[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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