diff --git a/.gitignore b/.gitignore index 50d5b288..fbcbdaea 100644 --- a/.gitignore +++ b/.gitignore @@ -54,7 +54,6 @@ helpsearch*/ # Non-complying tables and files # ################################## -*.xls* *.tab *.doc* *.ppt* diff --git a/README.md b/README.md index a3bca20e..b893ad11 100644 --- a/README.md +++ b/README.md @@ -33,7 +33,7 @@ This repository contains the current consensus genome-scale metabolic model of _ | Taxonomy | Latest update | Version | Reactions | Metabolites | Genes | |:-------|:--------------|:------|:------|:----------|:-----| -| _Saccharomyces cerevisiae_ | 07-Jun-2023 | develop | 4099 | 2768 | 1161 | +| _Saccharomyces cerevisiae_ | 08-Jul-2023 | 8.6.3 | 4099 | 2768 | 1161 | # Installation & usage diff --git a/growth.png b/growth.png new file mode 100644 index 00000000..89d235b6 Binary files /dev/null and b/growth.png differ diff --git a/history.md b/history.md new file mode 100644 index 00000000..e53247d2 --- /dev/null +++ b/history.md @@ -0,0 +1,267 @@ +# History + +### 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](https://www.metanetx.org) 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](https://github.com/SysBioChalmers/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](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). +* 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](http://www.maranasgroup.com/submission_models/iSce926.htm). 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`](https://github.com/SysBioChalmers/yeast-GEM/blob/master/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](http://www.genome.jp/kegg/) data + * `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 + * Boundary metabolites tracked (available in [`ComplementaryScripts`](https://github.com/SysBioChalmers/yeast-GEM/blob/master/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/ \ No newline at end of file diff --git a/model/dependencies.txt b/model/dependencies.txt index 72c82feb..36e35bef 100644 --- a/model/dependencies.txt +++ b/model/dependencies.txt @@ -1,4 +1,4 @@ MATLAB 9.12.0.2039608 (R2022a) Update 5 libSBML 5.19.0 -RAVEN_toolbox commit 8793679 -COBRA_toolbox unknown +RAVEN_toolbox 2.8.3 +COBRA_toolbox commit 28acb94 diff --git a/model/yeast-GEM.mat b/model/yeast-GEM.mat new file mode 100644 index 00000000..fc9b8e5e Binary files /dev/null and b/model/yeast-GEM.mat differ diff --git a/model/yeast-GEM.xlsx b/model/yeast-GEM.xlsx new file mode 100644 index 00000000..3c61caa5 Binary files /dev/null and b/model/yeast-GEM.xlsx differ diff --git a/model/yeast-GEM.xml b/model/yeast-GEM.xml index 03d606fb..61234a75 100644 --- a/model/yeast-GEM.xml +++ b/model/yeast-GEM.xml @@ -1,6 +1,6 @@ - +

Saccharomyces cerevisiae - strain S288C

@@ -8,7 +8,7 @@ - + @@ -24,10 +24,10 @@ - 2023-06-07T16:57:17Z + 2023-07-08T01:07:13Z - 2023-06-07T16:57:17Z + 2023-07-08T01:07:13Z @@ -166656,7 +166656,7 @@ - + @@ -166693,7 +166693,7 @@ - + @@ -166729,7 +166729,7 @@ - + diff --git a/model/yeast-GEM.yml b/model/yeast-GEM.yml index 25d73cef..4f43b052 100755 --- a/model/yeast-GEM.yml +++ b/model/yeast-GEM.yml @@ -1,9 +1,9 @@ --- !!omap - metaData: - id: "yeastGEM_develop" + id: "yeastGEM_v8.6.3" name: "The Consensus Genome-Scale Metabolic Model of Yeast" - date: "2023-06-07" + date: "2023-07-08" givenName: "Eduard" familyName: "Kerkhoven" email: "eduardk@chalmers.se" diff --git a/version.txt b/version.txt new file mode 100644 index 00000000..1de56fec --- /dev/null +++ b/version.txt @@ -0,0 +1 @@ +8.6.3 \ No newline at end of file