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Chris Fields | 3 Jun 2008 17:25
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[ANNOUNCEMENT] BioPerl and the Google Summer of Code

On behalf of the BioPerl core developers, Google, and the National  
Evolutionary Synthesis Center (NESCent), I would like to congratulate  
Mira Han on being accepted as a student for the Google Summer of Code  
(GSoC) and welcome her to the BioPerl community.  Mira's accepted  
project proposal involves developing phyloXML support for BioPerl.   
Following is the proposal abstract:

"PhyloXML is an XML document model for phylogenetic data that  
incorporates various annotation types, including user customized data.  
The format is currently not supported by BioPerl. I propose a SAX  
based data structure and interface for PhyloXML support in BioPerl. I  
will use most of the existing IO structures such as TreeIO and  
TreeEventBuilder and subclass them to extend the functions specific to  
PhyloXML. The objects will be connected to various existing BioPerl  
modules, such as SeqI, TaxonI, AnnotationI by reference in order to  
accommodate different phyloXML elements."

NESCent, under the Phyloinformatics Summer of Code, is participating  
as a mentoring organization in the GSoC for the second year.  This  
year, five projects (including Mira's) are being funded by Google,  
with a sixth project being funded by external sources.  Mira's co- 
mentors for this project are myself, Jason Stajich, Rutger Vos, and  
Christian Zmasek (the primary developer of phyloXML).  However, I  
encourage Mira to ask questions on the BioPerl mail list for feedback  
from the greater BioPerl community.

Further information on phyloXML:

http://www.phyloxml.org/
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miraceti | 3 Jun 2008 17:58
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Re: [ANNOUNCEMENT] BioPerl and the Google Summer of Code

Thanks for the welcome,
I'm very excited to be part of the great community,
Here is the wiki page for the project,
*http://www.bioperl.org/wiki/PhyloXML_support_in_BioPerl
*I'll look forward to interacting with you and getting lots of help!

Mira Han

On Tue, Jun 3, 2008 at 11:25 AM, Chris Fields <cjfields <at> uiuc.edu> wrote:

> On behalf of the BioPerl core developers, Google, and the National
> Evolutionary Synthesis Center (NESCent), I would like to congratulate Mira
> Han on being accepted as a student for the Google Summer of Code (GSoC) and
> welcome her to the BioPerl community.  Mira's accepted project proposal
> involves developing phyloXML support for BioPerl.  Following is the proposal
> abstract:
>
> "PhyloXML is an XML document model for phylogenetic data that incorporates
> various annotation types, including user customized data. The format is
> currently not supported by BioPerl. I propose a SAX based data structure and
> interface for PhyloXML support in BioPerl. I will use most of the existing
> IO structures such as TreeIO and TreeEventBuilder and subclass them to
> extend the functions specific to PhyloXML. The objects will be connected to
> various existing BioPerl modules, such as SeqI, TaxonI, AnnotationI by
> reference in order to accommodate different phyloXML elements."
>
> NESCent, under the Phyloinformatics Summer of Code, is participating as a
> mentoring organization in the GSoC for the second year.  This year, five
> projects (including Mira's) are being funded by Google, with a sixth project
> being funded by external sources.  Mira's co-mentors for this project are
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