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The Bayesian Conspiracy

The Bayesian Conspiracy is a multinational, interdisciplinary, and shadowy group of scientists. It is rumored that at the upper levels of the Bayesian Conspiracy exist nine silent figures known only as the Bayes Council.

This blog is produced by James Durbin, a Bayesian Initiate.

A simple Cytoscape Groovy example

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
  }
}

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