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
Is anyone else interested? If there is interest, I'll start a
planning document (TDWG phylo twiki?).
Arlin
On Aug 27, 2010, at 2:45 PM, Dan Rosauer wrote:
> Hi Arlin and others
>
> I think that idea 1 below is a really valuable topic to address.
> The ability to link tree tips to other sources of data by taxon name
> or identifier is a threshold step for automating a whole range of
> analyses and displays. For example, the software I work on,
> Biodiverse, links phylogenies to species location data for
> visualisation and analysis. It would be great to have it running
> automatically online, linking (for example) trees from treebase to
> distributions from GBIF. To do this (and many other things) however
> we need a better solution to the taxon matching problem you describe.
>
> cheers
> Dan
>
> From: tdwg-phylo-bounces(a)lists.tdwg.org [mailto:tdwg-phylo-bounces@lists.tdwg.org
> ] On Behalf Of Arlin Stoltzfus
> Sent: Friday, August 27, 2010 11:27 AM
> To: tdwg-phylo(a)lists.tdwg.org
> Subject: Re: [tdwg-phylo] Upcoming TDWG meeting
>
> 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.
>
> Arlin
>
> 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(a)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
>
> <ATT00001.txt>
-------
Arlin Stoltzfus (arlin(a)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
