[BioRuby] Google Summer of Code BioRuby project: Looking for co-mentors
Pjotr Prins
pjotr.public14 at thebird.nl
Wed Apr 1 08:08:08 UTC 2009
Hi Christian,
I am happy to help.
Pj.
On Tue, Mar 31, 2009 at 06:16:01PM -0700, Christian M Zmasek wrote:
> 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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