yeast 8.6.1

.github/CONTRIBUTING.md

@@ -1,6 +1,6 @@
 ## Contributor guidelines
 
-First of all, thank you for contributing to yeast-GEM!! Anybody is welcome to contribute, but please abide by the following guidelines.
+First of all, thank you for contributing to yeast-GEM! Anybody is welcome to contribute, but please abide by the following guidelines.
 
 You can contribute in 2 main ways: by creating issues, and by sending pull requests (PRs) with additions, deletions, corrections, etc. to the model.
 
@@ -14,7 +14,7 @@ Report an issue at https://github.com/SysBioChalmers/yeast-GEM/issues if you not
 * Lacking documentation.
 * Any type of feedback.
 
-If you are unsure about the issue, consider asking first in our [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM).
+If you are unsure about the issue, consider asking first in our [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) or [GitHub Discussion forum](https://github.com/SysBioChalmers/yeast-GEM/discussions).
 
 When creating the issue, please make sure:
 
@@ -29,11 +29,11 @@ Finally, if you like yeast-GEM please remember to 'star' our Github page (click
 
 ### Contributing to the model
 
-Want to contribute to the model with some additions or improvements? Consider starting by raising an issue and assign it to yourself to describe what you want to achieve. This way, we reduce the risk of duplicated efforts and you may also get suggestions on how to best proceed, e.g. there may be half-finished work in some branch that you could start with. Also, feel free to browse our [open issues](https://github.com/SysBioChalmers/yeast-GEM/issues) and our [ongoing projects](https://github.com/SysBioChalmers/yeast-GEM/projects): Anything tagged with "help wanted" is open to whoever wants to implement it!
+Do you want to contribute to the model with some additions or improvements? Consider starting by raising an issue and assign it to yourself to describe what you want to achieve. This way, we reduce the risk of duplicated efforts and you may also get suggestions on how to best proceed, e.g. there may be half-finished work in some branch that you could start with. Also, feel free to browse our [open issues](https://github.com/SysBioChalmers/yeast-GEM/issues) and our [ongoing projects](https://github.com/SysBioChalmers/yeast-GEM/projects): Anything tagged with "help wanted" is open to whoever wants to implement it!
 
-Here's how to set up yeast-GEM for local development to contribute smaller features or changes that you can implement yourself:
+Here is how to set up yeast-GEM for local development to contribute smaller features or changes that you can implement yourself:
 
-1. First of all, make sure that you have all [requirements](https://github.com/SysBioChalmers/yeast-GEM#required-software---contributor) for contributing to yeast-GEM. Note that COBRA and RAVEN should be cloned in your computer and not just downloaded.
+1. First of all, make sure that you have all [requirements](https://github.com/SysBioChalmers/yeast-GEM#developer) for contributing to yeast-GEM.
 
 2. Fork the yeast-GEM repository on GitHub (go to https://github.com/SysBioChalmers/yeast-GEM & click on the upper right corner).
 
@@ -53,15 +53,13 @@ Here's how to set up yeast-GEM for local development to contribute smaller featu
     ```
 
