Hi Paul,

This is cool stuff. I'm wondering why you went with the XML-RPC approach as
opposed to direct embedding via e.g. SJava? I guess it's a pure R solution,
without worrying about technical complications from the R-Java bridge. Do
you envision running Cytoscape and R in two separate processes?

I could see a two-tiered interface, with simple commands depending only on
the RPC interface, while more control could be gained through direct
embedding via the JNI, if the user wanted to deal with the complications.

Michael

On Thu, Jul 15, 2010 at 7:33 PM, Paul Shannon
<pshannon@systemsbiology.org>wrote:

> 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
>
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