Intro: GSOCer Elliott Hauser

[Elliott Hauser]

Hey all.

My name's Elliott and I'm developing MIAPA-related tools for NeXML and ISAtools in a Google Summer of Code project, with Hilmar serving as primary mentor.

My project homepage on NESCent's wiki is here.  On that page you'll find links to the GitHub repository for the project and the gfolder with all the docs I'll make and use during the project.  There's not much on GitHub yet, just a little testing and messing around with the treebase NeXML example file from NeXML.org, but by the end of the summer it will hopefully be a resource for the MIAPA community.

During the remainder of the community bonding period I'm dusting off my XML/XSL/XPath skills and learning the Java I'll need.  I'm also learning about NeXML and MIAPA.

One of the most important parts of my project will be determining what NeXML elements and attributes are MIAPA-relevant, so that I can then extract and transform them.  The extracted MIAPA information is intended as a quick way to researchers to submit MIAPA 'vitals' of their files, and the ISAtab transformation is intended to allow NeXML files to be used in ISAtools workflows.  Input and help from this group at any stage of the above would be much appreciated.  I'll of course ask for more specific feedback in the future but if anyone would like to be more directly involved in a particular section (beyond those of you I've spoken with already), please let me know.  I'd welcome any brain space you'd care to give.

Excited to get going in earnest next week!

Best

Elliott Hauser

UNC Chapel Hill

Information Science PhD Program 2012-2017

[Hilmar Lapp]

On May 9, 2012, at 2:59 PM, Elliott Hauser wrote:

On that page you'll find links to the GitHub repository for the project

I'll just add here that I also created a MIAPA organization on Github (http://github.com/miapa).

If you are developing tools for supporting MIAPA, I'd be happy to fork the repo under there, or to create a repo under the organization for your perusal, just as we did for Elliott's project. Simply let me know or post here.

-hilmar

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: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :

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[Rutger Vos]

Hi Elliott,

please be aware that there is an almost complete dump of all of
TreeBASE's studies, as NeXML, here:
https://github.com/rvosa/supertreebase

Cheers,

Rutger

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Dr. Rutger A. Vos
Bioinformaticist
NCB Naturalis
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[Arlin Stoltzfus]

Hi Elliot.  Sorry for the delayed response.  I certainly look forward to hearing more about the project as it develops.   If you need any help with interpreting specific publications to use as test-cases I am happy to lend a hand with such things.  

Arlin

On May 9, 2012, at 2:59 PM, Elliott Hauser wrote:

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Arlin Stoltzfus (ar...@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

[Elliott Hauser]

Thanks Arlin.  I will definitely take you up on that in the next week or two.

Rutger, thanks again for pointing me to Treebase.  I forked it today and will eventually be creating the nastiest valid NeXML Treebase files I can think of to make sure my XSLT is hardy.  

Finally, per Hilmar's recommendation I'll be posting my weekly updates to this list and nexml-discuss.  Apologies for cross posting for those of you who are on both.

Best, Elliott

[Jim Leebens-Mack]

Hi Elliot,

It is wonderful to have you working on this.  Your proposal and the other documents in your googledocs folder show that you have made a great start on a project that is likely to produce much needed infrastructure for advancing the principles of MIAPA.  As pointed out by Vos et al. and captured in your notes we need to identify or develop ontology concepts that NeXML and ISA can draw upon to describe aspects of analysis (alignment and tree inference) and the trees themselves (tree type, branch length units, branch support).  I look forward to working with you and others on this list to formalize a MIAPA 1.0 checklist for the phylogenetics community to use, evaluate and refine.  

Bests,

Jim

  

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Jim Leebens-Mack 

4505 Miller Plant Scinces
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Phone: 706-583-5573 
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email: jleebe...@plantbio.uga.edu 
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[Rutger Vos]

Hi Elliott,

are you also aware of this spreadsheet with the annotation predicates
that occur in the TreeBASE NeXML? Here is the link:

https://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw

Best wishes,

Rutger

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