[BiO BB] need help w/ VRML viewer for big graphs - Mozilla plug-in?

[Harry Mangalam]

Depending on how much programming you're willing to do, it sounds like 
some of the CAIDA tools may be of interest, particularly their java3d 
walrus visualizer (based on Tamara Munzner's work)
http://www.caida.org/tools/visualization/walrus/

Right now it doesn't support much support for identification of the 
nodes themselves but it provides a good framework for writing in your 
own node-handling functions.  We're evaluating it for doing some 
large network (IP as well as semantic) visualizations.

hjm



On Friday 11 May 2007 22:34, Ann Loraine wrote:
> A hyperbolic viewer might be just the thing. We do want to "drill
> down" into specific components of the graph.  So that could be what
> we need...
>
> Let me know if you would recommend a particular one (or two) to try
> out first. Maybe some-one on the list would know, as well?
>
> One nice side benefit of LGL is that in the process of building
> layouts for the graph, it seems to separate them into separate
> components, which is useful.
>
> Thanks for the suggestions!
>
> -Ann
>
> On 5/11/07, Joe Landman <landman at scalableinformatics.com> wrote:
> > Hi Ann
> >
> > Ann Loraine wrote:
> > > I'm just getting started with LGL, but it looks like it can
> > > give me a
> >
> > VRML
> >
> > > document that specifies the layout of large graphs (my biggest
> > > is 500K edges, 9k nodes), and I'd like to find a VRML viewer
> > > that might be able
> >
> > to
> >
> > > handle such a large graph. (I've got a machine w/ 3 gig memory,
> > > and
> >
> > access
> >
> > > to a few others with even more memory, but I don't have admin
> > > privs on those, so I'd like to avoid bugging the sysadmins
> > > about installing new software until I'm sure I've got something
> > > that will work...)
> > >
> > > If anyone on the list can recommend a good VRML plug-in (for
> > > Mozilla) or stand-alone viewer that might work for this
> > > application, I would be very grateful!
> >
> > Hmmm... Maybe my info is dated, but I had used inventor viewer
> > (the VRML 1.0 spec was effectively OpenInventor's spec) to view
> > some molecular structures I created out of PDB and other
> > coordinates.  Calls these fairly simple graphs, several thousand
> > nodes, and tens of thousands of edges.  Inventor viewer worked
> > fine for these, though I ran them on an SGI at the time.  I have
> > run ivview recently on the same files on my laptop without
> > problem.  So if they are v1.0 VRML compliant, you might try the
> > OpenInventor viewer as a stand-alone.
> >
> > > Also, if you have any tips on visualizing large graphs, I'd be
> > > grateful
> >
> > for
> >
> > > those as well!
> >
> > Get lots of RAM.  And a fast graphics card (accelerated OpenGL)
> > with lots of RAM :(
> >
> > > So far the only thing I've been able to find that appears
> > > capable of
> >
> > laying
> >
> > > out big graphs is LGL...but maybe there are some others?
> >
> > There are some hyperbolic space viewers for large connected
> > graphs, though these are more for drilling in to specific nodes,
> > than seeing the large scale structure of the system.
> >
> > > Thank you in advance for your help!!!
> > >
> > > -Ann
> >
> > --
> > Joseph Landman, Ph.D
> > Founder and CEO
> > Scalable Informatics LLC,
> > email: landman at scalableinformatics.com
> > web  : http://www.scalableinformatics.com
> > phone: +1 734 786 8423
> > fax  : +1 734 786 8452 or +1 866 888 3112
> > cell : +1 734 612 4615
> > _______________________________________________
> > General Forum at Bioinformatics.Org -
> > BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board

-- 
Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, 
UC Irvine 92697  949 824 0084(o), 949 285 4487(c) 
harry.mangalam at uci.edu