[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>
wrote:
> 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)
>>
>> -----------------------------------------------------
>>
>>
>>
>>
>>
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
More information about the BioRuby
mailing list