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

• Manual curation project:
  • 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)