[Tdwg-phylo] Publishing a trees in RDF

[Arlin Stoltzfus]

On Oct 22, 2010, at 10:29 AM, 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.

To clarify this-- I didn't mean to imply that there are no gaps.  In  
the *short-term*, there may be real gaps between what users want (or  
think they want) and what developers are providing and maintaining.   
I'm just saying that, by virtue of repeated failures, we should have  
learned by now that the way to close these gaps is NOT for the Nth  
independent developer to go out and developer the Mth independent tree  
viewer using the latest GUI fashions.

Arlin

> 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 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
>
> _______________________________________________
> 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