copasi / cytoscape-copasi

Example Cytoscape 3 plugin that imports COPASI files

Example COPASI Cytoscape application

This project hosts an example cytoscape application, that adds an importer for COPASI files to Cytoscape. The example borrows heavily from cy3sbml.

Building the app

Running:

mvn package

from the checked out project, will produce a file ./target/CopasiPlugin-1.0.jar, that then can be manually added to cytoscape. For this to work, the native library of the COPASI Java bindings needs to be in the java.library.path (On windows any directory in the PATH will do, on Linux /usr/lib will work).

Creating an artifact from the bindings

The COPASI bindings consist of a copasi.jar file and a corresponding shared library. To be able to use them the maven command:

mvn org.apache.maven.plugins:maven-install-plugin:2.5.2:install-file -Dfile=lib\copasi.jar -DgroupId=org.COPASI -DartifactId=copasi -Dversion=1 -Dpackaging=jar

was used, from there it is then picked up from the pom file, as the lib directory is marked as repository:

<repository>
  <id>in-project</id>
  <name>In project repository</name>
  <url>file://${project.basedir}/lib</url>
</repository>

and then the file is included like so:

<dependency>
  <groupId>org.COPASI</groupId>
  <artifactId>copasi</artifactId>
  <version>1</version>
</dependency>   

License

The packages available on this page are provided under the Artistic License 2.0, which is an OSI approved license. This license allows non-commercial and commercial use free of charge.