Re: [Treebase-devel] NeXML submissions to TreeBASE as GSOC project?

[Rutger V. <rut...@gm...>]

I'm interested in (co-)mentoring that.

On Thu, Mar 3, 2011 at 1:25 PM, Arlin Stoltzfus <ar...@um...> wrote:
> I'd like to suggest-- to anyone who might be interested in serving as a
> mentor-- implementing NeMXL submissions to TreeBASE as a possible GSOC
> project.   The idea would be to reduce the amount of user interaction with
> TreeBASE, supporting direct submission of critical information represented
> in the NeXML file, including the usual matrix and trees, as well as
> * GenBank accessions
> * links from OTUs to taxon concepts
> * methodological links from a matrix to a tree
> * authors and contact information
> This would open the door for the development of third-party annotation tools
> or phylogeny inference tools that generate submission-ready NeXML files that
> meet a minimal standard (like MIAPA if it exists).  A bioinformatics grad
> student in Jim Leebens-Mack's lab is gearing up to develop such a submission
> tool this spring.
> A further project might be to develop and implement a web services protocol
> so that annotation clients can submit to TreeBASE.
> Arlin
>
> Begin forwarded message:
>
> From: Rutger Vos <rut...@gm...>
> Date: March 3, 2011 5:38:55 AM EST
> To: Arlin Stoltzfus <ar...@um...>
> Cc: William Piel <wil...@ya...>, Enrico Pontelli
> <epo...@cs...>, Jim Leebens-Mack <jle...@pl...>,
> "mar...@gm... panahiazar" <mar...@gm...>
> Subject: Re: MIAPA demo & GSOC projects: TreeBASE, NeXML coordination
> It would be great if NeXML submissions to TreeBASE could be a GSoC
> project, but that does mean that whoever (else) wants to mentor that
> should sign themselves up to the PhyloSoC wiki in rather short order:
> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011
>
> On Wed, Mar 2, 2011 at 3:43 PM, Arlin Stoltzfus <ar...@um...> wrote:
>
> Enrico, Bill--
>
> Some of us (Jim, Maryam, Rutger and I) have been having a discussion about a
>
> MIAPA demo project this spring that may lead to GSOC projects and to
>
> long-term funding.
>
> A likely target is a submission tool that would facilitate the annotation of
>
> methods and the creation of an archive-ready record.  I did a
>
> proof-of-concept of this a few years ago
>
> (https://www.nescent.org/wg_evoinfo/Supporting_MIAPA#Proof-of-concept_.28annotation_software.29).
>
>  We would use external vocabularies (many useful sources have been
>
> identified) and represent annotations using meta statements in NeXML.
>
> Maryam (PhD student in bioinformatics, CS background) has some months to
>
> devote to this project while working with Jim.  So, this (or something like
>
> it) is really going to happen over the next few months.
>
> We agreed it would be good to get Enrico and Bill involved to talk about
>
> possible GSOC projects, and how to leverage this into other, larger plans.
>
> For instance, a GSOC project to modify TreeBASE to allow NeXML submissions
>
> would be timely.  More generally, it would be nice to demo a web services
>
> architecture for submission, so that various clients could submit records.
>
>  For several years, Enrico has wanted to apply computational intelligence to
>
> workflow description and execution.
>
> Here is one vision for an overall strategy:
>
>  http://www.evoio.org/wiki/DemonstrationProject#An_overall_strategy
>
> If you are interested, please join us for a teleconference on Friday at
>
> 10:00 am.  Enrico already has expressed interest.  Bill, let me know if you
>
> are interested.  Regards,
>
> 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
>
>
>
>
>
> --
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com
>
> -------
> 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
>
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-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com