Merge pull request #343 from SysBioChalmers/develop

yeast 8.7.0

.github/issue_template/bug_report.md

@@ -0,0 +1,37 @@
+---
+name: 🐞 Bug report
+about: If you have run into a bug/problem/error when using the model.
+labels: bug
+assignees: ''
+
+---
+<!-- Note: Please search to see if an issue already exists for the bug you encountered. -->
+
+<!-- Make sure you use the latest yeast-GEM version. -->
+
+<!-- For convenience, when referring to a particular reaction/metabolite/gene identifiers, you can link to Metabolic Atlas for quick reference.
+Examples:
+- Link to reaction [r_0061](https://metabolicatlas.org/explore/Yeast-GEM/gem-browser/reaction/r_0061)
+- Link to gene [YCL018W](https://metabolicatlas.org/explore/Yeast-GEM/gem-browser/gene/YCL018W)
+- Link to metabolite [s_0009](https://metabolicatlas.org/explore/Yeast-GEM/gem-browser/metabolite/s_0009)
+-->
+
+#### Current behavior:
+<!-- A concise description of what you're experiencing. Try to be as clear as possible: Is it something wrong/missing in the model? Is it a simulation issue? How does the reaction/metabolite/gene/simulation look like in the `main` branch? -->
+
+#### Expected feature/value/output:
+<!-- A concise description of what you expected to happen. How the reaction/metabolite/gene/simulation result should look (cite literature if needed). If you have a precise idea on how this should be fixed, then it might be better to use the "Propose curation" issue type (link to change this is above "Title").  -->
+
+#### Reproducing these results:
+<!-- If the bug is a result from simulation, model import/export or use of any of the functions in this repository, then make sure you report:
+1. What operating system you use (Windows/Mac).
+2. What version of MATLAB/RAVEN/COBRA/Python you use (provide what is relevant for your situation).
+3. If a simulation result, also report the solver (Gurobi/glpk/CPLEX etc.).
+3. What exact commands were done, so that we can try to reproduce the bug.
+4. The exact error message that is shown.
+-->
+
+#### Anything else:
+<!--
+Links? References? Anything that will give us more context about the issue that you are encountering!
+-->

