[Treebase-devel] application-to-TreeBASE direct submission?

[Arlin S. <ar...@um...>]

Hello all.  Yesterday I had a talk with Sudhir Kumar, author of MEGA,  
which probably is responsible for more published trees than any other  
phylogeny inference package (not necessarily the most trees among the  
phylogeny elite represented in TreeBASE).   I discovered that MEGA has  
a graphical name-reconciling interface for users to align mismatched  
OTU names between tree and alignment files-- this is a common problem  
and a barrier to re-use that I have encountered personally multiple  
times.

He suggested the idea that, to facilitate effective archiving, it  
might be useful to have a way for phylogeny applications to generate a  
submission in TreeBASE, providing metadata such as software version  
and run conditions.

Probably you have heard this suggestion before (I heard it earlier  
this week from Joseph Hughes in regard to BEAST).

I mentioned that TreeBASE has a top-secret interface that Dryad uses  
to submit NEXUS files, and that this could be the basis for a  
submission interface for other applications.  My understanding is that  
this is done via web-services, and that the user gets a link to a  
temporary submission that must be completed interactively.  I hope I  
didn't give the wrong impression.

Anyway, Sudhir was very interested in this.  He said that he has  
programmers with time to work on this kind of thing.   If the MEGA  
team prototyped a direct-submission interface, they could write a  
brief paper about it, and maybe we could get other developers together  
to hash out the metadata terms to support,  based on the recent MIAPA  
exercise at TDWG.   If we could get MEGA and the top 3 TreeBASE  
programs (PAUP, MB, RAXML-- right?), that would cover a very large  
segment of users.

I realize that this approach might not be the best way to promote  
archiving in the long-term.  However, it might be more effective in  
the short term, and we might learn a lot from it.

I'd like to hear any thoughts you have on this.  Would this be a  
useful exercise?  What are the disadvantages?  How could it fit into a  
larger strategy?

Arlin
-------
Arlin Stoltzfus (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org