[Tdwg-phylo] Publishing a trees in RDF

Arlin Stoltzfus arlin at umd.edu
Fri Oct 22 16:29:31 CEST 2010

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.


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
> _______________________________________________
> tdwg-phylo mailing list
> tdwg-phylo at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo

Arlin Stoltzfus (arlin at 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

More information about the tdwg-phylo mailing list