[Biopython-dev] Draft abstract for BOSC 2010 Biopython Project Update

[Peter Cock]

Hi all,

I should have circulated this earlier, but here is a draft abstract
for a "Biopython Project Update" talk at BOSC 2010, to be submitted
*today*.
http://www.open-bio.org/wiki/BOSC_2010

I'm hoping to attend BOSC again this year and give the talk, but
haven't sorted out the finances - Brad has offered to present if I
can't go, hence the talk author list. If anyone else wants to help
with slides etc (or as a standby speaker) please let me know.

This is based on the abstract from last year, included in this PDF:
http://www.open-bio.org/w/images/c/c7/BOSC2009_program_20090601.pdf

In the PDF version of the abstract I've made the logo smaller this time ;)

Comments welcome,

Thanks,

Peter

--

Biopython Project Update
Peter Cock, Brad Chapman

In this talk we present the current status of the Biopython project
(www.biopython.org), described in a application note published last
year (Cock et al., 2009). Biopython celebrated its 10th Birthday last
year, and has now been cited or referred to in over 150 scientific
publications (a list is included on our website).

At the end of 2009, following an extended evaluation period, Biopython
successfully migrated from using CVS for source code control to using
git, hosted on github.com. This has helped our existing developers to
work and test new features on publicly viewable branches before being
merged, and has also encouraged new contributors to work on additions
or improvements. Currently about fifty people have their own Biopython
repository on GitHub.

In summer 2009 we had two Google Summer of Code (GSoC) project
students working on phylogenetic code for Biopython in conjunction
with the National Evolutionary Synthesis Center (NESCent). Eric
Talevich’s work on phylogenetic trees including phyloXML support (Han
and Zamesk, 2009) was merged and included with Biopython 1.54, and he
continues to be actively involved with Biopython. We hope to include
Nick Matzke’s module for biogeographical data from the Global
Biodiversity Information Facility (GBIF) later this year. For summer
2010 we have Biopython related GSoC projects submitted via both
NESCent and the Open Bioinformatics Foundation (OBF), and hope to have
students working on Biopython once again.

Since BOSC 2009, Biopython has seen four releases. Biopython 1.51
(August 2009) was an important milestone in dropping support for
Python 2.3 and our legacy parsing infra-structure (Martel/Mindy), but
was most noteworthy for FASTQ support (Cock et al., 2010). Biopython
1.52 (September 2009) introduced indexing of most sequence file
formats for random access, and made interconverting sequence and
alignment files easier. Biopython 1.53 (December 2009) included
wrappers for the new NCBI BLAST+ command line tools, and much improved
support for running under Jython. Our latest release is Biopython 1.54
(April/May 2010), new features include Bio.Phylo for phylogenetic
trees (GSoC project), and support for Standard Flowgram Format (SFF)
files used for 454 Life Sciences (Roche) sequencing.

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).

References

Cock, P.J.A., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke,
A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., de Hoon,
M.J. (2009) Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
doi:10.1093/bioinformatics/btp163

Han, M.V. and Zmasek, C.M. (2009) phyloXML: XML for evolutionary
biology and comparative genomics. BMC Bioinformatics 10:356.
doi:10.1186/1471-2105-10-356

Cock, P.J.A., Fields, C.J., Goto N., Heuer, M.L., and Rice, P.M.
(2010) The Sanger FASTQ file format for sequences with quality scores,
and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38(6)
1767-71. doi:10.1093/nar/gkp1137