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Difference between revisions of "Google Summer of Code 2014 Ideas"

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(Copied from the main OBF GSoC page)
 
(Added project contact info, reformatted as subsections)
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==Cross-project ideas==
 
==Cross-project ideas==
  
:* [http://www.open-bio.org/wiki/Cross_Projects#Cross_BioInterchange BioInterchange: Convert and Exchange Biological File Formants using RESTful web service]
+
=== [http://www.open-bio.org/wiki/Cross_Projects#Cross_BioInterchange BioInterchange: Convert and Exchange Biological File Formants using RESTful web service] ===
:* [http://sbml.org/GSoC2014 Native and JVM-based support for the Systems Biology Markup Language (SMBL)]
+
 
 +
=== [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]==
 
==[http://bioperl.org/wiki/Google_Summer_of_Code BioPerl]==
  
:* [http://bioperl.org/wiki/Google_Summer_of_Code#NGS-friendly_BioPerl_code NGS-friendly BioPerl code]
+
[[Image:BioPerl_logo_tiny.jpg|right|link=bp:Google Summer of 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)]
+
* '''[[bp:Google Summer of Code | BioPerl GSoC Page]]''' - project ideas and mentors
:* [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]
+
* [[bp:Main Page|Project website]]
:* [http://bioperl.org/wiki/Google_Summer_of_Code#Lightweight.2FLazy_BioPerl_Classes Lightweight BioPerl modules]
+
* [[bp:Becoming_a_developer|Information for new developers]]
:* [http://bioperl.org/wiki/Google_Summer_of_Code#BioPerl_2.0_.28and_beyond.29 Modern BioPerl: BioPerl 2.0 and beyond]
+
* 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]
:* [http://bioperl.org/wiki/Google_Summer_of_Code#Bio::Assembly Bio::Assembly]
+
* [[bp:Project_priority_list|Priority list]] of things that need work, as another source for student-conceived project ideas
:* [http://bioperl.org/wiki/Google_Summer_of_Code#Semantic_Web_Support Semantic Web Support]
+
* [[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]==
 
==[http://biojava.org/wiki/Google_Summer_of_Code BioJava]==
:* [http://biojava.org/wiki/Google_Summer_of_Code#Port_the_BioJava_1_or_2_functionality_to_BioJava_3 Port the BioJava 1 or 2 functionality to BioJava 3]
+
 
:* [http://biojava.org/wiki/Google_Summer_of_Code#Improve_structural_alignment_datastructures_to_support_topology-independent_alignments Improve structural alignment datastructures to support topology-independent alignments]
+
[[Image:Biojava_logo_tiny.jpg|right|link=http://biojava.org/wiki/Google_Summer_of_Code]]
:* [http://biojava.org/wiki/Google_Summer_of_Code#Topology_Diagrams_of_Protein_Structures Topology Diagrams of Protein Structures]
+
 
:* [http://biojava.org/wiki/Google_Summer_of_Code#Sequence_Variation Sequence Variation]
+
* '''[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
 +
 
 +
=== [http://biojava.org/wiki/Google_Summer_of_Code#Port_the_BioJava_1_or_2_functionality_to_BioJava_3 Port the BioJava 1 or 2 functionality to BioJava 3] ===
 +
=== [http://biojava.org/wiki/Google_Summer_of_Code#Improve_structural_alignment_datastructures_to_support_topology-independent_alignments Improve structural alignment datastructures to support topology-independent alignments] ===
 +
=== [http://biojava.org/wiki/Google_Summer_of_Code#Topology_Diagrams_of_Protein_Structures Topology Diagrams of Protein Structures] ===
 +
=== [http://biojava.org/wiki/Google_Summer_of_Code#Sequence_Variation Sequence Variation] ===
 
-->
 
-->
==[http://biopython.org/wiki/Google_Summer_of_Code Biopython]==
+
 
:* [http://biopython.org/wiki/Google_Summer_of_Code#Indexing_.26_Lazy-loading_Sequence_Parsers Indexing & Lazy-loading Sequence Parsers]
+
==[[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]==
 
==[http://bioruby.open-bio.org/wiki/Google_Summer_of_Code BioRuby]==
:* [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]
+
 
 +
[[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/Google_Summer_of_Code BioHaskell]==
:* [http://biohaskell.org/Google_Summer_of_Code#Optimizing_transalign Optimizing a novel, very sensitive alignment method]
+
 
 +
:* [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] ===
 +
 
 +
<!--
 +
==BioSQL==
 +
 
 +
[[Image:BioSQL_logo.png|160px|right|link=biosql:Main Page]]
 +
; [[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
 +
-->

Revision as of 11:26, 14 February 2014

Interested mentors and students should subscribe to the OBF/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

Native and JVM-based support for the Systems Biology Markup Language (SMBL)

BioPerl

BioPerl logo tiny.jpg

NGS-friendly BioPerl code

Convert BioPerl-DB to use DBIx::Class

Major BioPerl Reorganization (Part II)

Perl Run Wrappers for External Programs in a Flash

Lightweight BioPerl modules

Modern BioPerl: BioPerl 2.0 and beyond

Bio::Assembly

Semantic Web Support

BioPython

Biopython logo tiny.png

Indexing & Lazy-loading Sequence Parsers

BioRuby

BioRuby logo tiny.png

An ultra-fast scalable RESTful API to query large numbers of genomic variations

BioHaskell

Optimizing a novel, very sensitive alignment method