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~\\Biopython Project Update}
\author{\underline{Eric Talevich}\footnote{Institute of Bioinformatics, University of Georgia, Athens, GA, USA},
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},
Jo\~ao Rodrigues\footnote{Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands},
\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,
With Biopython 1.58 (August 2011), we included support for ABI chromatogram
files, and also gained interoperability with PAML by merging an independent
project, Brandon Invergo's pypaml.
Biopython 1.59 (February 2012) added support for TogoWS, an integrated web
resource for bioinformatics databases and services, and new features in
GenomeDiagram \citep{GenomeDiagram}.
Biopython 1.60 is expected to have been released by BOSC 2012
[{\it NB: to be revised during abstract review}]. % XXX
All releases have seen more unit tests, more documentation, and more new
contributors. Additionally, we have submitted a paper describing the recent
\texttt{Bio.Phylo} module for phylogenetics.

In Summer 2011 we had three Google Summer of Code (GSoC) students, all building
features for protein structure analysis:
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\~ao Rodrigues and Eric Talevich are working to
refactor and merge the results of these projects under a unified API covering
the PDB, mmCIF and PBDML formats for 3D molecular structures.

Two additional students are expected to work with us for GSoC 2012
to implement a Biopython equivalent to BioPerl's SearchIO (covering BLAST, HMMER,
FASTA etc.~search results), and representation and manipulation of genomic
variants (HGVS, GFF, VCF files)
[{\it NB: to be revised during abstract review}]. % XXX

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[Talevich {\it et al}., 2012]{BioPhylo}Talevich, E., Invergo, B.M., Cock, P.J.A., and Chapman, B.A. (2012) Bio.Phylo: A unified phylogenetics toolkit for Biopython.  {\it BMC Bioinformatics} (submitted)

\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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