diff --git a/README.md b/README.md index b797a901..2c8c1845 100644 --- a/README.md +++ b/README.md @@ -33,21 +33,7 @@ This repository contains the current consensus genome-scale metabolic model of _ | Taxonomy | Latest update | Version | Reactions | Metabolites | Genes | |:-------|:--------------|:------|:------|:----------|:-----| -| _Saccharomyces cerevisiae_ | 05-Sep-2022 | 8.6.1 | 4063 | 2744 | 1163 | - -### Gene essentiality prediction - -- Accuracy: 0.881 -- True non-essential genes: 929 -- True essential genes: 63 -- False non-essential genes: 96 -- False essential genes: 38 - -### Growth prediction - -- Correlation coefficient R2: 0.865 - -![Growth curve](growth.png) +| _Saccharomyces cerevisiae_ | 05-Sep-2022 | develop | 4063 | 2744 | 1160 | # Installation & usage diff --git a/code/increaseVersion.m b/code/increaseVersion.m index a7b2ece9..97502c62 100644 --- a/code/increaseVersion.m +++ b/code/increaseVersion.m @@ -52,27 +52,29 @@ function increaseVersion(bumpType) %Run tests cd modelTests disp('Running gene essentiality analysis') -[new.accuracy,new.tp,new.tn,new.fn,new.fp] = essentialGenes(newModel); +[new.accuracy,new.tp,new.tn,new.fn,new.fp] = essentialGenes(model); disp('Run growth analysis') -new.R2=growth(newModel); +new.R2=growth(model); + saveas(gcf,'../../growth.png'); +cd .. copyfile('../README.md','backup.md') fin = fopen('backup.md','r'); fout = fopen('../README.md','w'); searchStats1 = '^(- Accuracy\: )0\.\d+'; -searchStats2 = '^(- True positive genes\: )\d+'; -searchStats3 = '^(- True negative genes\: )\d+'; -searchStats4 = '^(- False positive genes\: )\d+'; -searchStats5 = '^(- False negative genes\: )\d+'; -newStats1 = ['$1' num2str(new.accuracy)]; +searchStats2 = '^(- True non-essential genes\: )\d+'; +searchStats3 = '^(- True essential genes\: )\d+'; +searchStats4 = '^(- False non-essential genes\: )\d+'; +searchStats5 = '^(- False essential genes\: )\d+'; +newStats1 = ['$1' num2str(new.accuracy,'%.3f')]; newStats2 = ['$1' num2str(numel(new.tp))]; newStats3 = ['$1' num2str(numel(new.tn))]; newStats4 = ['$1' num2str(numel(new.fp))]; newStats5 = ['$1' num2str(numel(new.fn))]; -searchStats6 = '^(- R2<\/sup>\: )0\.\d+'; -newStats6 = ['$1' num2str(new.R2)]; +searchStats6 = '^(- Correlation coefficient R2<\/sup>\: )0\.\d+'; +newStats6 = ['$1' num2str(new.R2,'%.3f')]; while ~feof(fin) str = fgets(fin); @@ -105,10 +107,11 @@ function increaseVersion(bumpType) delete('backup'); %Include tag and save model: +disp('Write model files') model.id = ['yeastGEM_v' newVersion]; saveYeastModel(model,true,true,true) %only save if model can grow -%Check if any file changed (except for history.md and 1 line in yeast-GEM.xml): +%Check for any unexpected file changes [~,diff] = system('git diff --numstat'); diff = strsplit(diff,'\n'); change = false; @@ -117,18 +120,20 @@ function increaseVersion(bumpType) if length(diff_i) == 3 switch diff_i{3} case 'model/yeast-GEM.xml' - %.xml file: 2 lines should be added & 2 lines should be deleted - if eval([diff_i{1} ' > 2']) || eval([diff_i{2} ' > 2']) + %.xml file: 4 lines should be added & 4 lines should be + %deleted (2 with version information, 2 with current date) + if eval([diff_i{1} ' > 4']) || eval([diff_i{2} ' > 4']) disp(['NOTE: File ' diff_i{3} ' is changing more than expected']) change = true; end case 'model/yeast-GEM.yml' %.yml file: 2 lines should be added & 2 lines should be deleted + %(1 with version information, 1 with current date) if eval([diff_i{1} ' > 2']) || eval([diff_i{2} ' > 2']) disp(['NOTE: File ' diff_i{3} ' is changing more than expected']) change = true; end - case 'history.md' + case {'history.md','README.md','growth.png','model/yeast-GEM.mat'} otherwise disp(['NOTE: File ' diff_i{3} ' is changing']) change = true; diff --git a/code/modelCuration/TEMPLATEcuration.m b/code/modelCuration/TEMPLATEcuration.m index cd155bd8..f42dd6d5 100644 --- a/code/modelCuration/TEMPLATEcuration.m +++ b/code/modelCuration/TEMPLATEcuration.m @@ -18,6 +18,7 @@ cd .. model = getEarlierModelVersion('$VERSION'); model.id='yeastGEM_develop'; +dataDir=fullfile(pwd(),'..','data','modelCuration','v8.6.1'); %Modify to the correct version cd modelCuration %% Brief description of curation to be performed (PR #xxx) [include correct PR or Issue number] @@ -50,10 +51,10 @@ [new.accuracy,new.tp,new.tn,new.fn,new.fp] = essentialGenes(model); fprintf('Genes in model: %d\n',numel(model.genes)); fprintf('Gene essentiality accuracy: %.4f\n', new.accuracy); -fprintf('Gene essentiality TP: %d\n', numel(new.tp)); -fprintf('Gene essentiality TN: %d\n', numel(new.tn)); -fprintf('Gene essentiality FP: %d\n', numel(new.fp)); -fprintf('Gene essentiality FN: %d\n', numel(new.fn)); +fprintf('True non-essential genes: %d\n', numel(new.tp)); +fprintf('True essential genes: %d\n', numel(new.tn)); +fprintf('False non-essential genes: %d\n', numel(new.fp)); +fprintf('False essential genes: %d\n', numel(new.fn)); fprintf('\nRun growth analysis\n') R2=growth(model); fprintf('R2 of growth prediction: %.4f\n', R2); diff --git a/code/modelCuration/v8_6_1.m b/code/modelCuration/v8_6_1.m new file mode 100644 index 00000000..f1a4d4bb --- /dev/null +++ b/code/modelCuration/v8_6_1.m @@ -0,0 +1,42 @@ +% This scripts applies curations to be applied on yeast-GEM release 8.6.1. +% Indicate which Issue/PR are addressed. If multiple curations are performed +% before a new release is made, just add the required code to this script. If +% more extensive coding is required, you can write a separate (generic) function +% that can be kept in the /code/modelCuration folder. Otherwise, try to use +% existing functions whenever possible. In particular /code/curateMetsRxnsGenes +% can do many types of curation. + +%% Load yeast-GEM 8.6.1 (requires local yeast-GEM git repository) +cd .. +model = getEarlierModelVersion('8.6.1'); +model.id='yeastGEM_develop'; +dataDir=fullfile(pwd(),'..','data','modelCuration','v8.6.1'); +cd modelCuration + +%% Correct ATP synthase mitochondrial complex gene associations (PR #323) +model = changeGrRules(model, 'r_0226', ['Q0080 and Q0085 and Q0130 and ' ... + 'YBL099W and YBR039W and YDL004W and YDR298C and YDR377W and YJR121W ' ... + 'and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and ' ... + 'YDR322C-A and YPR020W and YOL077W-A'],true); +model = deleteUnusedGenes(model); +checkModelStruct(model,true,false) + +%% DO NOT CHANGE OR REMOVE THE CODE BELOW THIS LINE. +% Show some metrics: +cd ../modelTests +disp('Run gene essentiality analysis') +[new.accuracy,new.tp,new.tn,new.fn,new.fp] = essentialGenes(model); +fprintf('Genes in model: %d\n',numel(model.genes)); +fprintf('Gene essentiality accuracy: %.4f\n', new.accuracy); +fprintf('True non-essential genes: %d\n', numel(new.tp)); +fprintf('True essential genes: %d\n', numel(new.tn)); +fprintf('False non-essential genes: %d\n', numel(new.fp)); +fprintf('False essential genes: %d\n', numel(new.fn)); +fprintf('\nRun growth analysis\n') +R2=growth(model); +fprintf('R2 of growth prediction: %.4f\n', R2); + +% Save model: +cd .. +saveYeastModel(model) +cd modelCuration diff --git a/growth.png b/growth.png deleted file mode 100644 index 975229a9..00000000 Binary files a/growth.png and /dev/null differ diff --git a/history.md b/history.md deleted file mode 100644 index aca239a6..00000000 --- a/history.md +++ /dev/null @@ -1,259 +0,0 @@ -# History - -### 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/yeast-GEM.mat