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