Google Summer of Code 2012

GSoC 2012

The Open Bioinformatics Foundation has been accepted as a mentoring organization for Google Summer of Code 2012, with 5 student projects funded!

2012 Student Projects

Wibowo Arindrarto

mentored by Peter Cock

SearchIO Implementation in Biopython

Lenna Peterson

mentored by Brad Chapman

Diff My DNA: Development of a Genomic Variant Toolkit for BioPython

Marjan Povolni

mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal

The world's fastest parallelized GFF3/GTF parser in D, and an interfacing biogem plugin for Ruby

Artem Tarasov

mentored by Pjotr Prins, Francesco Strozzi, Raoul Bonnal

Robust and fast parallel BAM parser in D for binding against dynamic languages

Clayton Wheeler

mentored by Francesco Strozzi and Raoul Bonnal

Multiple Alignment Format parser for BioRuby

2012 Mentor Volunteers and Project Ideas

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:

BioPerl

• Lightweight Sequence objects and Lazy Parsing
• Perl Generic Wrappers for External Programs
• BioPerl 2.0: Modern::Perl, Perl6, and BioPerl
• Bio::Assembly updates
• Semantic web support

BioPython

• SearchIO
• Variant representation, parser, generator, and coordinate converter

BioJava

• Take BioJava into the Cloud
• New File Parsers
• Port an algorithm to BioJava

BioRuby

• Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI
• Testing framework for biogem plugins
• Extend bio-alignment plug-in with Multiple Alignment Format -MAF- parser (FFI?)
• Adding social networking functionality to BioRuby.org
• Update bio-images a plugin to represent bio-object with cool images
• Update to the Ruby Ensembl API

BioLib

• Mapping EMBOSS to Perl, Ruby or Python using BioLib+SWIG+EMBOSS
• Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI (together with the BioRuby project)

Note to students: project ideas on the wikis of member projects are only selected projects, albeit well thought-out ones. You are encouraged to propose your own project, just make sure it is still a contribution to one the OBF member projects (see list below)! If we like your proposal, we will try to find a mentor to help you with the project. Regardless of what you decide to do, make sure you read and follow the guidelines for students below.