[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.


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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