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

Raoul JP Bonnal bonnalraoul at ingm.it
Thu Apr 2 08:43:34 UTC 2009

Ok, probably was not so clear, I'm available for co-mentoring if you want.

Christian M Zmasek ha scritto:
> 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.
> Sincerely,
> Christian
> 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
>>> _______________________________________________
>>> BioRuby mailing list
>>> BioRuby at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioruby

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