[BioC] CRytoscape: an early release

[Paul Shannon]

Building upon some exemplary work by Jan Bot (the CytoscapeRPC plugin) and Duncan Lang (XMLRPC package) we now have a good start on controlling Cytoscape 2.7 from R.

Much remains to be done.  Once this version gets some mileage on it, I will convert its current procedural style into proper S4 classes, and submit the package to Bioconductor.  

The biggest deficit in the package that I am aware of occurs in sending large graphs from R to Cytoscape take longer than it should.  Some tuning of XMLRPC may be needed to fix this.

All the code (the Cytoscape plugin, the XMLRPC package (with some of my own modifications) and the new CRytoscape package) can be found here:

  http://db.systemsbiology.net:8080/cytoscape/gaggle/test/cy2rpc/public/index.html

Lots of documentation is provided, as well as a test script which demonstrates how to use the package.

Suggestions, complaints, rants and bug reports are all welcome.

 - Paul