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

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(BioInterchange: Convert and Exchange Biological File Formants using RESTful web service: Copied from the other wiki page)
(BioPerl: Revived the BioJava section with a stub for JSBML)
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=== [http://bioperl.org/wiki/Google_Summer_of_Code#Semantic_Web_Support Semantic Web Support] ===
=== [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]==
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* No IRC channel at present
* 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] ===
=== JVM support and improvements for the Systems Biology Markup Language ===
=== [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] ===
==[[biopython:Google Summer of Code |BioPython]]==
==[[biopython:Google Summer of Code |BioPython]]==

Revision as of 11:45, 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

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

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


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


Semantic Web Support


Biojava logo tiny.jpg

JVM support and improvements for the Systems Biology Markup Language


Biopython logo tiny.png

Indexing & Lazy-loading Sequence Parsers


BioRuby logo tiny.png

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


Optimizing a novel, very sensitive alignment method