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

Christian M Zmasek czmasek at burnham.org
Wed Apr 1 18:31:12 UTC 2009

Hi, Joel:

 From my own experience as a co-mentor last year, the time requirement 
is rather limited.
The project I co-mentored was "phyloXML in BioRuby". Since I am 
knowledgeable about phyloXML I mainly helped out with questions related 
to it.

Of course, for this year's project "phyloXML in BioRuby", it will be the 
opposite. Since I am the main-mentor I will/am handling all the issues 
related to the application process/midterm 
evaluation/final-evaluation/phyloXML. But I would feel more comfortable, 
if I had one or two co-mentors with significant Ruby and BioRuby 
experience who could help out if questions specific to these languages 


PS: The project still needs to be accepted by the Nescent organization. 
Last year, there were about 15 projects, and only five got accepted 
(since Google gave Nescent five slots, Nescent had to decide which 
projects they liked the most).

Joel Dudley wrote:
> I am interested. What's involved in being a co-mentor? I am one of the  
> authors of MEGA (http://www.megasoftware.net) and I have been  
> programming with Ruby daily for about 3 years now.
> -- Joel
> On Mar 31, 2009, at 6:16 PM, 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
>> _______________________________________________
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
> =============Email Policy=============
> I now only check mail at the following times:
> - 8 a.m., Noon, 5 p.m. Mon-Fri
> - 8 a.m. Sat-Sun
> If this is a true emergency, or you require an
> immediate response from me, please contact
> me via my mobile phone: (408) 464-8258
> ====================================

More information about the BioRuby mailing list