[Tdwg-phylo] Publishing a trees in RDF

Nico Cellinese ncellinese at flmnh.ufl.edu
Fri Oct 22 18:42:10 CEST 2010

Inevitable. Good thing inded. But not enough to make significant progress and fill the gaps. I agree with Hilmar.


On Oct 22, 2010, at 12:39 PM, Richard Ree wrote:

> Both technology and users' needs evolve rapidly - so the "gaps" will
> never be closed, at least in the time frame required by grants, etc.
> Also, in phylogenetics a lot of developers are themselves users, so
> quick and dirty solutions to scratch individual itches is inevitable.
> It's a good thing, IMO.
> -Rick
> On Fri, Oct 22, 2010 at 11:22 AM, William Piel <william.piel at yale.edu> wrote:
>> On Oct 22, 2010, at 11:00 AM, Roderic Page wrote:
>>> There are other issues here as well. Technology advances rapidly, and
>>> what once seemed a good choice may rapidly become dated
>> True.. but another aspect is just that in order to explore whether a particular graphical concept or tool will work, or will benefit people, you have to knock out prototypes and implementations. e.g., drag-and-drop branch rearrangement in MacClade was great for small trees but not for big ones, hence phylowidget was looking to implement something that worked for large trees (via concentric menus on nodes) and to experiment with auto-pruing, etc. People have to keep knocking out GUI software efforts to test the waters for new features. And the search is not over, for example:
>> - Do we really have a completely satisfying way of visualizing patterns of gene duplication within a species tree?
>> - If I handed you a tree with 200k nodes, is there a visual / GUI way that would allow you to easily find interesting patterns in it, such as points of incongruence with a conventional taxonomy?
>> -  If I gave you 1,000 trees, is there a visual / GUI way that would allow you to see which branches in each tree probably crossed an ancient land bridge together?
>> So I think we still have lots more GUI / visual / ergonomic challenges that still need to be solved (even if lots of challenges have already been solved). And we should not expect each new idea to be implemented in a pristine killer app that does everything that everyone wants out of a tree visualizer -- that takes too long to build, and the right person for dreaming up a new idea is not necessarily the best person for creating clean, robust, off-the-shelf software.
>> We need to be okay with seeing a rich plethora of quick-and-dirty efforts, each focusing on articulating/investigating sets of novel ideas -- despite some obvious redundancy in some of the more general functions.  And then periodically, someone's got to assemble the best of these ideas into a robust, jack-of-all-trades, off-the-shelf software package.
>> bp
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