[BioRuby] Google Summer of Code BioRuby project: Looking for co-mentors

Christian M Zmasek czmasek at burnham.org
Wed Apr 1 18:20:23 UTC 2009

Hi Raoul:

Thank you for your reply.
While your project sounds interesting and much needed, the project I was 
referring to is to implement phyloXML (www.phyloxml.org) support in BioRuby.
Given that the deadline for Google Summer of Code projects is April 3rd, 
I think it would be almost impossible to propose a new project and find 
a student for it before this deadline.



Raoul JP Bonnal wrote:
> Dear Christian,
> one of the outcomes from Biohackathon 09, for me, was to implement Phylo 
> into BioSQL, could be of interest for this proposal ?
> Let me know.
> Christian M Zmasek ha scritto:
>> Hi:
>> As you probably read on previous messages, NESCent is again having a 
>> Google Summer of Code program 
>> (http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009).
>> I am serving as the mentor of a project entitled "phyloXML support in 
>> BioRuby" (see: 
>> https://www.nescent.org/wg/phyloinformatics/index.php?title=Phyloinformatics_Summer_of_Code_2009#phyloXML_support_in_BioRuby). 
>> In order to ensure a successful outcome (should the project be 
>> accepted), as well as to improve the chances of being accepted, I am 
>> looking for people willing to serve as co-mentors.
>> Christian
>> PS: Here is the full description of the project:
>>      phyloXML support in BioRuby
>> Rationale    Evolutionary trees are central to comparative genomics 
>> studies.
>>    Trees used in this context are usually annotated with a variety of
>>    data elements, such as taxonomic information, genome-related data
>>    (gene names, functional annotations) and gene duplication events, as
>>    well as information related to the evolutionary tree itself (branch
>>    lengths, support values). phyloXML is an XML data exchange standard
>>    that can represent this data. Trees in phyloXML format can be
>>    displayed and analyzed with Archaeopteryx
>>    <http://www.phylosoft.org/archaeopteryx/> (the successor to ATV
>> <http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/4/383>), 
>>    which also allows manipulation and navigation of the tree. While
>>    tools exist to convert other formats (such as the widely used Newick
>>    and Nexus formats) to phyloXML, there is currently support for
>>    phyloXML in only one of the open source Bio* projects (in BioPerl
>>    <http://www.bioperl.org/wiki/Phyloxml_Project_Demo>, as a result of
>>    Google's Summer of Code 2008). Approach    Build phyloXML support 
>> in the increasingly popular, dynamic, and
>>    fully objected oriented language Ruby. More specifically, extend the
>>    open source BioRuby project to support phyloXML (BioRuby 1.3.0 has
>>    just been released). This will entail (i) the development of objects
>>    to represent all the elements of phyloXML (sequences, taxonomic
>>    data, annotations, etc), (ii) the development of a parser to read in
>>    phyloXML, and (iii) a phyloXML writer. Challenges    Relating the 
>> data elements specific to phyloXML to the tree classes
>>    already in BioRuby while maintaining the standards of the BioRuby
>>    project. Development of a time and memory efficient phyloXML parser
>>    (the parser has to be able to process trees with thousands of
>>    external nodes, at least). Involved toolkits or projects    BioRuby 
>> <http://www.bioruby.org/>, phyloXML <http://www.phyloxml.org> Degree 
>> of difficulty and needed skills    Medium. Requires experience in an 
>> object oriented programming
>>    language (such as C++, Java, or, ideally, Ruby). Experience in
>>    genomics or a related biological field is also critical. Knowledge
>>    of BioRuby will obviously help, as well as familiarity with XML. 
>> Mentors    Christian Zmasek
>> _______________________________________________
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>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby

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