On Wednesday, 29. September 2010 11:36:03 Adam Spargo wrote:
Hi Cedric, I have been trying to use a program called Tulip to visualise my graphs, it claims to work up to millions of nodes, but as yet I still get crashes for relatively small graphs. My main problem has been that all my machines with enough RAM are remote and the x-connection is too slow. I have put some more RAM in my desktop but now the graphics card seems to struggle. Waiting for a new graphics card ... Tulip does support batch mode, so I could run on a big memory machine and output hardcopy, but I haven't had a chance to really learn it interactively yet.
I'll let you know if I have any success.
Thank you, I will give it a try
How big a graph can you look at with cytoscape? I haven't tried that.
If I remember correctly, you can load graphs with > 10k edges (no clue about the number of vertices, sorry) into cytoscape, but when you try to create an actual representation of that data, even with a "decent" 4GB RAM, it crashes. But I think that this is rather related due to the fact that cytoscape (at least my installation) is based on Java and I get an Buffer-overflow. And I could imagine that for the special purposes in your case at the WTSI, you are handling way bigger graphs ;)
Best,
Adam.
Best, Cedric
-- Dr Adam Spargo High Performance Assembly Group email: aws@sanger.ac.uk Wellcome Trust Sanger Institute Tel: +44 (0)1223 834244 x7728 Hinxton, Cambridge CB10 1SA Fax: +44 (0)1223 494919
On Wed, 29 Sep 2010, Cedric Laczny wrote:
Hi,
although this might seem a bit off-topic, I think it is an important topic and might be very well interesting for some of us. The boost graph library provides methods to export graphs e.g. for the use with graphviz. However, this is a rather "one-way" solution. Besides that, it is difficult to handle large graphs with graphviz. Therefore, I was wondering if there have been some recent developments here? I would especially be interested in a solution that allows the direct visualisation of a graph (even previously serialized), possibly integrating ways to filter out some of the data in order to be able to visualize the graph in some way. It is clear to me that visualizing arbitrarily large graphs will be limited by physical limitations mostly (RAM etc.). But I would find it very convenient to at least load the graph, set some filters, so that I don't need to do this seperatly via a C++-program. Actually, I am writing my graph to a format that can be visualized by Cytoscape. Unfortunately, this suffers from large limitations on the size of the graph (number of edges and nodes). I am looking forward to hear your ideas about this and possible suggestions about libraries or programs that might achieve this goal. Thank you.
Best regards,
Cedric _______________________________________________ Boost-users mailing list Boost-users@lists.boost.org http://lists.boost.org/mailman/listinfo.cgi/boost-users