[Biopython-dev] BOSC 2009

[Peter]

Hello Biopythoneers,

Those of you following the dev-mailing list or the OBF news feed will
know that talk abstracts for BOSC 2009 are due in today, see
http://www.open-bio.org/wiki/BOSC_2009
I should to be able to attend and present the Biopython Project
Update, and a few other Biopython developers may also be around too,
so some sort of hackathon is in the air.

It is a bit unfortunate the deadline was scheduled on the Easter
break, as I'm sure quite a few of you will be on holiday, but here is
an outline abstract.  If anyone has comments, please let me know (on
the list or directly) in the next couple of hours...

Biopython Project Update (draft abstract for BOSC 2009)

In this talk we present the current status of the Biopython project,
focusing on features developed in the last year, and future plans for
the project.  The Oxford University Press journal Bioinformatics has
recently published an application note describing Biopython:

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I,
Hamelryck T, Kauff F, Wilczynski B, and de Hoon MJ. Biopython: freely
available Python tools for computational molecular biology and
bioinformatics. Bioinformatics 2009 Mar 20.
doi:10.1093/bioinformatics/btp163

Since BOSC 2008, Biopython 1.49 has been released.  This was an
important milestone in bringing support for Python 2.6, and in terms
of our dependence on Numerical Python as we made the transition from
the obsolete Numeric library to NumPy.  Biopython 1.49 also added more
biological methods to our core sequence object.

April 2009 will see the release of Biopython 1.50 (at the time of
writing, a beta has already been released).  Some of the new features
include:
1. GenomeDiagram by Leighton Pritchard has been integrated into
Biopython as the Bio.Graphics.GenomeDiagram module.
2. A new module Bio.Motif has been added, which is intended to replace
the existing Bio.AlignAce and Bio.MEME modules.
3. Bio.SeqIO can now read and write FASTQ and QUAL files used in
second generation sequencing work.

Biopython will celebrate its 10th Birthday later this year, we will
present a brief history of the project and current work.  This
includes the evaluation of git (and github) as a possible distributed
version control system (DVCS) to replace our existing very stable CVS
server hosted by the Open Bioinformatics Foundation, which we hope
will encourage more participation in the project.

--

Thanks,

Peter