Google Summer of Code 2011

Summer 2011 Projects

Here are links to the progress report pages for OBF's 2011 Google Summer of Code students:

BioPython

Justinas Vygintas Daugmaudis, Michele dos Santos da Silva (2 students), mentored by Thomas Hamelryck and Eric Talevich

Mocapy++Biopython: from data to probabilistic models of biomolecules

BioPython Integration

Mocapy++ Plugin System

BioJava

Chuan Hock Koh, mentored by Peter Troshin, Andreas Prlic, and Jay Vyas

Amino Acid Physico-Chemical Properties Calculation

BioRuby

Michał Koziarski, mentored by Raoul J.P. Bonnal and Francesco Strozzi

Represent bio-objects and related information with images

BioPerl

Sheena Scroggins, mentored by Robert Buels and Chris Fields

Major BioPerl reorganization

BioPython

Mikael Eric Trellet, mentored by João Rodrigues and Eric Talevich

Interface analysis module for BioPython

Mentors and Project Ideas

Mentors 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

• Major BioPerl reorganization
• 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

• Mocapy++Biopython: from data to probabilistic models of biomolecules
• Variant representation, parser, generator, and coordinate converter

BioJava

• Amino acids physico-chemical properties calculation
• Extend Sequence Viewer code to become a client for the Distributed Annotation System

BioRuby

• Support Next Generation Sequencing (NGS) in BioRuby
• BioRuby Wrapper for Command line application
• Represent bio-objects and related information with images
• Modular annotation knowledge base for BioRuby

BioLib

• Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI (2011)
• Mapping EMBOSS to Perl, Ruby or Python using BioLib+SWIG+EMBOSS (2011)

BioDAS

• Redesign of the DAS Registry
• DAS Server for large files on local filesystems

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.