yeast 8.6.3 (#339)

* chore: update workflows (#333) * chore: update gh workflow dependencies * revert: latest yamllint action has issues * fix: loosen python vesion requested by workflow * chore: relax workflow dependency * revert: use of git history in workflow * Volatile Esters & Polyphosphate Reactions (#337) * initial fork, xlsx data * allowing xlsx files * csv overview file v1 * feat-rxn: volatile esters & polyphosphate reactions * chore: remove additional model files * Revert "initial fork, xlsx data" This reverts commit 9699677. * refactor: reorganize reconstruction script and data files * fix: correct identifiers, subsystems, notes, EC numbers etc. * chore: rerun v8_6_2.m - change in reaction r_0226 is because previous run used model 8.6.1 as input, not 8.6.2 * fix: update mention to correct PR * fix: remove unused metabolites & correct subsystem --------- Co-authored-by: Ulf Liebal <[email protected]> * fix: install dependencies in workflow (#341) * fix: install dependencies in workflow * refactor: create .env in previous workflow step --------- Co-authored-by: Mihail Anton <[email protected]> Co-authored-by: Ulf Liebal <[email protected]>
SysBioChalmers · Jul 7, 2023 · 3eeeaa1 · 3eeeaa1
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diff --git a/.github/workflows/memote-history.yml b/.github/workflows/memote-history.yml
@@ -6,56 +6,55 @@ jobs:
   memote-history:
     runs-on: ubuntu-latest
     steps:
-
-    - name: Checkout
-      uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
-
-    - name: Set up Python 3
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.9.7'
-
-    - name: Install memote
-      run: pip install -r code/requirements/ci-requirements.txt
-
-    - name: Setup variables
-      id: setup
-      run: |
-        echo "::set-output name=history::history_report.html"
-        echo "::set-output name=deployment::$(awk -F '=' '{if (! ($0 ~ /^;/) && $0 ~ /deployment/) print $2}' memote.ini | tr -d ' ')"
-        echo "::set-output name=other-repo::gh-pages-repo"
-
-    - name: Checkout repo for gh-pages branch
-      uses: actions/checkout@v2
-      with:
-        repository: ${{ github.repository }}
-        ref: ${{ steps.setup.outputs.deployment }}
-        path: ${{ steps.setup.outputs.other-repo }}
-
-    # - name: Convert model
-    #   run: |
-    #     touch .env
-    #     python -c 'import code.io as io; model = io.read_yeast_model(make_bigg_compliant=True); io.write_yeast_model(model)'
-
-    - name: Memote short run
-      run: |
-        git config --global user.name "memote-bot"
-        memote run --skip-unchanged --solver-timeout 30
-
-    - name: Compute Memote history on push
-      run: |
-        # Generate the history report on the deployment branch
-        memote report history --filename="${{ steps.setup.outputs.other-repo }}/${{ steps.setup.outputs.history }}"
-
-    - name: Auto-commit results
-      uses: stefanzweifel/[email protected]
-      with:
-        commit_user_name: memote-bot
-        commit_message: "chore: update memote history report"
-        file_pattern: ${{ steps.setup.outputs.history }}
-        branch: ${{ steps.setup.outputs.deployment }}
-        repository: ${{ steps.setup.outputs.other-repo }}
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python 3
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+
+      - name: Install memote
+        run: pip install -r code/requirements/ci-requirements.txt
+
+      - name: Setup variables
+        id: setup
+        run: |
+          echo "::set-output name=history::history_report.html"
+          echo "::set-output name=deployment::$(awk -F '=' '{if (! ($0 ~ /^;/) && $0 ~ /deployment/) print $2}' memote.ini | tr -d ' ')"
+          echo "::set-output name=other-repo::gh-pages-repo"
+
+      - name: Checkout repo for gh-pages branch
+        uses: actions/checkout@v2
+        with:
+          repository: ${{ github.repository }}
+          ref: ${{ steps.setup.outputs.deployment }}
+          path: ${{ steps.setup.outputs.other-repo }}
+
+      # - name: Convert model
+      #   run: |
+      #     touch .env
+      #     python -c 'import code.io as io; model = io.read_yeast_model(make_bigg_compliant=True); io.write_yeast_model(model)'
+
+      - name: Memote short run
+        run: |
+          git config --global user.name "memote-bot"
+          memote run --skip-unchanged --solver-timeout 30
+
+      - name: Compute Memote history on push
+        run: |
+          # Generate the history report on the deployment branch
+          memote report history --filename="${{ steps.setup.outputs.other-repo }}/${{ steps.setup.outputs.history }}"
+
+      - name: Auto-commit results
+        uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          commit_user_name: memote-bot
+          commit_message: "chore: update memote history report"
+          file_pattern: ${{ steps.setup.outputs.history }}
+          branch: ${{ steps.setup.outputs.deployment }}
+          repository: ${{ steps.setup.outputs.other-repo }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/memote-release.yml b/.github/workflows/memote-release.yml
@@ -0,0 +1,43 @@
+name: memote release
+
+on:
+  release:
+    type: [published]
+
+jobs:
+  memote:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main branch
+        uses: actions/checkout@v3
+        with:
+          ref: main
+
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v3
+        with:
+          ref: gh-pages
+          path: gh-pages-repo
+
+      - name: Set up Python 3
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+
+      - name: Install memote
+        run: pip install -r code/requirements/requirements.txt
+
+      - name: Memote run
+        run: |
+          memote report snapshot --solver-timeout 30 --filename="gh-pages-repo/release_report.html"
+
+      - name: Auto-commit results
+        uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          commit_user_name: memote-bot
+          commit_message: "chore: update memote release report"
+          file_pattern: release_report.html
+          branch: gh-pages
+          repository: gh-pages-repo
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/memote-run.yml b/.github/workflows/memote-run.yml
@@ -6,24 +6,20 @@ jobs:
   memote-run:
     runs-on: ubuntu-latest
     steps:
+      - name: Checkout
+        uses: actions/checkout@v3
 
