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

Davide Rambaldi davide.rambaldi at ifom-ieo-campus.it
Tue Apr 7 09:09:46 UTC 2009

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?


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.
Bioinformatic Group IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy

[t] +39 02574303 066
[e] davide.rambaldi at ifom-ieo-campus.it
[i] http://ciccarelli.group.ifom-ieo-campus.it/fcwiki/DavideRambaldi  
[i] http://www.semm.it             (PhD school)
[i] http://www.btbs.unimib.it/     (Master)


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