 6. Now you can make your changes locally!
-    * Always make your changes in Matlab and never directly editing the model files. For loading the model use `loadYeastModel.m`, and for saving the model use `saveYeastModel.m`. The latter will ensure all 3 versions of the model (`.xml`, `.yml` & `.txt`) get updated in the same way.
-    * If your changes are minor (e.g. a single chemical formula you wish to correct), you can do it directly from the command line.
-    * If your changes are not so small and require several steps, create a script that loads the model, reads data (if applicable), changes the model accordingly, and saves the model back.
-    * Each script should start with a commented section describing the script, explaining the parameters, and indicating your name and the date it was written. Existing functions can clarify what style should be used.
+    * Always make your changes in MATLAB and never directly editing the model files. For loading the model use `loadYeastModel.m`, and for saving the model use `saveYeastModel.m`. The latter will ensure all 3 versions of the model (`.xml`, `.yml` & `.txt`) get updated in the same way.
+    * Curations to the model are consolidated in scripts that can convert a model from one yeast-GEM release (=version) to the next. Therefore, use the `/code/modelCuration/TEMPLATEcuration.m` file, or contribute directly to an existing `v$VERSION.m` script, where `$VERSION` matches the most recent yeast-GEM release. If the most recent release is 8.6.0, there will be a `/code/modelCuration/v8_6_0.m` script that consolidates curations to be applied to release 8.6.0.
+    * See the `TEMPLATEcuration.m` script with more description on how to use this file. Look at previous curations files (e.g. `v8_6_0.m`) to get an idea of how this works.
     * As much as possible follow the model conventions:
-      - For new metabolites and/or reactions, please use `/code/otherChanges/getNewIndex.m` for obtaining new ids.
       - For metabolite and/or reaction names, please avoid any unconventional characters (e.g. Greek letters).
       - For new genes, please use as id the [systematic names from SGD](http://seq.yeastgenome.org/help/community/nomenclature-conventions).
-    * Store scripts in the appropriate folder in `/code` and data (as `.tsv` files) in the appropriate folder in `/data`. If you think no folder is adequate for your script/data, feel free to create your own folder. Note that binary data such as `.mat` structures or `.xls` tables cannot be stored in the repo (as they cannot be version-controlled, and they increment too much the size of the repo).
+    * Store generic scripts in the appropriate folder in `/code` and data (as `.tsv` files) in the appropriate folder in `/data`. If a data file is just to apply one round of curation (for instance a table with selected gene associations to be corrected), it should be stored in the appropriate subfolder in `/code/modelCuration`. If you think no folder is adequate for your script/data, feel free to create your own folder. Note that binary data such as `.mat` structures or `.xls` tables cannot be stored in the repo (as they cannot be version-controlled, and they increment too much the size of the repo).
     * When you are done making changes, review locally your changes with `git diff` or any git client, to make sure you are modifying the model as you intended.
 
 7. Commit your changes and push your branch to GitHub.

.github/issue_template.md

@@ -1,23 +1,24 @@
 ### Description of the issue:
-*Try to be as clear as possible: Is it something wrong/missing in the model? Is it a simulation issue? PLEASE DELETE THIS LINE.*
+<!-- Try to be as clear as possible: Is it something wrong/missing in the model? Is it a simulation issue -->
 
 
 #### Expected feature/value/output:
-*How the reaction/metabolite/gene/simulation result should look (cite literature if needed). PLEASE DELETE THIS LINE.*
+<!-- How the reaction/metabolite/gene/simulation result should look (cite literature if needed). -->
 
 
 #### Current feature/value/output:
-*How the reaction/metabolite/gene/simulation actually looks in the `main` branch. PLEASE DELETE THIS LINE.*
+<!-- How the reaction/metabolite/gene/simulation actually looks in the `main` branch. -->
 
 
 #### Reproducing these results:
-*Please attach any code used below (if it's python code replace the word "matlab" with "python". PLEASE DELETE THIS LINE.*
+<!-- Please attach any code used below (if it's python code replace the word "matlab" with "python". -->
 ```matlab
 
 ```
 
 **I hereby confirm that I have:**
+<!-- Note: replace [ ] with [X] to check the box -->
 - [ ] Tested my code with [all requirements](https://github.com/SysBioChalmers/yeast-GEM#required-software---user) for running the model
-- [ ] Done this analysis in the `main` branch of the repository
+- [ ] Done this analysis in the `develop` branch of the repository
 - [ ] Checked that a similar issue does not exist already
 - [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) about the issue

.github/workflows/memote-history.yml

@@ -18,7 +18,7 @@ jobs:
         python-version: '3.9.7'
 
     - name: Install memote
-      run: pip install -r requirements/ci-requirements.txt
+      run: pip install -r code/requirements/ci-requirements.txt
 
     - name: Setup variables
       id: setup

.github/workflows/memote-run.yml

@@ -16,7 +16,7 @@ jobs:
         python-version: '3.9.7'
 
     - name: Install memote
-      run: pip install -r requirements/ci-requirements.txt
+      run: pip install -r code/requirements/ci-requirements.txt
 
     - name: Convert model
       run: |

.github/workflows/memote_release.yml

@@ -26,7 +26,7 @@ jobs:
         python-version: '3.9.7'
 
     - name: Install memote
-      run: pip install -r requirements/requirements.txt
+      run: pip install -r code/requirements/requirements.txt
 
     - name: Memote run
       run: |

.github/workflows/yaml-validation.yml

@@ -35,5 +35,5 @@ jobs:
 
     - name: Import with cobrapy
       run: |
-        pip install -r requirements/ci-requirements.txt
+        pip install -r code/requirements/ci-requirements.txt
         python -c "import cobra ; cobra.io.load_yaml_model('model/yeast-GEM.yml')"

