Gene Interaction Networks simulation

GINsim is a software tool for the design and analysis of qualitative dynamical models of biological interaction networks. For more info see http://ginsim.org

Build and Install

GINsim uses maven: mvn package will compile it and prepare a jar (executable Java archive) as well as dependancies into the target folder. To use it outside of the build dir, copy the jar and the lib folder or use mvn assembly::assembly to build a fat jar (with dependencies included).

Run and documentation

Run GINsim using with java -jar GINsim.jar command.

User documentation is available on the GINsim website.

Generate javadoc (in the "target/site" folder) using "mvn javadoc:javadoc".

Plugins

Most features in GINsim are implemented as internal extensions and declared using java annotations. See the developer documentation for more details. Note that out-of-tree plugins (i.e. plugins distributed as separate jar files) are not supported, but supporting such plugins should be easy if needed.