https://github.com/metexplore/met4j
Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks. It also came with a toolbox gathering CLI for several analyses relevant to metabolism-related research.
https://github.com/metexplore/met4j
Last synced: 8 months ago
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Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks. It also came with a toolbox gathering CLI for several analyses relevant to metabolism-related research.
- Host: GitHub
- URL: https://github.com/metexplore/met4j
- Owner: MetExplore
- Created: 2022-06-30T14:04:23.000Z (almost 4 years ago)
- Default Branch: master
- Last Pushed: 2025-10-05T19:57:14.000Z (8 months ago)
- Last Synced: 2025-10-13T19:17:35.844Z (8 months ago)
- Language: Java
- Size: 13.5 MB
- Stars: 2
- Watchers: 5
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
Awesome Lists containing this project
README
# Met4J : the Java library for metabolic networks
[](https://forgemia.inra.fr/metexplore/met4j/-/commits/master)
[](https://forgemia.inra.fr/metexplore/met4j/-/commits/master)
[](https://img.shields.io/maven-central/v/fr.inrae.toulouse.metexplore/met4j)
[](https://img.shields.io/gitlab/v/tag/metexplore/met4j?gitlab_url=https%3A%2F%2Fforgemia.inra.fr%2F&include_prereleases&label=version)
[](https://javadoc.io/doc/fr.inrae.toulouse.metexplore/met4j)
[](https://twitter.com/met4j)
**Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks. It also came with a toolbox gathering CLI for several analyses relevant to metabolism-related research.**
Met4j is composed by three main modules:
- [met4j-core](met4j-core/README.md): it's the key module which contains all the core
classes for handling metabolic networks
- [met4j-io](met4j-io/README.md): for importing/exporting metabolic networks in several
formats (SBML, KEGG, TSV)
- [met4j-graph](met4j-graph/README.md): for performing graph-based topological analysis of metabolic networks.
The package [met4j-toolbox](met4j-toolbox/README.md) contains high-level apps that can be run in command line by using either jar file or Singularity or Docker containers.
## Installation
### From Maven
Install all modules :
```
fr.inrae.toulouse.metexplore
met4j-toolbox
1.4.0
```
or a specific module (example : met4j-core ):
```
fr.inrae.toulouse.metexplore
met4j-core
1.4.0
```
### From Source
```
git clone https://forgemia.inra.fr/metexplore/met4j.git;
cd met4j;
mvn clean install
```
Read [met4j-toolbox](met4j-toolbox/README.md) to see how to get jar, Docker or Singularity packages containing all the met4-toolbox apps.
## Usage
User documentation for the library modules can be found in each module's own README.
Detailed code examples can be found at [here](https://forgemia.inra.fr/metexplore/tutorialmet4j).
Javadoc can be found at [https://javadoc.io/doc/fr.inrae.toulouse.metexplore](https://javadoc.io/doc/fr.inrae.toulouse.metexplore)
## Contributing
Pull requests are welcome **on the gitlab repo** ([https://forgemia.inra.fr/metexplore/met4j](https://forgemia.inra.fr/metexplore/met4j)). For major changes, please open an issue first to discuss what you would like to change.
Please make sure to update tests as appropriate.
## Issues
Issues or suggestions can be posted [here](https://github.com/MetExplore/met4j/issues).
## License
Met4J is distributed under the open license [CeCILL-2.1](https://cecill.info/licences/Licence_CeCILL_V2.1-en.html) (compatible GNU-GPL).