David--
This raises two issues that I don't quite understand.
The problem of visualizing large trees, e.g., hundreds of thousands or millions of nodes, has been solved again and again by computer scientists. We've all seen some visualizations of the internet done with such tools. There is no fundamental technology barrier. The technology exists to visualize large trees and zoom around and navigate and so on.
The problem has to do with how to develop stable and adaptable software for a community that is poor, dispersed, fractious (unable to agree on standards), and constantly changing in its needs.
Likewise, computer scientists and hackers have repeatedly solved the problem of designing a framework for automating bioinformatics workflows. So why don't more bioinformaticians use automated workflows?
Probably the group that is getting closest to what you want is the TreeViz group of EoL at the Field Museum. Karen Cranston (cc) has some cool slides on this.
The second issue that I don't understand is: what is the proper netiquette when a list message is cc'ed to half a dozen people? If we all keep repeating the cc pattern, recipients may be getting lots of messages that they don't want. If we stick to the list only, they could miss out.
Arlin
On Oct 21, 2010, at 5:20 AM, Kidd, David M wrote:
I am yet to consider the visualizing RDF trees, however, I have am interest in visualizing and interacting with trees and networks in a web context.
I've been looking at the various web tree visualizers, as well as more generic visualization libraries, for the last week or so. Understanding the functionality, maturity, user community and inter- browser compatability is time consuming, and not always simple to determine.
Specifically, I am looking for a tool that supports, or can extended to support;
- Both both trees and networks,
- The selection of multiple nodes, e.g. subtrees
- The browsing of large trees/networks - I get some weird effects
with large trees in jsPhyloSVG. 4. (Readable) Labels at all nodes. 5. Alternate layouts (circular, hyperbolic, etc.) 6. Works in as many browsers as possible. 7. A variety of I/O formats - I store my trees in PhyloDB, which I am thinking of generalizing for networks.
The ability to browse large trees seems to be a particular limitation of existing tools (I'd love to be corrected if I am wrong). Having a tree larger than the widget, as in Phylowidget, is one approach, however, an overview window would be nice to orientate your view in relation to the entire tree. I have also been considering displaying only a subset of nodes and then having 'expand', 'contract' and 'pan' (by expanding and contracting) functions for navagation. The ability to display node subsets is probably more important for networks than trees as reticulation will often result in visual occlusion.
I would be very interested in any comments regarding existing tools and the above issues (an others I have not thought about). I would be happy to compile all comments and perhaps some comparative demos somewhere.
- Dave
David M. Kidd
Research Associate Center for Population Biology Silwood Park Campus Imperial College London 0207 594 2470
-----Original Message----- From: tdwg-phylo-bounces@lists.tdwg.org [mailto:tdwg-phylo-bounces@lists.tdwg.org ] On Behalf Of Richard Ree Sent: 20 October 2010 21:47 To: Hilmar Lapp Cc: tdwg-phylo@lists.tdwg.org Interest Group; Chris Baron Subject: Re: [Tdwg-phylo] Publishing a tree in RDF
The purposes of tree visualization are many and varied, so it seems natural to me that tool development reflects that diversity. One distinction of tred is that it exposes server-side and client-side functionality.
-Rick
On Wed, Oct 20, 2010 at 3:17 PM, Hilmar Lapp hlapp@nescent.org wrote:
On Oct 20, 2010, at 2:43 PM, Chris Baron wrote:
Also, I've been working on a phylogentic tree editor called tred. http://code.google.com/p/tred/
Interesting. How does your editor compare to the dozens of tree editors and visualizers already available. For example PhyloWidget, or jsPhyloSVG? I may sound like a broken record here, and I don't want to discourage you at all from developing tools for phylogenetics. We certainly need more developers. I also do think though that as a community we make the most progress if we aren't sprouting new tools for the same purpose all the time.
-hilmar
=========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : ===========================================================
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------- Arlin Stoltzfus (arlin@umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org