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\usepackage{beamerthemeHannover, graphicx, clrscode, amsmath, amssymb, multicol} | |
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\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} |