.gitignore

@@ -35,6 +35,7 @@
 .Trashes
 ehthumbs.db
 Thumbs.db
+.idea
 
 # Matlab generated files #
 ##########################
@@ -51,7 +52,10 @@ helpsearch*/
 *.pyc
 *.env
 
-# Non-complying tables #
-########################
-*.xls
+# Non-complying tables and files #
+##################################
+*.xls*
 *.tab
+*.doc*
+*.ppt*
+*.bak

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_ | 18-May-2022 | 8.6.0 | 4069 | 2749 | 1151 |
+| _Saccharomyces cerevisiae_ | 15-Jun-2022 | develop | 4063 | 2744 | 1163 |
 
 # Installation & usage
 
@@ -69,7 +69,7 @@ Please see the installation instructions for each software package.
 
   If you want to use any of the [provided](https://github.com/SysBioChalmers/yeast-GEM/tree/main/code) Python functions, you may create an environment with all requirements:
   ```bash
-  pip install -r requirements/requirements.txt  # installs all dependencies
+  pip install -r code/requirements/requirements.txt  # installs all dependencies
   touch .env                                    # creates a .env file for locating the root
   ```
 

code/deprecated/modelCuration/addRxnSubsystem.m

@@ -0,0 +1,30 @@
+% This Function is for adding new subsystem into model.
+% Input: model, keggPathways.tsv.
+% NOTE: Before run the codes below, the file should be manually editted.
+%       COBRA required.
+%       New subsystem should be in .tsv format.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% Load model
+cd ..
+model = loadYeastModel;
+
+%newsubsystem:
+fid = fopen('../data/modelCuration/v8_6_0/keggPathways.tsv');
+sub_data = textscan(fid,'%s %s %s','Delimiter','\t','HeaderLines',1);
+id = sub_data{1};
+subSystems = sub_data{2};
+fclose(fid);
+for i = 1:length(model.rxns)
+    if i <= length(id)
+        subIndex = find(strcmp(model.rxns, id(i)));
+        model.subSystems{subIndex, 1} = subSystems{i};
+    else
+        model.subSystems{i, 1} = 'nan';
+    end
+end
+
+% Save model:
+cd ..
+saveYeastModel(model)
+cd modelCuration

code/getEarlierModelVersion.m

@@ -11,7 +11,7 @@
 
 if any(regexp(version,'^\d+\.\d+\.\d+$')) % Tag is a version number
     tagpath=['git show refs/tags/v' version ':'];
-elseif any(contains(tag,{'main','develop'}))
+elseif any(contains(version,{'main','develop'}))
     tagpath=['git show ' version ':'];
 else
     error('version should be ''main'', ''develop'', or a specific release, e.g. ''8.1.0''')

code/increaseVersion.m

@@ -12,7 +12,7 @@ function increaseVersion(bumpType)
 
 %Check if in main:
 [~,currentBranch] = system('git rev-parse --abbrev-ref HEAD');
-if ~strcmp(currentBranch,'main')
+if ~strcmp(strtrim(currentBranch),'main')
     error('ERROR: not in main')
 end
 
@@ -46,8 +46,48 @@ function increaseVersion(bumpType)
 end
 
 %Load model:
+disp('Loading model file')
 model = importModel('../model/yeast-GEM.xml');
 
+%Run tests
+cd modelTests
+disp('Running gene essentiality analysis')
+[new.accuracy,new.tp,new.tn,new.fn,new.fp] = essentialGenes(newModel);
+disp('Run growth analysis')
+new.R2=growth(newModel);
+saveas(gcf,'../../growth.png');
+
+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)];
+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 = '^(- R<sup>2<\/sup>\: )0\.\d+';
+newStats6 = ['$1' num2str(new.R2)];
+
+while ~feof(fin)
+    str = fgets(fin);
+    inline = regexprep(str,searchStats1,newStats1);
+    inline = regexprep(inline,searchStats2,newStats2);
+    inline = regexprep(inline,searchStats3,newStats3);
+    inline = regexprep(inline,searchStats4,newStats4);
+    inline = regexprep(inline,searchStats5,newStats5);
+    inline = regexprep(inline,searchStats6,newStats6);
+    inline = unicode2native(inline,'UTF-8');
+    fwrite(fout,inline);
+end
+fclose('all');
+delete('backup.md');
+
 %Allow .mat & .xlsx storage:
 copyfile('../.gitignore','backup')
 fin  = fopen('backup','r');
@@ -77,14 +117,14 @@ function increaseVersion(bumpType)
     if length(diff_i) == 3
         switch diff_i{3}
             case 'model/yeast-GEM.xml'
-                %.xml file: 2 line2 should be added & 2 line2 should be deleted
+                %.xml file: 2 lines should be added & 2 lines should be deleted
                 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 'model/yeast-GEM.yml'
-                %.yml file: 1 line should be added & 1 line should be deleted
-                if eval([diff_i{1} ' > 1']) || eval([diff_i{2} ' > 1'])
+                %.yml file: 2 lines should be added & 2 lines should be deleted
+                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                

