[tdwg-phylo] Upcoming TDWG meeting

Arlin Stoltzfus arlin at umd.edu
Fri Aug 27 17:27:07 CEST 2010

I'm sending this reply to only the tdwg-phylo list (sending to  
everyone seems like overkill).

Here are two ideas based on the use of phylogenies:

1.   For various reasons, its important to be able to associate valid  
species sources or other universal identifiers (e.g., NCBI gis) with  
the human-readable OTU identifiers used in tree files, but this  
typically isn't done and it's not always easy.  The goal of this  
project is to enable ordinary phylogenetics & systematics users to use  
current standards (Newick, NHX, phyloxml, ...) to associate species  
names (possibly other tax ids) with phylogenies in their usual  
workflows.  The focus is on developing short-term tools and strategies  
that might lead to better long-term solutions.  In some cases, its  
just a matter of knowing how to use the file format properly, possibly  
aided by better tools for data input.  For users whose workflows rely  
on Newick, we would need a way to keep a separate mapping of OTU ids  
and tax ids, along with tools to interconvert or translate to one of  
the other formats (this could be as simple as an Excel spreadsheet or  
as complex as a web service that maintains your mapping and does the  
translation for you).

2.  There is a huge variety of tree viewers.  To some extent, users  
need this variety due to their having different feature sets.  But  
users shouldn't have to choose the viewer based on data format  
restrictions.  The goal of this project is to improve the usability of  
tree viewers.   Assess the interoperability (standards compatibility)  
of tree viewing software, develop strategies to improve it, and get  
started on any strategies that can be implemented.  Its not possible  
to modify viewers whose source code is unavailable, but there may be  
ways to work around this with scripts and translation tools.


On Aug 26, 2010, at 9:40 PM, Nico Cellinese wrote:

> Hi all,
> we have reserved one full day for a Phylogenetics Standards hands-on  
> activity at the upcoming TDWG conference. We asked for power strips  
> and wireless network and tables that we can sit around and work  
> together. The only thing that's missing right now is what exactly we  
> should target. The options are wide open right now, with the two  
> only major constraints being that (a) we have no funding this year  
> to bring people in who wouldn't otherwise be there, and (b) abstract  
> submission deadline is next Wednesday.
> Any feedback or ideas, wild or not, that you have would be welcome -  
> send those our way.
> And BTW currently this workshops seems to be placed on the Wednesday  
> of the conference week, so those of you blitzing the local biosphere  
> will unfortunately have a conflict.
> Cheers,
> Nico & Hilmar
> <><><><><><><><><><><><><><><><><><><><>
> Nico Cellinese, Ph.D.
> Assistant Curator, Herbarium & Informatics
> Adjunct Assistant Professor, Department of Biology
> Florida Museum of Natural History
> University of Florida
> 354 Dickinson Hall, PO Box 117800
> Gainesville, FL 32611-7800, U.S.A.
> Tel. 352-273-1979
> Fax 352-846-1861
> http://www.flmnh.ufl.edu
> <ATT00001.txt>

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

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