[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.
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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