SysBioChalmers · edkerk · May 6, 2022 · Dec 17, 2021 · Mar 9, 2022 · Mar 9, 2022
diff --git a/README.md b/README.md
@@ -2,20 +2,20 @@
 
 [![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)
 
-## Description
+# Description
 
 This repository contains the current consensus genome-scale metabolic model of _Saccharomyces cerevisiae_. It is the continuation of the legacy project [yeastnet](https://sourceforge.net/projects/yeast/). For the latest release please [click here](https://github.com/SysBioChalmers/yeast-GEM/releases).
 
-## Citation
+# Citation
 
 * If you use yeast-GEM please cite the yeast8 paper:
-  > Lu, H. et al. _A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism._ Nature Communications 10, 3586 (2019). https://doi.org/10.1038/s41467-019-11581-3.
+  > 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:
   > _The yeast consensus genome-scale model [Lu et al. 2019], version 8.3.4 [Sánchez et al. 2019], was used._
 
   Find the citation details for your specific version [here](https://zenodo.org/search?page=1&size=20&q=conceptrecid:%221494182%22&sort=-publication_date&all_versions=True).
 
-## Keywords:
+# Keywords
 
 **Utilisation:** experimental data reconstruction; multi-omics integrative analysis; _in silico_ strain design; model template  
 **Field:** metabolic-network reconstruction  
@@ -31,55 +31,61 @@ This repository contains the current consensus genome-scale metabolic model of _
 
 ## Model overview
 
-|Taxonomy | Template model | Reactions | Metabolites| Genes |
-|:-------:|:--------------:|:---------:|:----------:|:-----:|
-|_Saccharomyces cerevisiae_|[Yeast 7.6](https://sourceforge.net/projects/yeast/)|4058|2742|1150|
+| Taxonomy | Latest update | Version | Reactions | Metabolites | Genes |
+|:-------|:--------------|:------|:------|:----------|:-----|
+| _Saccharomyces cerevisiae_ | 14-March-2022 | develop | 4058 | 2742 | 1150 |
 
-**Last update:** 2021-12-17
+# Installation & usage
 
-## Installation
+## Obtain model
 
-### Required software - User:
+You can obtained the model by any of the following methods:
+1. If you have a Git client installed on your computer, you can clone the [`main`](https://github.com/SysBioChalmers/yeast-GEM) branch of the yeast-GEM repository.
+2. You can directly download [the latest release](https://github.com/SysBioChalmers/yeast-GEM/releases) as a ZIP file.
+3. If you want to contribute to the development of yeast-GEM (see [below](#below)), it is best to [fork](https://github.com/SysBioChalmers/yeast-GEM/fork) the yeast-GEM repository to your own Github account.
 
-* Matlab user:
-  * A functional Matlab installation (MATLAB 7.3 or higher).
-  * The [COBRA toolbox for MATLAB](https://github.com/opencobra/cobratoolbox).
-* Python user: Python 3.4, 3.5, 3.6 or 3.7
+## Required software
 
-### Required software - Contributor:
+### Basic user
 
-* Both of the previous Matlab requirements.
-* The [RAVEN toolbox for MATLAB](https://github.com/SysBioChalmers/RAVEN).
-* A [git wrapper](https://github.com/manur/MATLAB-git) added to the search path.
+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 2.6.1 or later (recommended)  
+  * [COBRA Toolbox](https://github.com/opencobra/cobratoolbox)
 
-**NOTE:** You also require [git lfs](https://git-lfs.github.com/) if you wish to run locally any of the following two [memote](https://github.com/opencobra/memote) commands:
-* `memote run`
-* `memote report history`
+* Python-based
+  * [cobrapy](https://github.com/opencobra/cobrapy)  
 
-This is because `results.db` (the database that stores all memote results) is tracked with git lfs.
+Please see the installation instructions for each software package. You may need to install [libSBML](https://sourceforge.net/projects/sbml/files/libsbml/5.19.0/stable/MATLAB%20interface/) and an LP-solver (e.g. [Gurobi](https://www.gurobi.com/downloads/gurobi-optimizer-eula/)).
 
-### Dependencies - Recommended Software:
+### Developer
 
-* For Matlab, the [libSBML MATLAB API](https://sourceforge.net/projects/sbml/files/libsbml/MATLAB%20Interface/) (version 5.17.0 is recommended).
-* [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations.
+* 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 2.6.1 or later
+  * [git wrapper](https://github.com/manur/MATLAB-git)  
 
-### Installation instructions
-* For users: Clone it from [`main`](https://github.com/SysBioChalmers/yeast-GEM) in the Github repo, or just download [the latest release](https://github.com/SysBioChalmers/yeast-GEM/releases). If you work in python, please create an environment with all requirements:
+* 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 requirements/requirements.txt  # installs all dependencies
   touch .env                                    # creates a .env file for locating the root
   ```
-* For contributors: Fork it to your Github account, and create a new branch from [`develop`](https://github.com/SysBioChalmers/yeast-GEM/tree/develop).
 
-## Usage
+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:
   ```python
   import code.io as io
@@ -92,11 +98,10 @@ Make sure to load/save the model with the corresponding wrapper functions!
 * 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).
 
-## Contributing
+# Contributing
 
 Contributions are always welcome! Please read the [contributions guideline](https://github.com/SysBioChalmers/yeast-GEM/blob/main/.github/CONTRIBUTING.md) to get started.
 
 ## 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).
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