diff --git a/README.md b/README.md index bb50e833..422e0d5d 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ [![All Contributors](https://img.shields.io/badge/all_contributors-31-success.svg)](#contributors) -### Brief Model Description +### Brief model description This repository contains the latest version of Human-GEM, a human genome-scale metabolic model. We encourage [contributions](#contributing). @@ -23,7 +23,7 @@ If you use Mouse1, Rat1, Zebrafish1, Fruitfly1, or Worm1 in your research, pleas -### Model Keywords +### Model keywords **Utilisation:** predictive simulation, multi-omics integrative analysis, model template **Field:** metabolic-network reconstruction @@ -35,7 +35,7 @@ If you use Mouse1, Rat1, Zebrafish1, Fruitfly1, or Worm1 in your research, pleas **Condition:** generic metabolism -### Model Overview +### Model overview |Taxonomy | Template Model | Reactions | Metabolites| Genes | | ------------- |:-------------:|:-------------:|:-------------:|:-----:| @@ -47,25 +47,39 @@ If you use Mouse1, Rat1, Zebrafish1, Fruitfly1, or Worm1 in your research, pleas Contributions are always welcome! Read more about the project's philosophy in our [wiki](https://github.com/SysBioChalmers/Human-GEM/wiki) or have a look at the [Contributing guidelines](https://github.com/SysBioChalmers/Human-GEM/blob/main/.github/CONTRIBUTING.md) before starting. -## User Guide +## User guide Detailed instructions on the installation and use of the Human-GEM model and repository can be found in the [Human-GEM user guide](https://sysbiochalmers.github.io/Human-GEM-guide/). -## Installation +# Installation -### 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). +## Required software +### Basic user +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) v2.10.1+ (recommended, see [Installation instructions](https://github.com/SysBioChalmers/RAVEN/wiki/Installation#installation-instructions)) +* [COBRA Toolbox](https://github.com/opencobra/cobratoolbox) -### 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. +#### Python-based +* [cobrapy](https://github.com/opencobra/cobrapy) +Please see the installation instructions for each software package. -### Installation Instructions +### Developer + +#### MATLAB-based +If you want to contribute to the development of Human-GEM, or otherwise want to run any of the [provided](https://github.com/SysBioChalmers/Human-GEM/tree/main/code) MATLAB functions, then the following software is required: +* [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) v2.10.1+ (recommended, see [Installation instructions](https://github.com/SysBioChalmers/RAVEN/wiki/Installation#installation-instructions)) + +#### Python-based +You can also contribution to the development of Human-GEM via python (e.g. cobrapy), even if you would not be able to run any of the model-specific MATLAB functions. To curate the model, you can still edit `Human-GEM.yml`, `genes.tsv`, `metabolites.tsv` and `reactions.tsv`, all located in the `model/` folder. + +### Recommended solver +* When performing simulations with Human-GEM, you are encouraged to use [Gurobi Optimizer](https://www.gurobi.com/academia/academic-program-and-licenses/). + +## Installation instructions * Clone the [main branch](https://github.com/SysBioChalmers/Human-GEM/tree/main) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Human-GEM/releases/latest). * Add the directory to your MATLAB path either by using the lines below or manually (instructions [here](https://se.mathworks.com/help/matlab/ref/addpath.html?requestedDomain=www.mathworks.com)). ```matlab @@ -77,28 +91,27 @@ HumanGEMInstaller.install HumanGEMInstaller.uninstall ``` -## Model Files +## Model files The model is available as `.xml`, `.xlsx`, `.txt`, `.yml`, and `.mat` in the `model/` directory. Note that only the `.yml` version is available on branches other than `main` (e.g., `develop`), to facilitate tracking of model changes. - ## Usage -#### Loading/saving the model +#### Loading/saving the model in MATLAB `Human-GEM.mat` (Recommended if on `main` branch) * Load and save using the built-in MATLAB `load()` and `save()` functions. `Human-GEM.yml` (Recommended if on `develop` or other branches) -* Load using the `importYaml.m` function (in `code/io/`) -* Save using the `exportYaml.m` function (in `code/io/`) +* Load using the `readYAMLmodel.m` function (from [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN)) +* Save using the `writeYAMLmodel.m` function (from [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN)) `Human-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)) -## Reaction, Metabolite, and Gene Annotations +## Reaction, metabolite, and gene annotations Additional annotation information and external identifiers for Human-GEM reactions, metabolites, and genes are provided as `tsv` files in the `model/` directory (`reactions.tsv`, `metabolites.tsv`, and `genes.tsv`, respectively). @@ -111,7 +124,7 @@ To import/export this annotation data to/from MATLAB, use the `importTsvFile` an - The [Human-GEM user guide](https://sysbiochalmers.github.io/Human-GEM-guide/) provides detailed instructions and examples for using the Human-GEM model and repository. -## Metabolic Maps +## Metabolic maps A collection of manually curated 2D metabolic maps associated with Human-GEM are stored in the [Human-maps repository](https://github.com/SysBioChalmers/Human-maps). These maps can be downloaded from the repository or explored interactively using [Metabolic Atlas](https://metabolicatlas.org/explore/map-viewer/human1).