chore: version 8.5.0

.gitignore

@@ -43,7 +43,6 @@ Thumbs.db
 *.mex*
 *.mlappinstall
 *.mltbx
-*.mat
 helpsearch*/
 
 # Python-related things #
@@ -55,5 +54,4 @@ helpsearch*/
 # Non-complying tables #
 ########################
 *.xls
-*.xlsx
 *.tab

history.md

@@ -0,0 +1,238 @@
+# History
+
+### 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/

model/yeast-GEM.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" level="3" version="1" fbc:required="false" groups:required="false">
-  <model metaid="yeastGEM.xml" id="M_yeastGEM_develop" name="The Consensus Genome-Scale Metabolic Model of Yeast" fbc:strict="true">
+  <model metaid="yeast-GEM.xml" id="M_yeastGEM_v8__46__5__46__0" name="The Consensus Genome-Scale Metabolic Model of Yeast" fbc:strict="true">
     <listOfUnitDefinitions>
       <unitDefinition id="mmol_per_gDW_per_hr">
         <listOfUnits>

model/yeast-GEM.yml

@@ -1,9 +1,9 @@
 ---
 !!omap
 - metaData:
-    id: "yeastGEM_develop"
+    id: "yeastGEM_v8.5.0"
     name: "The Consensus Genome-Scale Metabolic Model of Yeast"
-    date: "2021-06-15"
+    date: "2021-07-02"
 - metabolites:
     - !!omap
       - id: "s_0001"

version.txt

@@ -0,0 +1 @@
+8.5.0