.github/issue_template/curation.md

@@ -0,0 +1,51 @@
+---
+name: ✏️ Propose curation
+about: If you want to suggest a specific change to the model (e.g. new reaction, correct gene association, remove duplicate metabolite).
+labels: curation
+assignees: ''
+
+---
+<!-- Note: Please search to see if an issue already exists for the curation you propose. -->
+
+<!-- Make sure you use the latest yeast-GEM version. -->
+
+<!-- For convenience, when referring to a particular reaction/metabolite/gene identifiers, you can link to Metabolic Atlas for quick reference.
+Examples:
+- Link to reaction [r_0061](https://metabolicatlas.org/explore/Yeast-GEM/gem-browser/reaction/r_0061)
+- Link to gene [YCL018W](https://metabolicatlas.org/explore/Yeast-GEM/gem-browser/gene/YCL018W)
+- Link to metabolite [s_0009](https://metabolicatlas.org/explore/Yeast-GEM/gem-browser/metabolite/s_0009)
+-->
+
+#### Brief description:
+<!-- A concise description on what curation you are proposing and for what purpose. Provide links to website or references that support your statement. For instance: "In yeast-GEM the reaction for 3-isopropylmalate dehydrogenase is split into two half-reactions, as the second half-reaction is spontaneous. However, the spontaneous half-reaction is incorrectly assigned to a wrong enzyme. See https://www.uniprot.org/uniprotkb/P04173 and https://www.uniprot.org/uniprotkb/P38891 for the two enzymes, and https://iubmb.qmul.ac.uk/enzyme/EC1/1/1/85.html for the spontaneous half-reaction.
+
+If you just want to report a problem with the model, but do not have a precise idea on how this should be fixed, then it might be better to use the "Bug report" issue type (link to change this is above "Title").
+-->
+
+#### Current status:
+<!-- Show what is the current status in the model of the reaction/metabolite/gene etc. that you propose to curate. If suitable, this can be done in table format, choose yourself what data is most informative to show (do not include more than necessary):
+
+Identifier | Reaction equation | Genes
+---|---|---
+r_0061 | (2R,3S)-3-isopropylmalate[c] + NAD[c] => (2S)-2-isopropyl-3-oxosuccinate[c] + H+[c] + NADH[c] | YCL018W
+r_0029 | (2S)-2-isopropyl-3-oxosuccinate[c] + H+[c] => 4-methyl-2-oxopentanoate[c] + carbon dioxide[c] | YJR148W
+
+Alternatively, this can also be written out in bullet points, linking to Metabolic Atlas:
+
+- [r_0061](https://metabolicatlas.org/explore/Yeast-GEM/gem-browser/reaction/r_0061), correct half-reaction.
+- [r_0029](https://metabolicatlas.org/explore/Yeast-GEM/gem-browser/reaction/r_0029), spontaneous half-reaction incorrectly annotated with [YJR148W](https://metabolicatlas.org/explore/Yeast-GEM/gem-browser/gene/YJR148W)
+
+-->
+
+#### Proposed status/to-do list:
+<!-- Give a very brief list of actions that need to be taken to curate the model. In some cases, it might be helpful to first show the proposed changes in table format:
+
+Identifier | Reaction equation | Genes
+---|---|---
+r_0061 | (2R,3S)-3-isopropylmalate[c] + NAD[c] => (2S)-2-isopropyl-3-oxosuccinate[c] + H+[c] + NADH[c] | YCL018W
+r_0029 | (2S)-2-isopropyl-3-oxosuccinate[c] + H+[c] => 4-methyl-2-oxopentanoate[c] + carbon dioxide[c] | 
+
+But a to-do list should always be present:
+- [ ] Leave r_0061 intact.
+- [ ] Remove YJR148W from r_0029.
+    -->

.github/issue_template/help.md

@@ -0,0 +1,21 @@
+---
+name: ❔ Question/help
+about: If you have a question about the model or need some help with its use.  
+labels: help
+assignees: ''
+
+---
+<!-- Note: Please search to see if an issue already exists for the bug you encountered. -->
+
+<!-- For convenience, when referring to a particular reaction/metabolite/gene identifiers, you can link to Metabolic Atlas for quick reference.
+Examples:
+- Link to reaction [r_0061](https://metabolicatlas.org/explore/Yeast-GEM/gem-browser/reaction/r_0061)
+- Link to gene [YCL018W](https://metabolicatlas.org/explore/Yeast-GEM/gem-browser/gene/YCL018W)
+- Link to metabolite [s_0009](https://metabolicatlas.org/explore/Yeast-GEM/gem-browser/metabolite/s_0009)
+-->
+
+#### Question 
+<!-- Write down your concise question. If you have run into a problem with the model, or have a specific suggestion on how to change the model, it is better to use the "Bug report" or "Propose curation" issue types (link to change this is above "Title").  -->
+
+#### Further information 
+<!-- Provide any further information that might be useful to consider. Any links or references that may help to answer your question?  -->

.github/pull_request_template.md

@@ -1,8 +1,7 @@
 ### Main improvements in this PR:
-*Try to be as clear as possible: Is it fixing/adding something in the model? Is it an additional test/function/dataset? PLEASE DELETE THIS LINE.*
+<!-- Try to be as clear as possible: Is it fixing/adding something in the model?
+Is it an additional test/function/dataset? -->
 
 **I hereby confirm that I have:**
-
-- [ ] Tested my code with [all requirements](https://github.com/SysBioChalmers/yeast-GEM#required-software---contributor) for running the model
+<!-- Note: replace [ ] with [X] to check the box -->
 - [ ] Selected `develop` as a target branch (top left drop-down menu)
-- [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/yeast-GEM) about this PR

.gitignore

@@ -1,3 +1,8 @@
+# yeast-GEM specific #
+###################
+yetfl_metG.csv
+yetfl_rxnG.csv
+
 # Compiled source #
 ###################
 *.com
@@ -44,6 +49,7 @@ Thumbs.db
 *.mex*
 *.mlappinstall
 *.mltbx
+*.mat
 helpsearch*/
 
