From 861e263e3845c2bc641f2bde4ad8e871cfad7d87 Mon Sep 17 00:00:00 2001 From: Hao Wang Date: Wed, 14 Oct 2020 13:40:10 +0200 Subject: [PATCH 1/3] doc: update README --- README.md | 16 +++------------- 1 file changed, 3 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index c62cc89..26fac72 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,5 @@ -> Please read the paragraph below and delete it: -This is the `README.md` template provided by [standard-GEM](https://github.com/SysBioChalmers/standard-GEM). -Blanks are indicated by `{{ }}`. Below are examples of blanks used throughout this file: -`{{organization or username}}` is the organization name or username for this GitHub repository, eg. `SysBioChalmers` -`{{repository name}}` is the name of this GitHub repository, eg. `yeast-GEM` - -## {{repository name}}: {{repository description}} +# Mouse-GEM: The generic genome-scale metabolic model of _Mus musculus_ [![Version](https://badge.fury.io/gh/{{organization or username}}%2F{{repository name}}.svg)](https://badge.fury.io/gh/sysbiochalmers/yeast-gem) [![Zenodo](https://zenodo.org/badge/{{Zenodo ID}}.svg)](https://zenodo.org/badge/latestdoi/{{Zenodo ID}}) @@ -14,16 +8,12 @@ Blanks are indicated by `{{ }}`. Below are examples of blanks used throughout th #### Brief Model Description -{{ fill in a short description or the paper abstract }} +This repository contains the latest version of Mouse-GEM, a mouse genome-scale metabolic model. #### Citation -{{ provide the citation once available, for example: - > Lu, H., Li, F., Sánchez, B.J. et al (2019). A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nat Commun 10, 3586 [doi:10.1038/s41467-019-11581-3](https://doi.org/10.1038/s41467-019-11581-3) - -}} - +Manuscript under preparation #### Model Keywords From e0237a6cbb2fc246431ffe7a53422692d46a1fc4 Mon Sep 17 00:00:00 2001 From: Hao-Chalmers Date: Wed, 14 Oct 2020 14:24:04 +0200 Subject: [PATCH 2/3] doc: update README --- README.md | 49 ++++++++++++++++++++++++++++++++++++++++--------- 1 file changed, 40 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 26fac72..877d058 100644 --- a/README.md +++ b/README.md @@ -17,29 +17,60 @@ Manuscript under preparation #### Model Keywords -**Utilisation:** experimental data reconstruction, multi-omics integrative analysis, _in silico_ strain design, model template +**Utilisation:** multi-omics integrative analysis, predictive simulation **Field:** metabolic-network reconstruction **Type of Model:** reconstruction, curated -**Model Source:** YeastMetabolicNetwork +**Model Source:** Human-GEM **Omic Source:** genomics, metabolomics -**Taxonomy:** _Saccharomyces cerevisiae_ +**Taxonomy:** _Mus musculus_ **Metabolic System:** general metabolism **Tissue:** **Bioreactor:** **Cell type:** **Cell line:** -**Strain:** S288C -**Condition:** aerobic, glucose-limited, defined media +**Condition:** generic metabolism -### Installation +### Model Overview -{{ Be mindful of users who do not have a typical background - provide a clear overview of the required software. Also, there might be different requirements for users and collaborators. }} +|Taxonomy | Template Model | Reactions | Metabolites| Genes | +| ------------- |:-------------:|:-------------:|:-------------:|:-----:| +|_Mus musculus_ | Human-GEM | | | | -### Usage +## Installation -{{ Describe how to load and save the model. }} +### Required Software +* A functional MATLAB installation (MATLAB 7.3 and higher). +* The [RAVEN toolbox](https://github.com/SysBioChalmers/RAVEN). +* The [COBRA toolbox](https://github.com/opencobra/cobratoolbox) (not necessary for most functionality). + + +### Dependencies - Recommended Software +* The libSBML MATLAB API (version [5.13.0](https://sourceforge.net/projects/sbml/files/libsbml/5.13.0/stable/MATLAB%20interface/) is recommended). +* [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations. + + +### Installation Instructions +* Clone the [master branch](https://github.com/SysBioChalmers/Human-GEM/tree/master) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Human-GEM/releases/latest). +* Add the directory to your MATLAB path (instructions [here](https://se.mathworks.com/help/matlab/ref/addpath.html?requestedDomain=www.mathworks.com)). + + +## Usage + +#### Loading/saving the model + +`Mouse-GEM.mat` (Recommended if on `master` branch) +* Load and save using the built-in MATLAB `load()` and `save()` functions. + +`Mouse-GEM.xml` (SBML format) +* Load using the `importModel.m` function (from [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN)) +* Save using the `exportModel.m` function (from [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN)) + + +## Websites + +- [Metabolic Atlas](https://metabolicatlas.org/) enables visualization and exploration of Human-GEM content. ### Contributing From 57d1cf1848d607a3dea6b84e79f41218a2c61815 Mon Sep 17 00:00:00 2001 From: Hao-Chalmers Date: Wed, 14 Oct 2020 19:43:21 +0200 Subject: [PATCH 3/3] doc: update taxonomy and genome ids --- README.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 877d058..c29b86b 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,6 @@ [![Version](https://badge.fury.io/gh/{{organization or username}}%2F{{repository name}}.svg)](https://badge.fury.io/gh/sysbiochalmers/yeast-gem) [![Zenodo](https://zenodo.org/badge/{{Zenodo ID}}.svg)](https://zenodo.org/badge/latestdoi/{{Zenodo ID}}) -[![Gitter chat](https://badges.gitter.im/{{organization or username}}/{{repository name}}.svg)](https://gitter.im/{{organization or username}}/{{repository name}}) #### Brief Model Description @@ -20,9 +19,11 @@ Manuscript under preparation **Utilisation:** multi-omics integrative analysis, predictive simulation **Field:** metabolic-network reconstruction **Type of Model:** reconstruction, curated -**Model Source:** Human-GEM -**Omic Source:** genomics, metabolomics -**Taxonomy:** _Mus musculus_ +**Model source:** [Human-GEM](https://doi.org/10.1126/scisignal.aaz1482) +**Omic source:** genomics; metabolomics +**Taxonomic name:** _Mus musculus_ +**Taxonomy ID:** [10090](https://identifiers.org/taxonomy:10090) +**Genome ID:** [GCA_000001635.8](https://identifiers.org/insdc.gca:GCA_000001635.8) **Metabolic System:** general metabolism **Tissue:** **Bioreactor:**