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

[Peter Cock]

2011/4/18 Peter Cock <p.j.a.cock at googlemail.com>:
> 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
>

I've uploaded an initial abstract (which I can still change until the
deadline later tonight), if there are suggestions for improvements:

In this talk we present the current status of the Biopython project
(www.biopython.org), described in a application (Cock et al., 2009).

Since BOSC 2010, we have made three releases. Touching on key
functionality, Biopython 1.55 (August 2010) made our command line
tool wrappers easier to use, Biopython 1.56 (November 2010) added
a UniProt XML parser, and Biopython 1.57 (April 2011) added an
SQLite based indexer for sequence flat files. All releases have seen
more unit tests, more documentation, and more new contributors.

In summer 2010 we had one Google Summer of Code (GSoC) project
student, Joao Rodrigues working on protein structure (PDB) code for
Biopython. Some of Joao’s work has already been included in Biopython
releases, and he and his mentor Eric Talevich (himself a GSoC 2009
student) are working to merge the rest of this work. Additionally they
hope to co-mentor a GSoC student this summer.

For the last six months, we have been running a BuildBot server
(see http://buildbot.net/), with the offline parts of the Biopython unit
test suite scheduled every night on build slaves running on Linux,
Windows and Mac OS X, and both “C” Python and Jython (using the
Java virtual machine). This has been beneficial in catching platform
specific regressions, for example under Python 3 which we are still
working towards fully supporting. The BuildBot server is running on
an OBF maintained Amazon cloud server, while the slaves are initially
all machines maintained by individual Biopython developers.

Biopython is free open source software available from www.biopython.org
under the Biopython License Agreement (an MIT style license,
http://www.biopython.org/DIST/LICENSE).

Peter