View source for Google Summer of Code 2014 Ideas

Interested mentors and students should subscribe to the OBF/GSoC [http://lists.open-bio.org/mailman/listinfo/gsoc mailing list] and announce their interest - that is the way we can track what is happening.

Mentor names and project ideas are hosted on each member project's wiki on a dedicated Google Summer of Code page.  See each of the member projects, linked below, for more details about any project:

==Cross-project ideas==

=== BioInterchange: Convert and Exchange Biological File Formants using RESTful web service ===

;  Rationale
: [http://www.biointerchange.org/index.html BioInterchange] Interchange data using the Resource Description Framework (RDF) and let BioInterchange automagically create RDF triples from your TSV, XML, GFF3, GVF, Newick and other files common in Bioinformatics. BioInterchange helps you transform your data sets into linked data for sharing and data integration via command line, web-service, or API. BioInterchange was conceived and designed during NBDC/DBCLS's [http://2012.biohackathon.org/ BioHackathon 2012]. Architecture and RDF serialization implementations were provided by Joachim Baran, Geraint Duck provided JSON and XML deserialization implementations and contributed to architecture decisions, guidance on ontology use and applications were given by Kevin B. Cohen and Michel Dumontier, where Michel brought forward and extended the Semanticscience Integrated Ontology (SIO). Jin-Dong Kim helped to define ontology relationships for RDFizing DBCLS' PubAnnotation category annotations. The main idea is to have a central service with can be used as a validator and as interchange service for different languages. 

;  Approach
:The project will identify the most common and used file formants for all the currently used language under OBF and will design a RESTful API and will project an implementation for all the supported languages. BioInterchange was developed with Ruby but the scope of the project is to have an agnostic system which let use implement a converter using the best language for that functionality. It expected to have a high traffic for the service so an appropriate refactoring or reimplementation using parallel techniques or languages devoted to parallel programming would be possible.
 
;  Difficulty and needed skills
:The project is mid / high difficulty, aimed at talented students. Previous knowledge of Ruby or other scripting language is preferred and flexibility in learning other languages is requireed.
;  The project requires
:Knowledge of advanced programming languages and meta-programming and some concept in parallelizing and web services design. 

;  Mentors
:  Raoul J.P. Bonnal, Francesco Strozzi, Toshiaki Katayama, Joachim Baran

=== [http://sbml.org/GSoC2014 Native and JVM-based support for the Systems Biology Markup Language (SMBL)] ===


==[http://bioperl.org/wiki/Google_Summer_of_Code BioPerl]==

[[Image:BioPerl_logo_tiny.jpg|right|link=bp:Google Summer of Code]]

* '''[[bp:Google Summer of Code | BioPerl GSoC Page]]''' - project ideas and mentors
* [[bp:Main Page|Project website]]
* [[bp:Becoming_a_developer|Information for new developers]]
* source code browser for [http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live/trunk bioperl-live] (the main BioPerl code base), and [http://code.open-bio.org/svnweb/index.cgi/bioperl/ all BioPerl sub-projects]
* [[bp:Project_priority_list|Priority list]] of things that need work, as another source for student-conceived project ideas 
* [[bp:Mailing_lists|Mailing lists]]
* IRC: <code>#bioperl</code> on [http://freenode.net Freenode]

=== [http://bioperl.org/wiki/Google_Summer_of_Code#NGS-friendly_BioPerl_code NGS-friendly BioPerl code] ===

=== [http://bioperl.org/wiki/Google_Summer_of_Code#Convert_BioPerl-DB_to_DBIx::Class Convert BioPerl-DB to use DBIx::Class] ===

=== [http://bioperl.org/wiki/Google_Summer_of_Code#Major_BioPerl_Reorganization.2C_part_2 Major BioPerl Reorganization (Part II)] ===

=== [http://bioperl.org/wiki/Google_Summer_of_Code#Perl_Run_Wrappers_for_External_Programs_in_a_Flash Perl Run Wrappers for External Programs in a Flash] ===

=== [http://bioperl.org/wiki/Google_Summer_of_Code#Lightweight.2FLazy_BioPerl_Classes Lightweight BioPerl modules] ===

=== [http://bioperl.org/wiki/Google_Summer_of_Code#BioPerl_2.0_.28and_beyond.29 Modern BioPerl: BioPerl 2.0 and beyond] ===

=== [http://bioperl.org/wiki/Google_Summer_of_Code#Bio::Assembly Bio::Assembly] ===

=== [http://bioperl.org/wiki/Google_Summer_of_Code#Semantic_Web_Support Semantic Web Support] ===

==[http://biojava.org/wiki/Google_Summer_of_Code BioJava]==

[[Image:Biojava_logo_tiny.jpg|right|link=http://biojava.org/wiki/Google_Summer_of_Code]]

* '''[http://biojava.org/wiki/Google_Summer_of_Code BioJava GSoC Page]''' - project ideas and mentors
* [http://biojava.org/wiki/BioJava:Modules BioJava modules] as another source for student-conceived project ideas
* source code for [http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk biojava-live] (the main BioJava code base) and [http://code.open-bio.org/svnweb/index.cgi/biojava/ all BioJava sub-projects]
* [http://biojava.org/wiki/BioJava:MailingLists Mailing lists]
* No IRC channel at present

=== JVM support and improvements for the Systems Biology Markup Language ===

==[[biopython:Google Summer of Code |BioPython]]==

[[Image:Biopython_logo_tiny.png|right|link=biopython:Google Summer of Code]]

* '''[[biopython:Google Summer of Code | BioPython GSoC Page]]''' - project ideas and mentors
* [[biopython:Main Page|Project website]]
* [[biopython:Contributing|Information for contributors]]
* [[biopython:Mailing lists|Mailing lists]]
* [[biopython:SourceCode| Source Code]]
* No IRC channel at present

=== [http://biopython.org/wiki/Google_Summer_of_Code#Indexing_.26_Lazy-loading_Sequence_Parsers Indexing & Lazy-loading Sequence Parsers] ===

==[http://bioruby.open-bio.org/wiki/Google_Summer_of_Code BioRuby]==

[[Image:BioRuby_logo_tiny.png|right|link=http://bioruby.org]]

* '''[http://bioruby.open-bio.org/wiki/Google_Summer_of_Code BioRuby GSoC Page]''' - project ideas and mentors
* [http://bioruby.org Project website]
* [http://lists.open-bio.org/mailman/listinfo/bioruby developers mailing list]
* [http://github.com/bioruby/bioruby/tree/master source code]
* IRC: <code>#bioruby</code> on [http://freenode.net Freenode]

=== [http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#An_ultra-fast_scalable_RESTful_API_to_query_large_numbers_of_genomic_variations An ultra-fast scalable RESTful API to query large numbers of genomic variations] ===

==[http://biohaskell.org/Google_Summer_of_Code BioHaskell]==

:* [http://biohaskell.org/ Project website]]
:* [http://hackage.haskell.org/packages/#cat:Bioinformatics Bioinformatics section on HackageDB]

=== [http://biohaskell.org/Google_Summer_of_Code#Optimizing_transalign Optimizing a novel, very sensitive alignment method] ===

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; [[biosql:Main Page|BioSQL]] :
:* [[biosql:Main Page|Project website]]
:* Current [http://biosql.org/wiki/Enhancement_Requests enhancement requests] as another source for student-conceived project ideas
:* [http://biosql.org/mailman/listinfo/biosql-l developers mailing list]
:* [http://code.open-bio.org/svnweb/index.cgi/biosql/browse/biosql-schema/trunk source code]
:* No IRC channel at present
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