\documentclass[10pt,oneside]{article}

%%%%%%%%%%%%%
\setlength{\textheight}{8.75in} %Letter is 11in, less 2 for margins, less 0.25 for footer
\setlength{\oddsidemargin}{0.0in} %gets +1inc
\setlength{\evensidemargin}{0.0in} %gets +1inch
\setlength{\textwidth}{6.50in} %Letter is 8.5, less 2 inches for margins
\setlength{\topmargin}{0.5in}
\setlength{\headheight}{0in}
\setlength{\headsep}{0in}
\setlength{\parindent}{0.25in}
%%%%%%%%%%%% 

\usepackage[numbers]{natbib}
\usepackage{graphicx}
\usepackage[colorlinks=true,citecolor=black,urlcolor=blue]{hyperref}

\title{%Hack to get the logo on the PDF front page:
\vspace{-1.5in}
\includegraphics[width=0.5\textwidth]{biopython.jpg}\\
%Hack to get some white space using a blank line:
~\\Biopython Project Update}
\author{Peter Cock\footnote{Information and Computational Sciences, James Hutton Institute (formerly SCRI), Invergowrie, Dundee DD2 5DA, UK},
\textit{et al.}}
\date{Bioinformatics Open Source Conference (BOSC) 2013, Berlin, Germany}

\begin{document}
%\pagestyle{empty}
%\thispagestyle{empty}
\maketitle
%\pagestyle{empty}
\thispagestyle{empty}

\vspace{-0.2in}
\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 2012, we will have made two releases, and a
manuscript describing the \texttt{Bio.Phylo} module for
phylogenetics has been published \citep{BioPhylo}.
All our releases have had more unit tests, more documentation,
and new contributors. In addition to nightly unit tests run on 
Linux, Windows and Mac OS X via an OBF hosted buildbot,
we now run continuous integration tests via TravisCI. Together
this covers the main operating systems (Linux, Mac OS X and
Windows) and Python implementations (Jython, PyPy and both
versions 2 and 3 of the primary Python implementation in C).

Biopython 1.61 (February 2013) included a number of small
enhancements and additions. This release also introduced the idea
of including some \textit{beta} modules within the standard install
for testing new experimental code, used to ship some of the GSoC
work (see below).

Biopython has for some time run under Python 3, and we have
been asking users to try this for testing purposes for some time.
Biopython 1.62 (expected May 2013) is intended be our first
release to officially support Python 3.
[{\it NB: to be revised during abstract review}]. % XXX

In Summer 2012 we had two Google Summer of Code (GSoC) students.
Wibowo `Bow' Arindrarto wrote a Biopython equivalent to BioPerl's SearchIO
covering sequence search results from BLAST, HMMER, FASTA etc able
to read and write multiple file formats with a common object model, and
index large files for memory efficient random access. Lenna Peterson
worked on the representation and manipulation of genomic variants
(HGVS, GFF, VCF files). Both students finished the GSoC programme
successfully, and have continued to be contribute to the project since.
Bow's SearchIO code has already been included in recent releases,
marked as experimental for wider testing and feedback.
Biopython hopes to mentor more students for GSoC 2013, for example
some phylogenetics project ideas have been put forward which would
be mentored under the NESCent project.
[{\it NB: to be revised during abstract review}]. % XXX

\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[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} {\bf 13}:209. \href{http://dx.doi.org/10.1186/1471-2105-13-209}{doi:10.1186/1471-2105-13-209}

\end{thebibliography}

\end{document}