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\documentclass[12pt]{beamer}
\usepackage{beamerthemeHannover, graphicx, clrscode, amsmath, amssymb, multicol}
\usepackage{verbatim}
\setbeamercolor{sidebar}{use=structure,bg=gray!60!green}
\title{ Slicing and Dicing Plant Genomes with Perl }
\author[@dukeleto]{Jonathan "Duke" Leto \\ Sol Genomics Network \\ http://solgenomics.net }
\date{}
\begin{document}
\frame{
\titlepage
\begin{center}
\includegraphics[scale=0.5]{sgn_logo}
\end{center}
}
\frame{
\frametitle{What is Sol Genomics Network? (SGN)}
SGN is an NSF-funded Model Organism Database on the web. \\
\begin{itemize}
\item A model organism is a species that is extensively studied to understand
particular biological phenomena, with the expectation that discoveries made
in the organism model will provide insight into the workings of other
organisms.
\end{itemize}
}
\frame{
\frametitle{What is Sol Genomics Network? (Continued)}
SGN is part of the Lukas Mueller research lab at Boyce Thompson Institute
for Plant Research (BTI), located on the Cornell University campus. \\
\begin{center}
\includegraphics[scale=0.3]{tomato}
\end{center}
We study the Solanaceae (Nightshade family): Tomato, Potato, Petunia, Eggplant, and many more
}
\frame{
\frametitle{Who uses SGN?}
\begin{itemize}
\item Evolutionary plant biologists
\item Plant biochemists
\item Plant disease researchers
\item Plant breeders
\end{itemize}
\begin{center}
\includegraphics[scale=0.7]{plant-study}
\end{center}
}
\frame{
\frametitle{Code By Numbers}
Every line of code goes on Github, anything reusable goes to CPAN. \\
\begin{itemize}
\item 29 public Github repos
\item 10 committers
\item $\sim$ 10 CPAN modules released (more on the way)
\item Over 200K lines of Perl
\begin{itemize}
\item Lots of legacy code, slowly modernizing
\item Converted to Catalyst last year
\end{itemize}
\end{itemize}
}
\frame{
\frametitle{Some CPAN Modules}
\begin{itemize}
\item Bio::Chado::Schema - DBIx::Class schema for Chado
\item Bio::GFF3 - Manipulate GFF3 data files
\item Bio::Blast - Interact with BLAST databases
\item Catalyst::View::Bio::Seqio - Catalyst view for Bioperl sequences
\item Yapri - Yet Another Perl R Interface
\end{itemize}
}
\frame{
\frametitle{What we depend on most}
\begin{itemize}
\item Moose
\item Catalyst
\item DBIx::Class
\item Plack
\item Starman
\item BioPerl
\item Mason
\item WWW::Mechanize
\item autodie
\item Test::*
\end{itemize}
}
\frame{
\frametitle{My current project}
Mimosa: Miniature Model Organism Sequence Aligner \\
\begin{center}
\includegraphics[scale=0.3]{mimosa2}
\end{center}
Web interface to not-so-friendly command-line utilities for evolutionary biologists
}
\frame{
\frametitle{ Resources }
\begin{center}
\begin{itemize}
\item http://solgenomics.net
\item http://github.com/solgenomics
\item \#cxgn on irc.perl.org
\end{itemize}
\end{center}
}
\frame{
\frametitle{ Thanks! }
\begin{itemize}
\item Boyce Thompson Institute for Plant Research
\item National Science Foundation
\item All the Perl + CPAN hackers that make SGN possible
\end{itemize}
\begin{center}
\includegraphics[scale=1.0]{tomato_happy}
\end{center}
}
\end{document}
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