diff --git a/good_research_practice/Git-Logo.png b/good_research_practice/Git-Logo.png new file mode 120000 index 0000000000000000000000000000000000000000..8fa419cfa699232e16d735ca2ecebbeb420c9de0 --- /dev/null +++ b/good_research_practice/Git-Logo.png @@ -0,0 +1 @@ +../presentation-pics/pics/Git-Logo.png \ No newline at end of file diff --git a/good_research_practice/Gitlab_Lumc.png b/good_research_practice/Gitlab_Lumc.png new file mode 120000 index 0000000000000000000000000000000000000000..4e9564cfc38262bf430e4df51ef48b9da827ed9d --- /dev/null +++ b/good_research_practice/Gitlab_Lumc.png @@ -0,0 +1 @@ +../presentation-pics/pics/Gitlab_Lumc.png \ No newline at end of file diff --git a/grp_for_data_analysis/Makefile b/good_research_practice/Makefile similarity index 100% rename from grp_for_data_analysis/Makefile rename to good_research_practice/Makefile diff --git a/grp_for_data_analysis/beamerthemelumc.sty b/good_research_practice/beamerthemelumc.sty similarity index 100% rename from grp_for_data_analysis/beamerthemelumc.sty rename to good_research_practice/beamerthemelumc.sty diff --git a/grp_for_data_analysis/gen2phen_logo.eps b/good_research_practice/gen2phen_logo.eps similarity index 100% rename from grp_for_data_analysis/gen2phen_logo.eps rename to good_research_practice/gen2phen_logo.eps diff --git a/good_research_practice/good_research_practice.tex b/good_research_practice/good_research_practice.tex new file mode 100644 index 0000000000000000000000000000000000000000..14e0bde7f6a66c6fa57c3f3d30c062258d431e13 --- /dev/null +++ b/good_research_practice/good_research_practice.tex @@ -0,0 +1,142 @@ +\documentclass[slidestop]{beamer} + +\title{Good research practice for data analysis} +\providecommand{\myConference}{NGS introduction} +\providecommand{\myDate}{Thursday, 22 May 2014} +\author{Michiel van Galen} +\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{Introduction} +\begin{pframe} + \begin{itemize} + \item Where and how to process my data? + \item What and where to store? + \item How to document this? + \item What about big data? + \end{itemize} +\end{pframe} + +\subsection{Git} +\begin{pframe} + We needed to select a system to track a project, analysis and data + \bigskip + + Git + \begin{figure} + \centering + \includegraphics[width=0.3\textwidth]{Git-Logo} + \end{figure} + \begin{itemize} + \item Distributed revision control and management system + \item Widely used for code tracking + \item Also very much capable for tracking analysis, documents, articles + \end{itemize} +\end{pframe} + +\subsection{With or without Git} +\begin{pframe} + \begin{itemize} + \item Track - who did what + \item Store + \item Collaborate + \item Centralize + \item Backup + \item Version historu + \item Secure your data + \item Share! + \end{itemize} + \bigskip + + One day Git course +\end{pframe} + +\subsection{Server} +\begin{pframe} + Local implementation of GitLab within the LUMC + \bigskip + + Log in with LUMC credentials + \bigskip + \begin{figure} + \centering + \includegraphics[width=0.5\textwidth]{Gitlab_Lumc} + \end{figure} +\end{pframe} + +\subsection{Ready to start} +\begin{pframe} + Project skeleton available to clone and hit the ground running. + \begin{itemize} + \item Describe the project + \item Document the pipelines + \item Data description + \item Select participants + \item Maintain big data + \item Folder structure + \item Log activities + \end{itemize} +\end{pframe} + +\subsection{Ipython notebook} +\begin{pframe} + \begin{figure} + \centering + \includegraphics[width=1.0\textwidth]{ipython_notebook} + \end{figure} +\end{pframe} + +\subsection{Scaling computation} +\begin{pframe} + \begin{figure} + \centering + \includegraphics[width=1.0\textwidth]{scaling_computation} + \end{figure} +\end{pframe} + +\section{Questions?