Met4J

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.

Modules

Met4j is composed by several maven 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, MetExploreXml, KEGG)
• met4j-graph: for performing graph-based topological analysis of metabolic networks.

The other modules are for the moment not documented or still in progress.

Installation

From Maven

Install all modules :

<dependency>
<groupId>fr.inrae.toulouse.metexplore</groupId>
<artifactId>met4j-toolbox</artifactId>
<version>0.5.2</version>
</dependency>

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

<dependency>
<groupId>fr.inrae.toulouse.metexplore</groupId>
<artifactId>met4j-core</artifactId>
<version>0.5.2</version>
</dependency>

Replace the version number by the last version of met4j.

From gitlab

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

Tutorial

You can find tutorials by clicking on the module links above. Examples can be found here: https://forgemia.inra.fr/metexplore/tutorialmet4j