That sounds great.  I've poked around with the source a bit, so I noticed a
couple of those efficiencies, but I wasn't having much luck making the
changes myself.  You can send the updated version to chburrus@indiana.edu or
just give me a link to download.  Thanks for the help.

------------------------------------------
Chad Burrus
MS Bioinformatics, Candidate
School of Informatics and Computing
Indiana University, Bloomington
Phone: (812) 783-9127


On Fri, Nov 12, 2010 at 10:24 AM, Paul Shannon
<pshannon@systemsbiology.org>wrote:

> 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
> >
> >
> > *
>

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