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

[Naohisa GOTO]

Hi Christian,

I'll answer any questions about BioRuby as much as I can.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Wed, 1 Apr 2009 11:31:12 -0700
Christian M Zmasek <czmasek at burnham.org> wrote:

> 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 
> arise.
> 
> Christian
> 
> 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
> >>