subSystems and rxnECnumbers added to reactions based on KEGG & Swissprot data
  • Boundary metabolites tracked (available in ComplementaryScripts)
• Simulation improvements:
  • Glucan composition fixed in biomass pseudo-rxn
  • Proton balance in membrane restored
  • Ox.Pho. stoichiometry fixed
  • NGAM rxn introduced
  • GAM in biomass pseudo-rxn fixed and refitted to chemostat data

yeast 7.6.0:

First release of the yeast model in GitHub, identical to the last model available at https://sourceforge.net/projects/yeast/