From 95a8eeac526e12ab44a10590c91d9256b014ffd5 Mon Sep 17 00:00:00 2001
From: Michiel van Galen <m.van_galen@lumc.nl>
Date: Wed, 21 May 2014 17:43:19 +0200
Subject: [PATCH] Adding a presentation
---
good_research_practice/Git-Logo.png | 1 +
good_research_practice/Gitlab_Lumc.png | 1 +
.../Makefile | 0
.../beamerthemelumc.sty | 0
.../gen2phen_logo.eps | 0
.../good_research_practice.tex | 142 ++++++++++++++++++
good_research_practice/ipython_notebook.png | 1 +
.../lgtc_logo.eps | 0
.../lumc_logo.eps | 0
.../lumc_logo_small.eps | 0
.../nbic_logo.eps | 0
.../ngi_logo.eps | 0
.../nwo_logo_en.eps | 0
.../nwo_logo_nl.eps | 0
.../scaling_computation.png | 1 +
.../ul_logo.eps | 0
.../grp_for_data_analysis.tex | 65 --------
17 files changed, 146 insertions(+), 65 deletions(-)
create mode 120000 good_research_practice/Git-Logo.png
create mode 120000 good_research_practice/Gitlab_Lumc.png
rename {grp_for_data_analysis => good_research_practice}/Makefile (100%)
rename {grp_for_data_analysis => good_research_practice}/beamerthemelumc.sty (100%)
rename {grp_for_data_analysis => good_research_practice}/gen2phen_logo.eps (100%)
create mode 100644 good_research_practice/good_research_practice.tex
create mode 120000 good_research_practice/ipython_notebook.png
rename {grp_for_data_analysis => good_research_practice}/lgtc_logo.eps (100%)
rename {grp_for_data_analysis => good_research_practice}/lumc_logo.eps (100%)
rename {grp_for_data_analysis => good_research_practice}/lumc_logo_small.eps (100%)
rename {grp_for_data_analysis => good_research_practice}/nbic_logo.eps (100%)
rename {grp_for_data_analysis => good_research_practice}/ngi_logo.eps (100%)
rename {grp_for_data_analysis => good_research_practice}/nwo_logo_en.eps (100%)
rename {grp_for_data_analysis => good_research_practice}/nwo_logo_nl.eps (100%)
create mode 120000 good_research_practice/scaling_computation.png
rename {grp_for_data_analysis => good_research_practice}/ul_logo.eps (100%)
delete mode 100644 grp_for_data_analysis/grp_for_data_analysis.tex
diff --git a/good_research_practice/Git-Logo.png b/good_research_practice/Git-Logo.png
new file mode 120000
index 0000000..8fa419c
--- /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 0000000..4e9564c
--- /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 0000000..14e0bde
--- /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 0000000..78d32a3
--- /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 0000000..86258f8
--- /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 075f8aa..0000000
--- 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}
--
GitLab