Met4J : the Java library for metabolic networks

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: it's the key module which contains all the core classes for handling metabolic networks
• met4j-io: for importing/exporting metabolic networks in several formats (SBML, KEGG, TSV)
• met4j-graph: for performing graph-based topological analysis of metabolic networks.

The package met4j-toolbox 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 :

<dependency>
<groupId>fr.inrae.toulouse.metexplore</groupId>
<artifactId>met4j-toolbox</artifactId>
<version>0.12.0</version>
</dependency>

or a specific module (example : met4j-core ):

<dependency>
<groupId>fr.inrae.toulouse.metexplore</groupId>
<artifactId>met4j-core</artifactId>
<version>0.12.0</version>
</dependency>

From Source

git clone https://forgemia.inra.fr/metexplore/met4j.git;
cd met4j;
mvn clean install 

Read met4j-toolbox 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. Javadoc can be found at https://javadoc.io/doc/fr.inrae.toulouse.metexplore

Contributing

Pull requests are welcome on the gitlab repo (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.

License

Met4J is distributed under the open license CeCILL-2.1 (compatible GNU-GPL).