} +\lastpagetemplate +\begin{pframe} + \begin{center} + Acknowledgements: + \bigskip + \bigskip + + Jeroen Laros + \bigskip + + Martijn Vermaat + \bigskip + + Jeroen Frank + \bigskip + + LGTC + + \end{center} +\end{pframe} + +\end{document} diff --git a/good_research_practice/ipython_notebook.png b/good_research_practice/ipython_notebook.png new file mode 120000 index 0000000000000000000000000000000000000000..78d32a3ce503fd4d5ab631c9ec6ed1fe9cbc86b9 --- /dev/null +++ b/good_research_practice/ipython_notebook.png @@ -0,0 +1 @@ +../presentation-pics/pics/ipython_notebook.png \ No newline at end of file diff --git a/grp_for_data_analysis/lgtc_logo.eps b/good_research_practice/lgtc_logo.eps similarity index 100% rename from grp_for_data_analysis/lgtc_logo.eps rename to good_research_practice/lgtc_logo.eps diff --git a/grp_for_data_analysis/lumc_logo.eps b/good_research_practice/lumc_logo.eps similarity index 100% rename from grp_for_data_analysis/lumc_logo.eps rename to good_research_practice/lumc_logo.eps diff --git a/grp_for_data_analysis/lumc_logo_small.eps b/good_research_practice/lumc_logo_small.eps similarity index 100% rename from grp_for_data_analysis/lumc_logo_small.eps rename to good_research_practice/lumc_logo_small.eps diff --git a/grp_for_data_analysis/nbic_logo.eps b/good_research_practice/nbic_logo.eps similarity index 100% rename from grp_for_data_analysis/nbic_logo.eps rename to good_research_practice/nbic_logo.eps diff --git a/grp_for_data_analysis/ngi_logo.eps b/good_research_practice/ngi_logo.eps similarity index 100% rename from grp_for_data_analysis/ngi_logo.eps rename to good_research_practice/ngi_logo.eps diff --git a/grp_for_data_analysis/nwo_logo_en.eps b/good_research_practice/nwo_logo_en.eps similarity index 100% rename from grp_for_data_analysis/nwo_logo_en.eps rename to good_research_practice/nwo_logo_en.eps diff --git a/grp_for_data_analysis/nwo_logo_nl.eps b/good_research_practice/nwo_logo_nl.eps similarity index 100% rename from grp_for_data_analysis/nwo_logo_nl.eps rename to good_research_practice/nwo_logo_nl.eps diff --git a/good_research_practice/scaling_computation.png b/good_research_practice/scaling_computation.png new file mode 120000 index 0000000000000000000000000000000000000000..86258f87ccea293b6260faaf94580ebaa7ff3ae5 --- /dev/null +++ b/good_research_practice/scaling_computation.png @@ -0,0 +1 @@ +../presentation-pics/pics/scaling_computation.png \ No newline at end of file diff --git a/grp_for_data_analysis/ul_logo.eps b/good_research_practice/ul_logo.eps similarity index 100% rename from grp_for_data_analysis/ul_logo.eps rename to good_research_practice/ul_logo.eps diff --git a/grp_for_data_analysis/grp_for_data_analysis.tex b/grp_for_data_analysis/grp_for_data_analysis.tex deleted file mode 100644 index 075f8aa5b0d8014b2318baf79900547bec342ec0..0000000000000000000000000000000000000000 --- a/grp_for_data_analysis/grp_for_data_analysis.tex +++ /dev/null @@ -1,65 +0,0 @@ -\documentclass[slidestop]{beamer} - -\title{Phylogenetic reconstruction} -\providecommand{\myConference}{NGS introduction} -\providecommand{\myDate}{Thursday, 22 May 2014} -\author{Michiel van Galen} -\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{Introduction} -\subsection{Some slide} -\begin{pframe} - - \begin{itemize} - \item The \emph{section} command controls the title. - \item The \emph{subsection} command controls the frametitle. - \end{itemize} -\end{pframe} - -\section{Questions?} -\lastpagetemplate -\begin{pframe} - \begin{center} - Acknowledgements: - \bigskip - \bigskip - - Jeroen Laros - \bigskip - - Martijn Vermaat - \bigskip - - Jeroen Frank - \bigskip - - LGTC - - \end{center} -\end{pframe} - -\end{document}