There are other issues here as well. Technology advances rapidly, and what once seemed a good choice may rapidly become dated. Without wishing to start a flame war, I think Java applets are dead (sorry Phylowidget), Flash is fading away (thank you Steve), and increasingly we will see lightweight SVG and Canvas-based browsers, non-web based browsers that exploit specific hardware (iPad anyone), and Google- Earth based browsers.
I doubt one-size-fits all will work. Standards themselves won't address this issue, and I personally doubt RDF is where we want to be focussing efforts anyway. A decent JSON format for trees and associated metadata would be much more palatable for developers. It's worth remembering that the great success of Newick (and Nexus) was largely due to the ease of parsing.
Regards
Rod
On 22 Oct 2010, at 15:29, Arlin Stoltzfus wrote:
QED. The technology is out there. IMHO, the continual propagation of new tree-viewers by developers, and the sense of users that there is no tree viewer that satisfies their needs, is (in the medium-term and long-term) a cultural-organizational-educational problem and not at all a technical problem.
If this is true, then in order to solve the real problem, we need to think about things like changes in funding structure, standards development, and modes of user engagement, not new graphics libraries that do just the right thing with only a few commands.
Arlin
On Oct 21, 2010, at 12:57 PM, Christian M Zmasek wrote:
Hi, Dave and Rutger:
My own tree viewer "Archaeopteryx" provides such an overview when zoomed in, plus some other features described as "missing" in most current tools.
See: http://www.phylosoft.org/archaeopteryx/
Example: http://www.phylosoft.org/archaeopteryx/examples/ mollusca.html
Archaeopteryx also provides other useful features (at least for comparative genomics use cases). For example, the ability to infer internal taxonomies (if all external nodes have _some_ taxonomic information associated with them; standalone version only; via uniprot taxonomy database).
Please let me know if you'd like to know more or have suggestions for improvement (although keep in mind that this Archaeopteryx is just a peculiar hobby of mine).
Christian
On 10/21/2010 3:39 AM, Rutger Vos wrote:
Hi Dave,
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.
Rod Page has coded a web widget (I believe all javascript) that has a small preview window for the whole tree and a larger "zoomed in" view. "TreeJuxtaposer" is a java app(let?) that allows you to contract and expand selections of nodes/clades. I think these come closest to what you are talking about, though neither operates on networks.
Cheers,
Rutger
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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
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--------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK
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