Merge pull request #369 from SysBioChalmers/develop

README.md

@@ -1,6 +1,10 @@
 # yeast-GEM: The consensus genome-scale metabolic model of _Saccharomyces cerevisiae_
 
-[![DOI](https://zenodo.org/badge/52777598.svg)](https://zenodo.org/badge/latestdoi/52777598) [![GitHub version](https://badge.fury.io/gh/sysbiochalmers%2Fyeast-gem.svg)](https://badge.fury.io/gh/sysbiochalmers%2Fyeast-gem) [![Join the chat at https://gitter.im/SysBioChalmers/yeast-GEM](https://badges.gitter.im/SysBioChalmers/yeast-GEM.svg)](https://gitter.im/SysBioChalmers/yeast-GEM?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)[![Memote history](https://github.com/SysBioChalmers/yeast-GEM/workflows/Memote%20history/badge.svg)](https://sysbiochalmers.github.io/yeast-GEM/history_report.html)
+[![Current release](https://img.shields.io/github/release/SysBioChalmers/yeast-GEM/all.svg)](https://github.com/SysBioChalmers/yeast-GEM/releases/)
+[![GitHub Discussions](https://img.shields.io/github/discussions/sysbiochalmers/yeast-gem)](https://github.com/SysBioChalmers/yeast-GEM/discussions)
+[![Memote report](https://github.com/SysBioChalmers/yeast-GEM/actions/workflows/memote-release.yml/badge.svg)](https://sysbiochalmers.github.io/yeast-GEM/release_report.html)
+[![DOI](https://zenodo.org/badge/52777598.svg)](https://zenodo.org/badge/latestdoi/52777598)
+
 
 # Description
 
@@ -9,7 +13,7 @@ This repository contains the current consensus genome-scale metabolic model of _
 # Citation
 
 * If you use yeast-GEM please cite the yeast9 paper:
-  > Zhang, C. et al. _Yeast9: a consensus yeast metabolic model enables quantitative analysis of cellular metabolism by incorporating big data._ bioRxiv (2023) doi:[10.1101/2023.12.03.569754](https://doi.org/10.1101/2023.12.03.569754)
+  > Zhang, C. et al. _Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community._ Molecular Systems Biology (2024) doi:[10.1038/s44320-024-00060-7](https://doi.org/10.1038/s44320-024-00060-7)
 * For pre-yeast9 versions:
   > Lu, H. et al. _A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism._ Nature Communications 10, 3586 (2019). doi:[10.1038/s41467-019-11581-3](https://doi.org/10.1038/s41467-019-11581-3)
 * Additionally, all yeast-GEM releases are archived in [Zenodo](https://zenodo.org/badge/latestdoi/52777598), for you to cite the specific version of yeast-GEM that you used in your study, to ensure reproducibility. You should always cite the original publication + the specific version, for instance:
@@ -113,10 +117,9 @@ Before opening Python, the following command should (once) be run in the yeast-G
   io.write_yeast_model(model)   # saving
   ```
 
-### Online visualization/simulation
+### Online visualization
 
-* You can visualize selected pathways of yeast-GEM and perform online constraint-based simulations using [Caffeine](https://caffeine.dd-decaf.eu/interactive-map), by creating a simulation with the latest yeast-GEM version available, and choosing any _S. cerevisiae_ map (currently only `iMM904` maps are available). Learn more [about Caffeine](https://caffeine.dd-decaf.eu).
-* Additionally, you can interactively navigate model components and visualize 3D representations of all compartments and subsystems of yeast-GEM at [Metabolic Atlas](https://metabolicatlas.org/explore?selected=Yeast-GEM). Learn more [about Metabolic Atlas](https://www.metabolicatlas.org/about).
+You can interactively navigate model components and visualize 3D representations of all compartments and subsystems of yeast-GEM at [Metabolic Atlas](https://metabolicatlas.org/explore?selected=Yeast-GEM). Learn more [about Metabolic Atlas](https://www.metabolicatlas.org/about).
 
 # Contributing
 

code/saveYeastModel.m

@@ -1,22 +1,21 @@
 function saveYeastModel(model,upDATE,allowNoGrowth,binaryFiles)
 % saveYeastModel
-%   Saves model as a .xml, .txt and .yml file. Also updates complementary
-%   files (boundaryMets.txt, README.md and dependencies.txt).
+%   Saves model as .xml, .txt and .yml file (.mat and .xlsx on demand). 
+%   It also updates README.md, dependencies.txt and checks for growth.
 %
-%   Inputs: model           (struct) model to save. Preferably RAVEN
-%                           format, although COBRA format is also allowed,
-%                           but some fields might be lost in the
-%                           conversion.
-%           upDATE          (bool, opt) If updating the date in the README file
-%                           is needed (default true)
-%           allowNoGrowth   (bool, opt) if saving should be allowed whenever
-%                           the model cannot grow, returning a warning (default
-%                           = true), otherwise will error
-%           binaryFiles     (bool, opt) if the model should be stored in
-%                           binary file formats (= xlsx and mat)
-%
-%   Usage: saveYeastModel(model,upDATE,allowNoGrowth,binaryFiles)
+% Inputs:
+%   model           (struct) model to save. Preferably RAVEN format,
+%                   although COBRA format is also allowed, but some fields
+%                   might be lost in the conversion.
+%   upDATE          (bool, opt) If updating the date in the README file is
+%                   needed (default true)
+%   allowNoGrowth   (bool, opt) if saving should be allowed whenever the
+%                   model cannot grow, returning a warning (default true),
+%                   otherwise will error
+%   binaryFiles     (bool, opt) if the model should be stored in binary
+%                   file formats (= xlsx and mat)
 %
+% Usage: saveYeastModel(model,upDATE,allowNoGrowth,binaryFiles)
 
 if nargin < 2
     upDATE = true;
@@ -56,7 +55,11 @@ function saveYeastModel(model,upDATE,allowNoGrowth,binaryFiles)
 
 %Check if model is a valid SBML structure:
 exportModel(model,'tempModel.xml',false,false,true);
-[~,~,errors] = evalc('TranslateSBML(''tempModel.xml'',1,0)');
+try
+    [~,~,errors] = evalc('TranslateSBML_RAVEN(''tempModel.xml'',1,0)');
+catch
+    [~,~,errors] = evalc('TranslateSBML(''tempModel.xml'',1,0)');
+end
 if any(strcmp({errors.severity},'Error'))
     delete('tempModel.xml');
     error('Model should be a valid SBML structure. Please fix all errors before saving.')