-    - name: Checkout
-      uses: actions/checkout@v2
+      - name: Create .env
+        run: touch .env
 
-    - name: Set up Python 3
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.9.7'
-
-    - name: Install memote
-      run: pip install -r code/requirements/ci-requirements.txt
-
-    - name: Convert model
-      run: |
-        touch .env
-        python -c 'import code.io as io; model = io.read_yeast_model(make_bigg_compliant=True); io.write_yeast_model(model)'
-
-    - name: Memote on PR
-      run: |
-        # Untracked build, skip saving to gh-pages
-        memote run --ignore-git --solver-timeout 30
+      - name: Memote on PR
+        uses: addnab/docker-run-action@v3
+        with:
+          image: ghcr.io/metabolicatlas/memote-docker:0.13
+          options: -v ${{ github.workspace }}:/opt
+          shell: bash
+          run: |
+            cd /opt
+            pip install -r code/requirements/ci-requirements.txt
+            python -c 'import code.io as io; model = io.read_yeast_model(make_bigg_compliant=True); io.write_yeast_model(model)'
+            memote run --ignore-git --solver-timeout 30
diff --git a/.github/workflows/memote_release.yml b/.github/workflows/memote_release.yml
diff --git a/.github/workflows/yaml-validation.yml b/.github/workflows/yaml-validation.yml
@@ -2,38 +2,35 @@ name: YAML validation
 
 on:
   push:
-    branches: [ develop ]
+    branches: [develop]
   pull_request:
-    branches: [ main, develop ]
+    branches: [main, develop]
 
 jobs:
   yaml-validation:
     runs-on: ubuntu-latest
     steps:
+      - name: Checkout
+        uses: actions/checkout@v3
 
-    - name: Checkout
-      uses: actions/checkout@v2
-      with:
-        fetch-depth: 1
+      - name: YAML Lint
+        uses: ibiqlik/action-yamllint@v1
+        with:
+          ## File(s) or Directory, separate by space if multiple files or folder are specified
+          file_or_dir: model/
+          ## Custom configuration (as YAML source)
+          config_data: "{extends: default, rules: {line-length: disable}}"
+          ## Format for parsing output [parsable,standard,colored,auto]
+          # format: # optional, default is colored
+          ## Return non-zero exit code on warnings as well as errors
+          # strict: # optional, default is false
 
