[BioC] CRytoscape: an early release

[Paul Shannon]

Hi Michael,

Thanks for your comments.

In an earlier version of a bridge between Cytoscape & R I used an approach much like you suggest:  I used RJava and RMI.  Two problems kept cropping up.  First, linux users (and sometimes others) often reported a lot of fuss installing RJava; perhaps SJava would have been better.  Second, though RMI allowed Cytoscape & R to run loosely coupled, the connection was fragile, and both programs had to be restarted if the connection was lost.

With XML-RPC, we seem to have the best of both worlds:  control of Cytoscape as if it and R were running in-process; robustness when the connection gets lost, or if either program is shut down.  I admit to a bias towards loose coupling.  Tying two complicated programs tightly together scares me a bit.

That said, your suggestion of a two-tiered interface is intriguing.  Could your elaborate on "more control could be gained through direct embedding"?  What kinds of control are you thinking of?  I would be glad to consider this.

Thanks!

 - Paul


On Jul 16, 2010, at 5:02 AM, Michael Lawrence wrote:

> 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 at 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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