 # Python-related things #
@@ -54,6 +60,7 @@ helpsearch*/
 
 # Non-complying tables and files #
 ##################################
+*.xls*
 *.tab
 *.doc*
 *.ppt*

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_ | 08-Jul-2023 | 8.6.3 | 4099 | 2768 | 1161 |
+| _Saccharomyces cerevisiae_ | 15-Jul-2023 | develop | 4131 | 2806 | 1163 |
 
 # Installation & usage
 
@@ -50,7 +50,7 @@ You can obtained the model by any of the following methods:
 
 If you want to use the model for your own model simulations, you can use **any software** that accepts SBML L3V1 FBCv3 formatted model files. This includes any of the following:
 * MATLAB-based
-  * [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) version 2.7.1 or later (recommended)  
+  * [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) version 2.8.3 or later (recommended)  
   * [COBRA Toolbox](https://github.com/opencobra/cobratoolbox)
 
 * Python-based
@@ -62,30 +62,35 @@ Please see the installation instructions for each software package.
 
 * MATLAB-based  
   If you want to contribute to the development of yeast-GEM, or otherwise want to run any of the [provided](https://github.com/SysBioChalmers/yeast-GEM/tree/main/code) MATLAB functions, then the following software is required:
-  * [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) version 2.7.1 or later
+  * [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) version 2.8.3 or later
 
 * Python-based  
   Contribution via python (cobrapy) is not yet functional. In essence, if you can retain the same format of the model files, you can still contribute to the development of yeast-GEM. However, you cannot use the MATLAB functions.
 
   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 code/requirements/requirements.txt  # installs all dependencies
-  touch .env                                    # creates a .env file for locating the root
+  pip install -r code/requirements/requirements.txt  # install all dependencies
+  touch .env # create a .env file for locating the root
   ```
 
 If you want to locally run `memote run` or `memote report history`, you should also install [git lfs](https://git-lfs.github.com/), as `results.db` (the database that stores all memote results) is tracked with git lfs.
 
 ## Model usage
 
-Make sure to load/save the model with the corresponding wrapper functions
+Make sure to load/save the model with the corresponding wrapper functions:
 * In Matlab:
   ```matlab
   cd ./code
   model = loadYeastModel(); % loading
   saveYeastModel(model);    % saving
   ```
   * If RAVEN is not installed, you can also use COBRA-native functions (`readCbModel`, `writeCbModel`), but these model-files cannot be committed back to the GitHub repository.
-* In Python:
+* In Python:  
+Before opening Python, the following command should (once) be run in the yeast-GEM root folder:  
+  ```bash
+  touch .env # create a .env file for locating the root
+  ```
+  Afterwards, the model can be loaded in Python with:
   ```python
   import code.io as io
   model = io.read_yeast_model() # loading

code/.deprecated/modelCuration/UpdateDBnewRxn.m

@@ -0,0 +1,16 @@
+% This script is adds new database annotated reactions to the model.
+% =MORE DETAILED DESCRIPTION REQUIRED. WHICH DATABASES? WHICH DATE? WHAT
+% CRITERIA OR SEARCH TERMS WERE USED? ANY ADDITIONAL FILTERING?=
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+cd ..
+model = loadYeastModel;
+metsInfo = '../data/modelCuration/DBnewRxns/DBnewRxnsMets.tsv';
+rxnsCoeffs = '../data/modelCuration/DBnewRxns/DBnewRxnsCoeffs.tsv';
+rxnsInfo = '../data/modelCuration/DBnewRxns/DBnewRxnsRxns.tsv';
+genesInfo = '../data/modelCuration/DBnewRxns/DBnewRxnsGenes.tsv';
+newModel = curateMetsRxnsGenes(model,metsInfo,genesInfo,rxnsCoeffs,rxnsInfo);
+checkModelStruct(newModel,true,false)
+saveYeastModel(newModel)
+cd modelCuration
+newModel=model;