Cytoscape is a network analysis package used quite often in systems biology. Cytoscape has scripting support for Python, Ruby, and Groovy. There wasn't a meaningful Groovy example so I made a couple of minor changes to the Ruby example, along with logging added for debugging:

import cytoscape.Cytoscape;
import cytoscape.layout.CyLayouts;
import cytoscape.layout.LayoutAlgorithm;
import cytoscape.CytoscapeInit

errFile = new File("test.out").withWriter{w->
  w.println "CYTOSCAPE SCRIPT LOG"

  try{
    props = CytoscapeInit.getProperties()
    props.setProperty("layout.default", "force-directed")

    new File("sampleData").eachFileMatch(~/.*\.sif/){f->
      w.println "Loading $f"
      Cytoscape.createNetworkFromFile(f.canonicalPath)
      Cytoscape.getCurrentNetworkView().redrawGraph(false,true)
    }
  }catch(Exception e){
    w.println e
  }
}

Labels: bioinformatics, Cytoscape, groovy