code/loadYeastModel.m

@@ -36,4 +36,5 @@
         model = ravenCobraWrapper(model);
     end
 end
+disp('If there is only 1 warning and no errors, it can savely be ignored.')
 end

code/missingFields/README.md

@@ -1,5 +1,3 @@
-## Missing Fields
+## Missing fields
 
-Scripts for adding fields to the model.
-
-**NOTE:** These scripts are provided as documentation + eventual re-use for developers. They are NOT intended to be used by regular users.
+Various scripts for adding and curating various annotation fields to the model, that are useful for model curation. These functions should be written in a generic format, so that they could be reused for future curations.

code/modelCuration/README.md

@@ -1,5 +1,9 @@
-## Model Curation
+## Model curation
 
 Scripts for curating different parts of the model.
 
-**NOTE:** These scripts are provided as documentation + eventual re-use for developers. They are NOT intended to be used by regular users.
+Curations between each model release are gathered in consolidated curation scripts that are named after the model version that they are curation. E.g. v8_6_0.m includes updates that should be applied to model version 8.6.0 to result in the next model release.
+
+TEMPLATEcuration.m is the template script that should be used to generate a new consolidated curation script after a new model has just been released.
+
+In addition, this folder contains generic functions that are useful for model curation. These functions should be written in a generic format, so that they could be reused for future curations.

code/modelCuration/TEMPLATEcuration.m

@@ -0,0 +1,64 @@
+%% TEMPLATE FOR SCRIPT THAT CONSOLIDATES CURATIONS THAT ARE MADE TO A MODEL
+% RELEASE. EACH RELEASE (e.g. yeast-GEM v8.6.1) WILL HAVE ITS OWN SCRIPT WHERE
+% CURATIONS TO THAT MODEL RELEASE ARE CONSOLIDATED, MATCHING A DEDICATED FOLDER
+% WITH DATA IN code/modelCuration/. SEE EARLIER SCRIPTS AS EXAMPLE. AFTER A NEW
+% RELEASE IS MADE ON GITHUB, COPY-PASTE THIS TEMPLATE, REMOVE THIS LEADING
+% CAPITALIZED TEXT, AND REPLACE $VERSION WITH THE VERSION NUMBER OF THE RECENT
+% YEAST-GEM RELEASE (e.g. $VERSION --> 8.6.1).
+
+% This scripts applies curations to be applied on yeast-GEM release $VERSION.
+% 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 $VERSION (requires local yeast-GEM git repository)
+cd ..
+model = getEarlierModelVersion('$VERSION');
+model.id='yeastGEM_develop';
+cd modelCuration
+
+%% Brief description of curation to be performed (PR #xxx) [include correct PR or Issue number]
+% Potential longer description of curation to be performed.
+% If any data files need to be loaded, keep these in the dedicated folder at
+% data/modelCuration/v$VERSION
+
+% Example [DELETE WHEN NOT USED]:
+
+%% Curate gene association for transport rxns (PR #306)
+% Add new genes
+model       = curateMetsRxnsGenes(model,'none','../../data/modelCuration/curationsOnV8_6_0/transRxnNewGPRGenes.tsv');
+
+% Change GPR relations
+fid           = fopen('../../data/modelCuration/curationsOnV8_6_0/TransRxnNewGPR.tsv');
+changegpr     = textscan(fid,'%q %q %q %q %q %q %q %q','Delimiter','\t','HeaderLines',1);
+newGPR.ID     = changegpr{1};
+newGPR.GPR    = changegpr{2};
+fclose(fid);
+
+model=changeGrRules(model,newGPR.ID,newGPR.GPR);
+
+% Delete unused genes (if any)
+model = deleteUnusedGenes(model);
+
+%% 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('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('\nRun growth analysis\n')
+R2=growth(model);
+fprintf('R2 of growth prediction: %.4f\n', R2);
+
+% Save model:
+cd ..
+saveYeastModel(model)
+cd modelCuration