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~\\Biopython Project Update}
\author{\underline{Eric Talevich}\footnote{XXX},
Peter Cock\footnote{Information and Computational Sciences, James Hutton Institute (formerly SCRI), Invergowrie, Dundee DD2 5DA, UK},
Brad Chapman\footnote{Bioinformatics Core Facility, Harvard School of Public Health, Harvard University, Boston, MA, USA},
\textit{et al.}}
\date{Bioinformatics Open Source Conference (BOSC) 2012, Long Beach, California, USA}

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\noindent
Website: \url{http://biopython.org} \\
Repository: \url{https://github.com/biopython/biopython} \\
License: Biopython License Agreement (MIT style, see \url{http://www.biopython.org/DIST/LICENSE}) \\

In this talk we present the current status of the Biopython project, a
long running distributed collaboration producing a freely available
Python library for biological computation \citep{AppNote}.
Biopython is supported by the Open Bioinformatics Foundation (OBF).

Since BOSC 2011, we have made two releases. Touching on key functionality,
Biopython 1.58 (August 2011) included support for ABI files and PAML,
Biopython 1.59 (February 2011) added TogoWS support \citep{TogoWS} and
new functionality to GenomeDiagram \citep{GenomeDiagram}. Biopython 1.60
is expected to have been released by BOSC 2012 [to be revised prior to BOSC].
All releases have seen more unit tests, more documentation, and more new
contributors. Additionally a paper has been submitted describing
the recent \texttt{Bio.Phylo} module for phylogenetics.

In summer 2011 we had three Google Summer of Code (GSoC) students, all
working on protein structure related projects: Mikael Trellet (biomolecular
interface analysis for \texttt{Bio.PDB}), Michele Silva (Python bridge for
Mocapy++ \citep{Mocapy} and linking it to \texttt{Bio.PDB} to enable statistical analysis
of protein structures), and Justinas Daugmaudis (Python-based extension
system for Mocapy++). Previous GSoC students Jo�o Rodrigues and Eric
Talevich are working to refactor and merge this work with a unified API
for dealing with structures in PDB, mmCIF and PBDML formats.

Two additional students are expected to work on Biopython for GSoC 2012
for a Biopython equilivent to BioPerl's SearchIO (covering BLAST, HMMER,
FASTA etc search results), and representation and manipulation of genomic
variants (HGVS, GFF, VCF files) [to be revised prior to BOSC].

We are now encouraging early adopters to help beta test Biopython under
Python 3 and PyPy. The use of nightly unit tests via the OBF BuildBot
server (\url{http://http://testing.open-bio.org/}) continue to be very
helpful for cross-platform validation (covering Windows, Linux and Mac OS X
for Python 2.5 -- 2.7, Jython 2.5, plus Python 3.1 -- 3.2 and soon PyPy)
as well as catching general regressions.

Mailing list discussions continue to be active, with lots of new work
and new contributors coming forward.

\begin{thebibliography}{}

\bibitem[Cock {\it et al}., 2009]{AppNote}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. {\it Bioinformatics} {\bf 25}(11) 1422-3. \href{http://dx.doi.org/10.1093/bioinformatics/btp163}{doi:10.1093/bioinformatics/btp163}

\bibitem[Katayama {\it et al}., 2010]{TogoWS}Katayama, T., Nakao, M., and Takagi, T. (2010) TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services. {\it Nucleic Acids Research} {\bf 38} W706-11. \href{http://dx.doi.org/10.1093/nar/gkq386}{doi:10.1093/nar/gkq386}

\bibitem[Pritchard {\it et al}., 2010]{GenomeDiagram}Pritchard, L., White, J.A., Birch, P.R., Toth, I. (2010) GenomeDiagram: a python package for the visualization of large-scale genomic data. {\it Bioinformatics} {\bf 2}(5) 616-7. \href{http://dx.doi.org/10.1093/bioinformatics/btk021}{doi:10.1093/bioinformatics/btk021}

\bibitem[Paluszewski and Hamelryck, 2010]{Mocapy}Paluszewski, M., and Hamelryck, T. (2010) Mocapy++--a toolkit for inference and learning in dynamic Bayesian networks. {\it BMC Bioinformatics} {\bf 11} 126. \href{http://dx.doi.org/10.1186/1471-2105-11-126}{doi:10.1186/1471-2105-11-126}


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