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![](https://forgemia.inra.fr/uploads/-/system/project/avatar/864/met4J_logo.png?width=64)
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# Met4J : the Java library for metabolic networks
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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.**

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 
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formats (SBML, KEGG, TSV)
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- [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.
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## Installation
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### From Maven
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Install all modules :  
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```
<dependency>
<groupId>fr.inrae.toulouse.metexplore</groupId>
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<artifactId>met4j-toolbox</artifactId>
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<version>1.4.0</version>
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</dependency>
```

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or a specific module (example : met4j-core ):  
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```
<dependency>
<groupId>fr.inrae.toulouse.metexplore</groupId>
<artifactId>met4j-core</artifactId>
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<version>1.4.0</version>
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</dependency>
```

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### From Source

```
git clone https://forgemia.inra.fr/metexplore/met4j.git;
cd met4j;
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mvn clean install 
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Read [met4j-toolbox](met4j-toolbox/README.md) to see how to get jar, Docker or Singularity packages containing all the met4-toolbox apps.

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## 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)
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## Contributing
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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 or suggestions can be posted [here](https://github.com/MetExplore/met4j/issues).
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## License
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Met4J is distributed under the open license [CeCILL-2.1](https://cecill.info/licences/Licence_CeCILL_V2.1-en.html) (compatible GNU-GPL).