b/model/yeast-GEM.mat deleted file mode 100644 index 1c649e3d..00000000 Binary files a/model/yeast-GEM.mat and /dev/null differ diff --git a/model/yeast-GEM.txt b/model/yeast-GEM.txt index 259abdad..ff5b5a95 100755 --- a/model/yeast-GEM.txt +++ b/model/yeast-GEM.txt @@ -201,7 +201,7 @@ r_0222 ADP[c] + ATP[c] + H+[c] => P(1),P(4)-bis(5'-adenosyl) tetraphosphate[c] + r_0223 ADP[c] + GTP[c] + H+[c] => P1-(5'-adenosyl),P4-(5'-guanosyl) tetraphosphate[c] + phosphate[c] YCL050C 0.00 1000.00 0.00 r_0224 GDP[c] + GTP[c] + H+[c] => P(1),P(4)-bis(5'-guanosyl) tetraphosphate[c] + phosphate[c] YCL050C 0.00 1000.00 0.00 r_0225 ATP[c] + PRPP[c] => 5-phosphoribosyl-ATP[c] + diphosphate[c] YER055C 0.00 1000.00 0.00 -r_0226 ADP[m] + 3 H+[c] + phosphate[m] => ATP[m] + 2 H+[m] + H2O[m] (Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR322C-A and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W) or (Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and YPR020W) or (Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR322C-A and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and YJL180C and YLR393W and YNL315C and YOL077W-A and YCL005W-A) 0.00 1000.00 0.00 +r_0226 ADP[m] + 3 H+[c] + phosphate[m] => ATP[m] + 2 H+[m] + H2O[m] Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and YDR322C-A and YPR020W and YOL077W-A 0.00 1000.00 0.00 r_0227 ATP[c] + H2O[c] => ADP[c] + H+[e] + phosphate[c] (YCR024C-A and YEL017C-A and YGL008C) or (YCR024C-A and YEL017C-A and YPL036W) or YER005W 0.00 1000.00 0.00 r_0228 GDP-alpha-D-mannose[c] + N,N'-diacetylchitobiosyldiphosphodolichol[c] => beta-D-mannosyldiacetylchitobiosyldiphosphodolichol[c] + GDP[c] + H+[c] YBR110W 0.00 1000.00 0.00 r_0229 dethiobiotin[c] + polysulphur[c] <=> biotin[c] + 2 H+[c] YGR286C -1000.00 1000.00 0.00 diff --git a/model/yeast-GEM.xml b/model/yeast-GEM.xml index c4043210..c0a605c0 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 @@ - 2022-09-05T15:35:26Z + 2022-09-05T17:01:46Z - 2022-09-05T15:35:26Z + 2022-09-05T17:01:46Z @@ -48329,64 +48329,25 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + @@ -166689,7 +166650,6 @@ - @@ -166939,7 +166899,6 @@ - @@ -167086,7 +167045,6 @@ - diff --git a/model/yeast-GEM.yml b/model/yeast-GEM.yml index 5d5ced0e..452e5051 100755 --- a/model/yeast-GEM.yml +++ b/model/yeast-GEM.yml @@ -1,7 +1,7 @@ --- !!omap - metaData: - id: "yeastGEM_v8.6.1" + id: "yeastGEM_develop" name: "The Consensus Genome-Scale Metabolic Model of Yeast" date: "2022-09-05" givenName: "Eduard" @@ -34954,7 +34954,7 @@ - s_1326: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR322C-A and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W) or (Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and YPR020W) or (Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR322C-A and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and YJL180C and YLR393W and YNL315C and YOL077W-A and YCL005W-A)" + - gene_reaction_rule: "Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and YDR322C-A and YPR020W and YOL077W-A" - eccodes: "3.6.3.14" - subsystem: - "Oxidative phosphorylation" @@ -109828,9 +109828,6 @@ - !!omap - id: "YJL168C" - name: "SET2" - - !!omap - - id: "YJL180C" - - name: "ATP12" - !!omap - id: "YJL196C" - name: "ELO1" @@ -110452,9 +110449,6 @@ - !!omap - id: "YLR386W" - name: "VAC14" - - !!omap - - id: "YLR393W" - - name: "ATP10" - !!omap - id: "YLR395C" - name: "COX8" @@ -110851,9 +110845,6 @@ - !!omap - id: "YNL292W" - name: "PUS4" - - !!omap - - id: "YNL315C" - - name: "ATP11" - !!omap - id: "YNL316C" - name: "PHA2" diff --git a/version.txt b/version.txt deleted file mode 100644 index 3edbce7b..00000000 --- a/version.txt +++ /dev/null @@ -1 +0,0 @@ -8.6.1 \ No newline at end of file