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

S M ixpata at gmail.com
Wed Apr 8 23:23:47 UTC 2009

I'd be interested in helping test too or in any other way I could  
help. I'm not experienced enough to program but maybe I can help on  
other ways.

Sent from my iPhone

On Apr 8, 2009, at 7:14 PM, Christian M Zmasek <czmasek at burnham.org>  

> Hi, Davide:
> Yes, help in testing code is always very welcome!
> Hopefully the project will get accepted!
> Christian
> 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.
>> -----------------------------------------------------
>> 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  (homepage)
>> [i] http://www.semm.it             (PhD school)
>> [i] http://www.btbs.unimib.it/     (Master)
>> -----------------------------------------------------
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