|
| 1 | +# History |
| 2 | + |
| 3 | +### yeast 8.6.0: |
| 4 | +- Fixes: |
| 5 | + - Closes #265: Make `r_0446` (formate-tetrahydrofolate ligase) irreversible, to prevent non-zero flux through TCA cycle. (PR #290) |
| 6 | +- Features: |
| 7 | + - Add pathways responsible for the formation of hydrogen sulfide as well as other volatile sulfur compounds during fermentation (PR #300) |
| 8 | + - Closes #302: Simplify model curation with `curateRxnsGenesMets` function (PR #300) |
| 9 | + - Remove COBRA Toolbox and MATLAB-git dependencies for the MATLAB-based curation pipeline (PR #303) |
| 10 | + - Closes #308: Distribute `yeast-GEM.mat` in RAVEN's format, to include `grRules` and `metComps` fields (PR #301) |
| 11 | +- Refactor: |
| 12 | + - 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) |
| 13 | + |
| 14 | +### yeast 8.5.0: |
| 15 | +- Features: |
| 16 | + - Set up memote as GitHub Action for pull requests (PR #162) |
| 17 | + - Moved old subSystems to reaction annotations (in `rxnMiriams` or `rxnKEGGpathways`) (PR #253) |
| 18 | +- Fixes: |
| 19 | + - Combine glycolysis + gluconeogenesis as single KEGG pathway annotations (PR #251). |
| 20 | + - Closes #252: Correct grRule of r_4590 (PR #255). |
| 21 | + - Closes #254: Corrects name of s_1218 (PR #255). |
| 22 | + - `saveYeastModel.m` now correctly handles Unicode characters (PR #255). |
| 23 | + - Closes #238: Correct indentation of `yeastGEM.yml` (PR #236 and #255). |
| 24 | +- Chore: |
| 25 | + - Update dependencies in `*requirements.txt` (PR #256). |
| 26 | + - Minor changes in model file formatting due to updates in COBRA+RAVEN toolboxes (PR #253). |
| 27 | +- Refactor: |
| 28 | + - Closes #232: Follow `standard-GEM` specifications (PR #257). |
| 29 | + - Closes #258: Rename git branches `master` and `devel` to `main` and `develop` (PR #261). |
| 30 | + |
| 31 | +### yeast 8.4.2: |
| 32 | +* Features: |
| 33 | + * `saveYeastModel.m` now checks if the model can grow and, based on the `allowNoGrowth` flag, returns either warnings or errors if not (PR #244). |
| 34 | + * Added several fatty acid ester producing reactions to the model, for improved simulation of alcoholic fermentation conditions (PRs #190 and #248). |
| 35 | +* Fixes: |
| 36 | + * Closes #242: Fixed a bug that prevented the model from growing (PR #243). |
| 37 | + * Corrected directionality of 23 reactions and removed a generic reaction (PR #228). |
| 38 | + |
| 39 | +### yeast 8.4.1: |
| 40 | +* Features: |
| 41 | + * Switched to `pip-tools` for managing python dependencies, distinguishing between user requirements `/requirements/requirements.txt` and developer requirements `/requirements/dev-requirements.txt` (PR #235). |
| 42 | +* Fixes: |
| 43 | + * Closes #201: Changed generic protein name to avoid confusion (PR #237). |
| 44 | + * Closes #205: Finished correcting reactions' stoichiometry based on KEGG data (PR #237). |
| 45 | + * Closes #215: Corrected wrong gene rule in reaction (PR #237). |
| 46 | + * Closes #225: Moved MNX rxn ids from notes to the proper annotation field (PR #226). |
| 47 | +* Documentation: |
| 48 | + * Closes #223: Clarified releasing steps, including authorship criteria for Zenodo releases, in contributing guidelines (PR #233). |
| 49 | + * Closes #227: Removed authorships/dates from all scripts, as it is redundant information (PR #230). |
| 50 | + * Added admin guidelines for managing python dependencies (PR #235). |
| 51 | + * Included links for model visualization in README file (PR #240). |
| 52 | + |
| 53 | +### yeast 8.4.0: |
| 54 | +* Features: |
| 55 | + * 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). |
| 56 | + * Solves #197: Added missing MetaNetX ids using KEGG ids and ChEBI ids (PR #220). |
| 57 | + * 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). |
| 58 | + * New functions `read_yeast_model` and `write_yeast_model` for easier usage in python (PR #224). |
