Add 2018 abstract

Author: Ben Fulton

2018_BOSC/abstract/abstract.tex

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+\documentclass[10pt,oneside]{article}
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+\setlength{\textheight}{8.75in} %Letter is 11in, less 2 for margins, less 0.25 for footer
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+\setlength{\textwidth}{6.50in} %Letter is 8.5, less 2 inches for margins
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+%%%%%%%%%%%%
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+% use letters instead of symbols to accommodate >7 authors
+\makeatletter
+\let\@fnsymbol\@alph
+\makeatother
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+\usepackage[utf8]{inputenc}
+\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=0.4\textwidth]{../presentation/figures/biopython.jpg} \\
+\vspace{3mm}Biopython Project Update 2018}
+\author{
+	\underline{Ben Fulton}\thanks{Research Technologies, Indiana University, Bloomington, Indiana. Email: \href{mailto:[email protected]}{[email protected]}},
+    Christian Brueffer\thanks{Department of Clinical Sciences, Lund University, Lund, SE},
+    Peter Cock\thanks{Information and Computational Sciences, James Hutton Institute, Invergowrie, Dundee, UK},\\
+    and the Biopython Contributors\thanks{See \href{https://github.com/biopython/biopython/blob/master/CONTRIB.rst}{contributor listing on GitHub}.}}
+\date{18\textsuperscript{th} Bioinformatics Open Source Conference (BOSC) 2018, Portland, OR}
+
+\begin{document}
+\maketitle
+\thispagestyle{empty}
+
+\vspace{-0.2in}
+\noindent
+Website: \url{http://biopython.org} \\
+Repository: \url{https://github.com/biopython/biopython} \\
+License: Biopython License Agreement (BSD like, see \url{http://www.biopython.org/DIST/LICENSE}) \\
+
+The Biopython Project is a long-running distributed collaborative effort,
+supported by the Open Bioinformatics Foundation, which develops a freely
+available Python library for biological computation \cite{AppNote}.
+We present here details of the Biopython releases since BOSC 2017,
+namely Biopython 1.68, 1.69 and 1.70. Together these had 82 named
+contributors including 51 newcomers which reflects our policy of
+trying to encourage even small contributions.
+
+Biopython 1.68 (August 2016) was a relatively small release,
+with the main new feature being support for RSSB's new binary
+Macromolecular Transmission Format (MMTF) for structural data.
+
+Biopython 1.69 (April 2017) represents the start of our re-licensing plan, to transition away
+from our liberal but unique \emph{Biopython License Agreement} to the similar
+but very widely used \emph{3-Clause BSD License}. We are reviewing the code
+base authorship file-by-file, in order to gradually dual license the entire
+project.
+
+Major new features include: a new parser for the ExPASy Cellosaurus cell line
+database, catalogue and ontology; support for the UCSC Multiple Alignment Format (MAF),
+FSA sequencing files, version 4 of the Affymetrix CEL format; updates to the
+REBASE February 2017 restriction enzyme list;
+Bio.PDB.PDBList now can download more formats including MMTF;
+enhanced PyPy support by taking advantage of NumPy and compiling most of the Biopython C code modules.
+
+Biopython 1.70 (July 2017) has internal changes to better support the
+now standard \verb|pip| tool for Python package installation.
+Major new features include:
+support for Mauve's eXtended Multi-FastA (XMFA) file format,
+updates to our BLAST XML and MEME parsers, ExPASy support,
+and phylogenetic distance matrices.
+This release is noteworthy for our new logo (below),
+contributed by Patrick Kunzmann. This draws on our original double helix logo
+(above), and the blue and yellow colors of the current Python logo:
+
+\begin{center}
+\includegraphics[height=2.5cm]{../presentation/figures/biopython_logo_s.png}
+\end{center}
+
+All releases fixed miscellaneous bugs, enhanced the test suite,
+and continued efforts to follow the PEP8 and PEP257 coding style guidelines
+which is now checked automatically with GitHub-integrated continuous integration
+testing using \href{https://travis-ci.org/biopython/biopython/builds}{TravisCI}.
+We now also use \href{https://ci.appveyor.com/project/biopython/biopython/history}{AppVeyor}
+for continuous integration testing under Windows.
+Current efforts include improving the unit test coverage, which is easily viewed
+online at \href{https://codecov.io/github/biopython/biopython/}{CodeCov.io}.
+
+\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}
+
+\end{thebibliography}
+
+\end{document}