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

Christian M Zmasek czmasek at burnham.org
Wed Apr 8 23:14:35 UTC 2009

Hi, Davide:

Yes, help in testing code is always very welcome!

Hopefully the project will get accepted!


Davide Rambaldi wrote:
> Hi, I am available to help is there is need.
> I have a small experience with bioruby but I am really interested in  
> partecipate in a project with bioruby.
> May be I can help in testing the code?
> Davide
> Il giorno 01/apr/09, alle ore 03:16, 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
> Davide Rambaldi,
> Bioinformatics PhD student.
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