[BioRuby] Google Summer of Code project ideas

[Pjotr Prins]

Thanks Raoul. I added:

Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI

Rationale 

    GFF3/GTF parsers are used by genome browsers and next-gen sequencing
tools. Current parsers are slow and use a lot of memory. A fast low-memory
parser would be beneficial to many bio-medical projects 

Approach 

    Based on existing implementation we can design a fast parser using the D
programming language. D provides capabilities for hand-crafting
high-performance parsers. If required, parallelization of records can be
introduced by using Actors. D can compile libraries which can be bound to Ruby
using a C-style interface. This means the GFF3/GTF parser can be used from
Ruby. The design will focus on iterating records and feeding them back to the
Ruby environment. The library will also be useful for Python, Perl and the
JVM. 

Difficulty and needed skills 

    This is a challenging project. Advanced programming concepts, concurrency,
foreign language bindings. 

The project requires

    An interest in high performance computing. Some affinity with coding in C
and one or more interpreted languages 

Mentors 

    Pjotr Prins (author of bio-gff3), Raoul Bonnal 

Other interested parties 

    Naohisa Goto (author BioRuby's GFF3 parser), Brad Chapman (author
Biopython's GFF3 parser) and Peter Cock (Biopython), Chris Fields (BioPerl). 


On Fri, Feb 17, 2012 at 01:07:11PM +0100, Raoul Bonnal wrote:
> Quick update. I added some new project, MAF parser and BioImage
> * Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI
> * Extend bio-alignment plug-in with Multiple Alignment Format -MAF- parser
> (FFI?) 
> * Testing framework for biogem plugins
> * Restyling BioRuby.org
> * Update bio-images a plugin to represent bio-object with cool images
> 
> I'm thinking about biongs but I need to figure out and "easy" task for a
> student. 
> 
> As usual, please login and make contributes to all of them, do not hesitate
> to propose new projects. There is something you miss in BioRuby ? Propose a
> a project for a new Biogem (BioRuby plugin)!
> 
> http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Proposal_2012
> 
> 
> --
> Ra
> 
> 
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