| 59 | + * Solves #172: Model can now be loaded with BiGG ids as main ids, for better compliance with cobrapy (PR #224). |
| 60 | +* Fixes: |
| 61 | + * Solves #102: Every component of the model is now preserved when the model is opened with cobrapy, including gene names (PR #216). |
| 62 | + * Manual curation of MetaNetX, KEGG and ChEBI ids for metabolites/reactions (PRs #188 and #220). |
| 63 | + * Solves #187: Removed some duplicate reactions in the model (PR #188). |
| 64 | + * Mass/charge balanced most unbalanced reactions in model using `checkSmatrixMNX.m`, bringing the number down to 17 reactions (PR #222). |
| 65 | +* Others: |
| 66 | + * Configured repo to ensure that files always use `LF` as EOL character (PR #221). |
| 67 | + * Gene SBO terms are now recorded, after update in COBRA toolbox (PR #188). |
| 68 | + |
| 69 | +### yeast 8.3.5: |
| 70 | +* Fixes: |
| 71 | + * Closes #129: Removed non-S288C genes (PR #211). |
| 72 | + * Closes #198: Fixes function for converting model to anaerobic (PR #199). |
| 73 | +* Tests: |
| 74 | + * Added growth tests for carbon & nitrogen limitation (#199). |
| 75 | + * Added test for computing gene essentiality (PR #200). |
| 76 | +* Documentation/Others: |
| 77 | + * Clarified with README's the purpose of each script/data folder (#209). |
| 78 | + * Closes #206: Updated citation guidelines (PR #210). |
| 79 | + * Updated contribution guidelines + issue/PR templates (PR #210). |
| 80 | + * Created folders with deprecated scripts (PR #209). |
| 81 | + |
| 82 | +### yeast 8.3.4: |
| 83 | +* Features: |
| 84 | + * Fixes #171: Added 101 GPR rules to transport rxns according to TCDB database (PR #178). |
| 85 | + * Added 18 met formulas from manual search (PR #155). |
| 86 | + * 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. |
| 87 | +* Fixes: |
| 88 | + * Corrected typo in gene ID (PR #186). |
| 89 | + |
| 90 | +### yeast 8.3.3: |
| 91 | +* Features: |
| 92 | + * Fixes #107: Two new pseudoreactions (`cofactor pseudoreaction` and `ion pseudoreaction`) added to the model as extra requirements to the biomass pseudoreaction (PRs #174 & #183). |
| 93 | +* Fixes: |
| 94 | + * `addSBOterms.m` adapted to identify new pseudoreactions (PR #180). |
| 95 | + * Removed non-compliant symbol from a reaction name to avoid parsing errors (PR #179). |
| 96 | +* Documentation: |
| 97 | + * Model keywords modified to comply with the sysbio rulebook (PR #173). |
| 98 | + * Added citation guidelines (PR #181). |
| 99 | + |
| 100 | +### yeast 8.3.2: |
| 101 | +* Features: |
| 102 | + * Fixes #154: MetaNetX IDs added from the yeast7.6 [MetaNetX](https://www.metanetx.org) model & from existing ChEBI and KEGG IDs in the model (PR #167). |
| 103 | + * Introduced contributing guidelines + code of conduct (PR #175). |
| 104 | +* Fixes: |
| 105 | + * 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). |
| 106 | + * Fixes #169: Compartment error for `r_4238` (PR #170). |
| 107 | + * Corrected confidence score of rxns from PR #142 (PR #170). |
| 108 | + |
| 109 | +### yeast 8.3.1: |
| 110 | +* Features: |
| 111 | + * Added 21 reactions & 14 metabolites based on metabolomics data (PR #156). |
| 112 | + * Added metadata to the excel version of the model (PR #163). |
| 113 | + * Added `ComplementaryData/physiology` with biological data of yeast (PR #159). |
| 114 | +* Fixes/Others: |
| 115 | + * Fixed bug that underestimated the biomass content (PR #159). |
| 116 | + * Fitted GAM to chemostat data (PR #159). |
| 117 | + |
| 118 | +### yeast 8.3.0: |
| 119 | +* Features: |
| 120 | + * 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). |
| 121 | +* Fixes/Others: |
| 122 | + * Removed verbose details from `README.md` (PR #150). |
| 123 | + * Updated RAVEN, which added extra annotation to the `.yml` file (PR #151). |
