Updated grp deck

good_research_practice/good_research_practice.tex

@@ -40,12 +40,12 @@
   \end{itemize}
 \end{pframe}
 
-\subsection{Git}
+\section{Git}
+\subsection{Version control}
 \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}
@@ -65,7 +65,7 @@
     \item Collaborate
     \item Centralize
     \item Backup
-    \item Version historu
+    \item Version history
     \item Secure your data
     \item Share!
   \end{itemize}
@@ -89,7 +89,7 @@
 
 \subsection{Ready to start}
 \begin{pframe}
-  Project skeleton available to clone and hit the ground running.
+  Project skeleton available to clone and hit the ground running, offering a platform to:
   \begin{itemize}
     \item Describe the project 
     \item Document the pipelines
@@ -109,7 +109,7 @@
   \end{figure}
 \end{pframe}
 
-\subsection{Scaling computation}
+\section{Scaling computation}
 \begin{pframe}
   \begin{figure}
     \centering
@@ -117,6 +117,144 @@
   \end{figure}
 \end{pframe}
 
+\subsection{Desktop workstation}
+\begin{pframe}
+  Good for writing, browsing and testing  
+  \begin{itemize}
+    \item Lacking power
+    \item Interface to real computers
+    \item No proper storage
+  \end{itemize}
+  Pretty interface
+\end{pframe}
+
+\subsection{Shark cluster}
+\begin{pframe}
+  \begin{itemize}
+    \item Part of the LUMC network
+    \item 700 CPU
+    \item 4Tb RAM
+    \item Top node 256GB RAM, 24 CPU
+  \end{itemize}
+  \begin{figure}
+    \centering
+    \includegraphics[width=0.45\textwidth]{shark_schematic}
+  \end{figure}
+\end{pframe}
+
+\subsection{Why the Shark cluster}
+\begin{pframe}
+  \begin{itemize}
+    \item Useful for most research projects that need computing power
+    \item NGS, R, GWAS...
+    \item Local, secure and powerful
+    \item Relatively simple to use (Course available)
+    \item Plenty of resources and disk space
+      \begin{itemize}
+      \item Isilon storage nodes (37Tb) for analysis
+      \item Long term storage (0.5Pb) for archiving
+    \end{itemize}
+    \item Still being expanded
+  \end{itemize}
+\end{pframe}
+
+\subsection{Working on the Shark cluster}
+\begin{pframe}
+  \begin{itemize}
+    \item Easy access with your LUMC account
+    \item Pipelines and knowledge available
+      \begin{itemize}
+      \item LGTC, SASC and other departments run many analyses
+      \item Very little downtime in recent years
+    \end{itemize}
+    \item Qlogin to work on a single node
+    \item Parallel analysis using makefiles and qsub
+  \end{itemize}
+\end{pframe}
+
+\subsection{Shark limitations}
+\begin{pframe}
+  \begin{itemize}
+    \item 'Only' 256GB top node
+    \item Some graphical limitations
+    \item Queues can be full
+    \item Access from outside is difficult
+      \begin{itemize}
+      \item Only BAM export
+      \item Research network
+    \end{itemize}
+  \end{itemize}
+\end{pframe}
+
+\subsection{Dutch lifescience grid}
+\begin{pframe}
+  \begin{itemize}
+    \item Across NL, 11 sites
+    \item ~1500 cpus, ~5Tb RAM
+  \end{itemize}
+  \begin{figure}
+    \centering
+    \includegraphics[width=0.5\textwidth]{lifesciencegrid_NL}
+  \end{figure}
+\end{pframe}
+
+\subsection{Working on the grid}
+\begin{pframe}
+  \begin{figure}
+    \centering
+    \includegraphics[width=1.0\textwidth]{rp3_grid}
+  \end{figure}
+\end{pframe}
+
+\subsection{Working on the grid}
+\begin{pframe}
+  Getting the grid to work is not easy but worthwhile
+  \begin{itemize}
+    \item 2300 RNA-seq samples
+    \item 300 jobs in parallel across the country
+    \item 10 cores, 40GB RAM for 36 hours
+    \item One sample at a time
+  \end{itemize}
+  \bigskip
+
+  \emph{150.000 core hours in 4 days}
+\end{pframe}
+
+\section{Recap}
+\begin{pframe}
+  \begin{itemize}
+    \item Data analysis, management and storage is changing into more centralized and powerful platforms
+    \item Due to the demand of larger studies and higher throughput
+  \end{itemize}
+  \bigskip
+
+  \begin{itemize}
+    \item Git offers a useful platform for project management
+    \item Remote resources are available reducing desktop machines to terminals
+    \item Storage and guidelines need considerations
+    \item Solutions are being worked on, LUMC 'Best Research Practices'
+  \end{itemize}
+\end{pframe}
+
+\subsection{Courses and documents}
+\begin{pframe}
+  \begin{itemize}
+    \item Linux
+    \item Shark
+    \item Python
+    \item Scripting
+    \item Git
+  \end{itemize}
+  \bigskip
+
+  Documentation and wikis available at:
+  \bigskip
+
+  humgenprojects.lumc.nl
+\end{pframe}
+
+
+
 \section{Questions?}
 \lastpagetemplate
 \begin{pframe}

good_research_practice/lifesciencegrid_NL.png

+../presentation-pics/pics/lifesciencegrid_NL.png
\ No newline at end of file

good_research_practice/rp3_grid.png

+../presentation-pics/pics/rp3_grid.png
\ No newline at end of file

good_research_practice/shark_schematic.png

+../presentation-pics/pics/shark_schematic.png
\ No newline at end of file