[Biopython-dev] Biopython project update at BOSC 2011?

[Peter Cock]

2011/4/17 Brad Chapman <chapmanb at 50mail.com>:
> Peter and Tiago;
>
>> > I realise the BOSC abstract deadline is now tomorrow (!)
>> > http://www.open-bio.org/wiki/BOSC_2011
>> >
>> > I think it may be just me and Brad going - and we could
>> > certainly put together something... Who else is planning
>> > to attend BOSC 2011 in Vienna, and would you like to
>> > be involved?
>
> It would be great if you wanted to do a Biopython talk. BOSC was
> trying to deviate a bit from the project update format, but anything
> you are working on with respect to Biopython or new features added
> would be perfect.

One idea would be to go over the Bio.SeqIO.index_db(...) code
and how this SQLite3 backend could be the basis of a new Bio*
OBF version of OBDA (to supplement the existing flat file and
BDB specifications).

> Personally, I'd be interested in hearing about the
> NGS work you are doing with Biopython and Galaxy. Democratizing
> analysis methods to allow biologists access is always a challenge,
> and I'd love to hear about how you've been approaching this.

I'll be talking after BOSC during ISMB proper about some of
my Galaxy work, but it isn't NGS focused - see Workshop 6
"Genomics for Non-Model Organisms" being organised by James
Taylor and Anton Nekrutenko from Galaxy:
http://www.iscb.org/ismbeccb2011-program/workshops#w6

In terms of Galaxy and NGS, I've finding my sequence file filtering
tool very handy (FASTA, FASTQ and SFF) for a number of workflows
including removing read contamination, mapped reads etc. This is
on the Galaxy toolshed and uses Biopython (for SFF filtering):
http://community.g2.bx.psu.edu/

>> I might go the codefest. It all depends if my PhD is done or not and
>> if I have to go nearby (I might visit south .CH, and thus it would be
>> just a small deviation).
>
> Tiago, good luck finishing up the degree. Hope you are done by the
> summer can make it out to Codefest,

+1

Peter