| 124 | + * Minor changes to `saveYeastModel.m` (PR #152). |
| 125 | + * Model is now stored simulating minimal media conditions (PR #157). |
| 126 | + |
| 127 | +### yeast 8.2.0: |
| 128 | +* Features: |
| 129 | + * 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). |
| 130 | +* Fixes: |
| 131 | + * `grRules` deleted from pseudoreactions, removing with this 49 genes (PR #145). |
| 132 | +* Chores: |
| 133 | + * Updated COBRA, which changed the number of decimals in some stoichiometric coefficients in `.txt` (PR #143) |
| 134 | + |
| 135 | +### yeast 8.1.3: |
| 136 | +* Features: |
| 137 | + * Added SBO terms for all metabolites and reactions, based on an automatic script now part of `saveYeastModel.m` (PR #132). |
| 138 | + * `increaseVersion.m` now avoids conflicts between `devel` and `master` by erroring before releasing and guiding the admin to change first `devel` (PR #133). |
| 139 | + * Website now available in `gh-pages` branch: http://sysbiochalmers.github.io/yeast-GEM/ |
| 140 | +* Fixes: |
| 141 | + * Standardize naming of pseudo-metabolites "lipid backbone" & "lipid chain" (PR #130). |
| 142 | +* Chores: |
| 143 | + * Updated COBRA, which swapped around the order of the `bqbiol:is` and `bqbiol:isDescribedBy` qualifiers in the `.xml` file (PR #131). |
| 144 | + |
| 145 | +### yeast 8.1.2: |
| 146 | +* New features: |
| 147 | + * `saveYeastModel.m` now checks if the model is a valid SBML structure; if it isn't it will error (PR #126). |
| 148 | + * Date + model size in `README.md` updates automatically when saving the model (PR #123). |
| 149 | + * Added `modelName` and `modelID`; the latter which will now store the version number (PR #127). |
| 150 | +* Fixes: |
| 151 | + * Fixes #60: New GPR relations for existing reactions were added according to new annotation from 5 different databases (PR #124). |
| 152 | + * Various fixes in `README.md` (PR #123). |
| 153 | + |
| 154 | +### yeast 8.1.1: |
| 155 | +* Fixes: |
| 156 | + * 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. |
| 157 | + * 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). |
| 158 | + * Remade function for defining confidence scores, which fixed 38 scores in `rxnConfidenceScores` (most of them from pseudoreactions). |
| 159 | + * `loadYeastModel` and `saveYeastModel` were improved to allow their use also when outside of the actual folder. |
| 160 | + |
| 161 | +### yeast 8.1.0: |
| 162 | +* New features: |
| 163 | + * SLIME reactions added to the model using [SLIMEr](https://github.com/SysBioChalmers/SLIMEr), to properly account for constraints on lipid metabolism (fixes #21): |
| 164 | + * SLIME rxns replace old ISA rxns for lumping lipids. They create 2 types of lipid pseudometabolites: backbones and acyl chains. |
| 165 | + * There are now 3 lipid pseudoreactions: 1 constrains backbones, 1 constrains acyl chains, 1 merges both. |
| 166 | +* Fixes: |
| 167 | + * All metabolite formulas made compliant with SBML (fixes #19). Model is now a valid SBML object. |
| 168 | + * Biomass composition was rescaled to experimental data from [Lahtvee et al. 2017](https://www.sciencedirect.com/science/article/pii/S2405471217300881), 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). |
| 169 | +* Refactoring: |
| 170 | + * Organized all files in `ComplementaryData` |
| 171 | + |
| 172 | +### yeast 8.0.2: |
| 173 | +* New features: |
| 174 | + * Model can now be used with cobrapy by running `loadYeastModel.py` |
| 175 | + * `loadYeastModel.m` now adds the `rxnGeneMat` field to the model |
| 176 | +* Refactoring: |
| 177 | + * Moved `pmids` of model from `rxnNotes` to `rxnReferences` (COBRA-compliant) |
| 178 | + * `yeastGEM.yml` and `dependencies.txt` are now updated by RAVEN (a few dependencies added) |
| 179 | + * Moved `boundaryMets.txt` and `dependencies.txt` to the `ModelFiles` folder |
| 180 | +* Documentation: |
