Commit 2b516e4e authored by Laros's avatar Laros
Browse files

Added humgen_staff slides.

parent 7bbc13a5
../../submodules/presentation/Makefile
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../../submodules/presentation/beamerthemelumc.sty
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\documentclass[slidestop]{beamer}
\title{\ldots}
\providecommand{\myConference}{Staff meeting}
\providecommand{\myDate}{Monday, September 9, 2013}
\author{Jeroen F. J. Laros}
\providecommand{\myGroup}{Leiden Genome Technology Center}
\providecommand{\myDepartment}{Department of Human Genetics}
\providecommand{\myCenter}{Center for Human and Clinical Genetics}
\providecommand{\lastCenterLogo}{
\raisebox{-0.1cm}{
\includegraphics[height=1cm]{lgtc_logo}
%\includegraphics[height=0.7cm]{ngi_logo}
}
}
\providecommand{\lastRightLogo}{
%\includegraphics[height=0.7cm]{nbic_logo}
%\includegraphics[height=0.8cm]{nwo_logo_en}
%\hspace{1.5cm}\includegraphics[height=0.7cm]{gen2phen_logo}
}
\usetheme{lumc}
\begin{document}
% This disables the \pause command, handy in the editing phase.
%\renewcommand{\pause}{}
% Make the title page.
\bodytemplate
% First page of the presentation.
\section{Version control}
\begin{fframe}
\frametitle{Central place for storing code.}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.8\textheight]{gitlab}
\end{center}
\caption{Gitlab.}
\label{}
\vspace{-0.5cm}
\end{figure}
\vfill
\permfoot{https://git.lumc.nl/}
\end{fframe}
\begin{frame}
\frametitle{Gitlab.}
Features:
\begin{itemize}
\item Accessible from within as well as outside of the LUMC.
\item Low maintenance.
\begin{itemize}
\item Use your LUMC username/password.
\item Create your own projects.
\end{itemize}
\item Supports both public as well as private projects.
\item Supports teams working on a project.
\end{itemize}
\end{frame}
\section{LUMC software packages}
\begin{fframe}
\frametitle{Distributing programs.}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.8\textheight]{pypi}
\end{center}
\caption{The Python Package Index.}
\label{}
\vspace{-0.5cm}
\end{figure}
\vfill
\permfoot{https://pypi.python.org/}
\end{fframe}
\begin{frame}[fragile]
\frametitle{Distributing programs.}
Via PyPI - the Python Package Index.
\bigskip
\begin{itemize}
\item Anyone can install your software easily.
\item Dependencies are automatically installed.
\item No more sharing of scripts.
\begin{itemize}
\item \ldots that need the help of the developer to run.
\end{itemize}
\end{itemize}
\bigskip
\bigskip
\pause
\begin{lstlisting}[language=bash]
pip install tssv
\end{lstlisting}
\end{frame}
\begin{fframe}
\frametitle{Released packages.}
We currently have released the following packages:
\begin{table}
{\small
\begin{tabular}{lp{8cm}}
wiggelen & Working with wiggle tracks in Python.\\
fastools & FASTA/FASTQ analysis and manipulation.\\
piletools & Mpileup analysis toolkit.\\
barcode & Design NGS barcodes.\\
tssv & Targeted characterisation of short structural variation.\\
kMer & k-mer analysis toolkit and programming library.\\
monoseq & A Python library for pretty-printing DNA and protein
sequences using a monospace font.\\
memoise & Memoise decorator.\\
\end{tabular}
}
\caption{Packages.}
\end{table}
\vfill
\permfoot{https://pypi.python.org/}
\end{fframe}
\section{Documentation}
\begin{frame}[fragile]
\frametitle{Command line help.}
Make it easy for users to use our tools.
\bigskip
\begin{lstlisting}[numbers=none, basicstyle=\tiny, caption={Help for the
diff option.}, language=none]
> kMer diff -h
usage: kMer diff [-h] -i INPUT INPUT [-d] [-s SUMMARY] [-t THRESHOLD] [-b]
[-p] [-S] [-m] [-e] [-P PAIRWISE] [-n PRECISION]
Calculate the difference between two k-mer profiles.
optional arguments:
-h, --help show this help message and exit
-i INPUT INPUT pair of input files
-d scale down (default=False)
-s SUMMARY summary function for dynamic smoothing (int default=0)
-t THRESHOLD threshold for the summary function (int default=0)
-b balance the profiles (default=False)
-p use only positive values (default=False)
-S scale the profiles (default=False)
-m smooth the profiles (default=False)
-e use the euclidean distance metric (default=False)
-P PAIRWISE paiwise distance function for the multiset distance (int
default=0)
-n PRECISION number of decimals (int default=3)
\end{lstlisting}
\end{frame}
\begin{frame}
\frametitle{Documentation for programmers.}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.8\textheight]{epydoc_1}
\end{center}
\caption{API documentation.}
\label{}
\end{figure}
\end{frame}
\begin{frame}
\frametitle{Documentation for programmers.}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.8\textheight]{epydoc_2}
\end{center}
\caption{API documentation (2).}
\label{}
\end{figure}
\end{frame}
\section{User-friendly interfaces}
\begin{fframe}
\frametitle{CLI-mate.}
Interface generator for command line programs.
\begin{itemize}
\item Web form to define the CLI of a program.
\item Definition is saved in RDF.
\pause
\item From the definition multiple user friendly interfaces can be
generated.
\begin{itemize}
\item Galaxy.
\item Moteur.
\end{itemize}
\pause
\item But it doesn't end there.
\begin{itemize}
\item User manual.
\item HTML webinterface.
\item Webservices.
\item \ldots
\end{itemize}
\end{itemize}
\vfill
\permfoot{http://www.humgen.nl/cli-mate}
\end{fframe}
\begin{frame}
\frametitle{CLI-mate.}
\begin{figure}
\includegraphics[width=\textwidth, height=0.85\textheight]{ifgen_home}
\caption{CLI-mate homepage.}
\end{figure}
\end{frame}
\begin{frame}
\frametitle{CLI-mate.}
\begin{figure}
\includegraphics[width=\textwidth, height=0.85\textheight]{ifgen_mpileup}
\caption{Defining a tool.}
\end{figure}
\end{frame}
\begin{frame}
\frametitle{CLI-mate.}
\begin{figure}
\includegraphics[width=\textwidth, height=0.85\textheight]{galaxy_mpileup}
\caption{Generated interface.}
\end{figure}
\end{frame}
\section{Education}
\begin{frame}
\frametitle{Courses given in the last year.}
\begin{table}[]
\begin{center}
{\small
\begin{tabular}{rl}
21--23-10-2013 & Introduction Linux and command line scripting\\
28--30-08-2013 & Next generation sequencing (NGS) data analysis\\
05--09-08-2013 & Python programming\\
05-04-2013 & Introduction to NGS data analysis\\
\end{tabular}
}
\end{center}
\caption{Regular courses.}
\label{}
\end{table}
\end{frame}
\section{Questions?}
\lastpagetemplate
\begin{frame}
\begin{center}
Acknowledgements:
\bigskip
\bigskip
\end{center}
\end{frame}
\end{document}
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