[GSoC] Bionode project at GSOC 2014

[Raoul Bonnal]

Dear Christoph,
it is very simple, just start,  and maybe create a google document, you could later share that document ONLY with mentors.
I would suggest to not write yet another set of parsers in javascript, as Eric suggested there are very good parsers as external tools

http://samtools.sourceforge.net/tabix.shtml
http://bedtools.readthedocs.org/en/latest/

and 
http://rubygems.org/gems/bio-maf
http://rubygems.org/gems/bio-gff3
https://github.com/mamarjan/gff3-pltools
https://github.com/lomereiter/sambamba

and I am sure java, python and perl have other outperforming parsers.  
I think a great value would come from a clean and nice API.

Consider also the possibility to use JS functions inside NoSQL db like couch there you can write js functions the map/reduce paradigm. Actually I do not know if it possible to call bio javascript functionalities inside the definition of a reduce or map function but I think that would be useful.


Raoul

On Mar 15, 2014, at 5:17 PM, Christoph Neuroth <christoph.neuroth at gmail.com> wrote:

> Thanks for the input everyone! I agree with the high-level goals
> (KISS, functional > OOP, idiomatic node, small modules, etc) and I got
> some more ideas but I'm struggling to create a project plan that is as
> detailed as required - as the project is new, there are just too many
> possibilites and because I'm new to the domain, it's hard to identify
> the most important things.
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