-    - name: YAML Lint
-      uses: ibiqlik/[email protected]
-      with:
-        ## File(s) or Directory, separate by space if multiple files or folder are specified
-        file_or_dir: model/
-        ## Custom configuration (as YAML source)
-        config_data: "{extends: default, rules: {line-length: disable}}"
-        ## Format for parsing output [parsable,standard,colored,auto]
-        # format: # optional, default is colored
-        ## Return non-zero exit code on warnings as well as errors
-        # strict: # optional, default is false
-
-    - name: Set up Python 3
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.9.7'
-
-    - name: Import with cobrapy
-      run: |
-        pip install -r code/requirements/ci-requirements.txt
-        python -c "import cobra ; cobra.io.load_yaml_model('model/yeast-GEM.yml')"
+      - name: Import with cobrapy
+        uses: addnab/docker-run-action@v3
+        with:
+          image: ghcr.io/metabolicatlas/memote-docker:0.13
+          options: -v ${{ github.workspace }}:/opt
+          shell: bash
+          run: |
+            cd /opt
+            python -c "import cobra ; cobra.io.load_yaml_model('model/yeast-GEM.yml')"
diff --git 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 | 8.6.2 | 4063 | 2744 | 1160 |
-
-### Gene essentiality prediction
-
-- Accuracy: 0.881
-- True non-essential genes: 926
-- True essential genes: 63
-- False non-essential genes: 96
-- False essential genes: 38
-
-### Growth prediction
-
-- Correlation coefficient R<sup>2</sup>: 0.865
-
-![Growth curve](growth.png)
+| _Saccharomyces cerevisiae_ | 07-Jun-2023 | develop | 4099 | 2768 | 1161 |
 
 # Installation & usage
 
@@ -117,4 +103,4 @@ Contributions are always welcome! Please read the [contributions guideline](http
 
 ## Contributors
 
-Code contributors are reported automatically by GitHub under [Contributors](https://github.com/SysBioChalmers/yeast-GEM/graphs/contributors), while other contributions come in as [Issues](https://github.com/SysBioChalmers/yeast-GEM/issues).
+Code contributors are reported automatically by GitHub under [Contributors](https://github.com/SysBioChalmers/yeast-GEM/graphs/contributors), while other contributions come in as [Issues](https://github.com/SysBioChalmers/yeast-GEM/issues).
diff --git a/code/modelCuration/v8_6_2.m b/code/modelCuration/v8_6_2.m
@@ -0,0 +1,49 @@
+% This scripts applies curations to be applied on yeast-GEM release 8.6.2.
+% 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 8.6.2 (requires local yeast-GEM git repository)
+cd ..
+model = getEarlierModelVersion('8.6.2');
+model.id='yeastGEM_develop';
+dataDir=fullfile(pwd(),'..','data','modelCuration','v8_6_2');
+cd modelCuration
+
+%% Volatile Esters & Polyphosphate Reactions (PR #336)
+% See https://github.com/SysBioChalmers/yeast-GEM/pull/336 for more detailed
+% explanation of what changes were made by including 8 new distinct ester
+% reactions and  polyphosphate synthesis and transport reactions.
+
+%% Curate gene association for transport rxns (PR #306)
+% Add new reactions and genes
+metsInfo = fullfile(dataDir,'VolPolyPMets.tsv');
+genesInfo = fullfile(dataDir,'VolPolyPGenes.tsv');
+rxnsCoeffs = fullfile(dataDir,'VolPolyPRxnsCoeffs.tsv');
+rxnsInfo = fullfile(dataDir,'VolPolyPRxns.tsv');
+
+model = curateMetsRxnsGenes(model, metsInfo, genesInfo, rxnsCoeffs, rxnsInfo);
+
+
+%% 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/data/modelCuration/v8_6_2/VolPolyPGenes.tsv b/data/modelCuration/v8_6_2/VolPolyPGenes.tsv
@@ -0,0 +1,2 @@
+genes	geneShortName	ncbigene	refseq	uniprot	kegg.genes	ecogene	hprd	asap	ccds	ncbiprotein
+YJL012C	VTC4	853441	NM_001181446	P47075	sce:YJL012C					NP_012522
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		genes geneShortName ncbigene refseq uniprot kegg.genes ecogene hprd asap ccds ncbiprotein
		YJL012C VTC4 853441 NM_001181446 P47075 sce:YJL012C NP_012522