chore: update citation (#368)

* chore: update citation

* fix: refer to gh discussions instead of gitter

* chore: remove reference to dd-decaf caffeine

has closed down since Aug 2023

* fix: links to badges

* fix: readme link to memote release report

* fix: citation year

---------

Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>

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:
@@ -99,10 +103,9 @@ 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