[BioC] RCytoscape performance

[Paul Shannon]

Hi Chad,

This should be vastly improved after changes I checked into the release branch yesterday.  My code for sending edges to Cytoscape was extraordinarily inefficient.

I can send you RCytoscape 1.0.1 offline if that would be any help.

- Paul


> Does anyone have any experience with the RCytoscape package and highly
> connected graphs?? I've got a graph being built dynamically with R and
> then pushed over to Cytoscape via the RCytoscape plugin.? However, the
> communication between R and Cytoscape is taking an incredibly long
> time--3-4 days for a graph with 362 nodes and 65703 edges, to be
> precise.? I'm still working on figuring out exactly which of the
> commands is taking so long (or if it's a combination of all of them,
> as I'm coming to suspect), but I've reproduced the code I'm using to
> interact with RCytoscape below.  It's basically just the tutorial
> code, though (from
> http://db.systemsbiology.net:8080/cytoscape/RCytoscape/vignette/RCytoscape.html).
> 
> Some context:  I'm running R 2.11.1, Cytoscape 2.7.0, and CytoscapeRPC
> 1.2 on a Linux box with a manual install of the RCytoscape and XMLRPC
> packages as described at
> http://db.systemsbiology.net:8080/cytoscape/RCytoscape/installation/index.html.
> I can get more information if you need it.
> 
> Thanks in advance for any help.
> 
> ------------------------------------------
> Chad Burrus
> MS Bioinformatics, Candidate
> School of Informatics and Computing
> Indiana University, Bloomington
> Phone: (812) 783-9127
> 
> 
> *