| 181 | + * Added badges and adapted README ro reflect new features |
| 182 | + |
| 183 | +### yeast 8.0.1: |
| 184 | +* `.yml` format included for easier visualization of model changes |
| 185 | +* Empty notes removed from model |
| 186 | +* Issue and PR templates included |
| 187 | +* `README.md` updated to comply with new repo's name |
| 188 | + |
| 189 | +### yeast 8.0.0: |
| 190 | +First version of the yeast8 model, to separate it from previous versions: |
| 191 | + |
| 192 | +* Manual curation project: |
| 193 | + * All metabolite information manually curated (names, charges, kegg IDs, chebi IDs) |
| 194 | + * Reaction gene rules updated with curation from [the iSce926 model](http://www.maranasgroup.com/submission_models/iSce926.htm). 13 genes added in this process |
| 195 | +* Format changes: |
| 196 | + * Folder `ComplementaryData` introduced |
| 197 | + * All data is stored in `.tsv` format now (can be navigated in Github) |
| 198 | + * Releases now come in `.xlsx` as well |
| 199 | +* Other new features: |
| 200 | + * Added `loadYeastModel.m` |
| 201 | + * A much smarter `increaseVersion.m` |
| 202 | + * Lots of refactoring |
| 203 | + |
| 204 | +### yeast 7.8.3: |
| 205 | +* curated tRNA's formulas |
| 206 | +* started tracking COBRA and RAVEN versions |
| 207 | +* dropped SBML toolbox as requirement |
| 208 | +* reorganized `complementaryScripts` |
| 209 | +* switched to a CC-BY-4.0 license |
| 210 | + |
| 211 | +### yeast 7.8.2: |
| 212 | +* fixed subSystems bug: now they are saved as individual groups |
| 213 | +* solved inter-OS issues |
| 214 | +* remade license to follow GitHub format |
| 215 | +* added `history.md` and made it a requirement to update when increasing version |
| 216 | + |
| 217 | +### yeast 7.8.1: |
| 218 | +* started following dependencies |
| 219 | +* started keeping track of the version in the repo (`version.txt`) |
| 220 | +* included `.gitignore` |
| 221 | +* dropped `.mat` storage for `devel` + feature branches (but kept it in `master`) |
| 222 | + |
| 223 | +### yeast 7.8.0: |
| 224 | +* Added information: |
| 225 | + * `metFormulas` added for all lipids |
| 226 | + * `rxnKEGGID` added from old version |
| 227 | + * `rxnNotes` enriched with Pubmed ids (`pmid`) from old version |
| 228 | + * `rxnConfidenceScores` added based on automatic script (available in [`ComplementaryScripts`](https://github.com/SysBioChalmers/yeast-GEM/blob/master/ComplementaryScripts)) |
| 229 | +* Format changes: |
| 230 | + * Biomass clustered by 5 main groups: protein, carbohydrate, lipid, RNA and DNA |
| 231 | + |
| 232 | +### yeast 7.7.0: |
| 233 | +* Format changes: |
| 234 | + * FBCv2 compliant |
| 235 | + * Compatible with latest COBRA and RAVEN parsers |
| 236 | + * Created main structure of repository |
| 237 | +* Added information: |
| 238 | + * `geneNames` added to genes based on [KEGG](http://www.genome.jp/kegg/) data |
| 239 | + * `subSystems` and `rxnECnumbers` added to reactions based on [KEGG](http://www.genome.jp/kegg/) & [Swissprot](http://www.uniprot.org/uniprot/?query=*&fil=organism%3A%22Saccharomyces+cerevisiae+%28strain+ATCC+204508+%2F+S288c%29+%28Baker%27s+yeast%29+%5B559292%5D%22+AND+reviewed%3Ayes) data |
| 240 | + * Boundary metabolites tracked (available in [`ComplementaryScripts`](https://github.com/SysBioChalmers/yeast-GEM/blob/master/ComplementaryScripts)) |
| 241 | +* Simulation improvements: |
| 242 | + * Glucan composition fixed in biomass pseudo-rxn |
| 243 | + * Proton balance in membrane restored |
| 244 | + * Ox.Pho. stoichiometry fixed |
| 245 | + * NGAM rxn introduced |
| 246 | + * GAM in biomass pseudo-rxn fixed and refitted to chemostat data |
| 247 | + |
| 248 | +### yeast 7.6.0: |
| 249 | +First release of the yeast model in GitHub, identical to the last model available at https://sourceforge.net/projects/yeast/ |
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