Commit 99045c88 authored by Laros's avatar Laros
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Added ict_research lecture.

parent 6daba0db
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\documentclass[slidestop]{beamer}
\title{ICT and research at the LUMC}
\providecommand{\myConference}{BULL / DICT}
\providecommand{\myDate}{Thursday, 18 October 2012}
\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{Introduction}
\begin{frame}
\frametitle{ICT and research}
Division 5.
\pause
\begin{itemize}
\item Center for Human and Clinical Genetics.
\pause
\begin{itemize}
\item Human Genetics.
\pause
\begin{itemize}
\item Leiden Genome Technology Center.
\end{itemize}
\end{itemize}
\end{itemize}
\bigskip
\pause
High throughput sequencing.
\end{frame}
\section{Illumina sequencing}
\begin{frame}
\frametitle{DNA sequencing}
\begin{minipage}[t]{0.45\textwidth}
\begin{figure}
\includegraphics[width=\textwidth]{hiseq_2000}
\caption{HiSeq 2000.}
\end{figure}
\end{minipage}
\hfill
\pause
\begin{minipage}[t]{0.53\textwidth}
\begin{figure}[]
\begin{center}
\includegraphics[width=0.8\textwidth, height=0.3\textheight]
{k_flowcell}
\end{center}
\caption{Flowcell.}
\end{figure}
\vspace{-1cm}
\pause
\begin{figure}[]
\begin{center}
\includegraphics[width=0.8\textwidth]{k_bridge2}
\end{center}
\caption{Amplification.}
\end{figure}
\end{minipage}
\end{frame}
\begin{frame}
\frametitle{Raw data analysis}
\begin{figure}[]
\begin{center}
\includegraphics[width=\textwidth]{k_basecall}
\end{center}
\caption{Base calling.}
\label{}
\end{figure}
\end{frame}
\begin{frame}[fragile]
\frametitle{Result of base calling}
\begin{lstlisting}[language=none, caption=FastQ file.]
@FCC0ADRACXX:2:1101:1684:1875#GCGGAACT/1
AGGGGATGCAACCTCGAGGAGGAAAGGAACGAAAGAGGAAGGGAG...
+
BS\ceeeegggggiihfhighihiiiihiihhhihfhighiiiii...
@FCC0ADRACXX:2:1101:1714:1885#GCGGAACT/1
ATTTTCTCAATGTCTACCACTGCGGGTAACACTTTGTGTTTCCCA...
+
bbbeeeeegggggiihiiiiiiiiiighiiiiiiiiggfghiihi...
\end{lstlisting}
\bigskip
These files are around $1$T big.
\end{frame}
\begin{frame}
\frametitle{Some figures}
Runtime $2$ weeks ($5$-$10$ full genomes).
\bigskip
Produces $6$T of pictures per flowcell, $500$G base calling.
\bigskip
Needs continuous connection to the storage, otherwise it stalls.
\bigskip
\pause
Basecalling:
\begin{tabular}{r@{\,}l@{\,}ll}
$24$ & & & time in hours for base calling per flowcell\\
$12$ & $\times$ & & number of cores\\ \cline{1-1}
$2$ & $\times$ & & number of flowcells\\ \cline{1-1}
$576$ & & & CPU hours per flowcell\\
\end{tabular}
\bigskip
On a desktop machine this would take $48$ days.
\end{frame}
\begin{frame}
\frametitle{Some figures}
Cost:
\bigskip
\begin{tabular}{lr@{\,}l@{\,}ll}
\euro & $13,000$ & & & sequencing\\
\euro & $6,400$ & & & sample preparation\\
\euro & $1,200$ & $+$ & & personnel\\ \cline{1-2}
\euro & $20,600$ & & &\\
& $2$ & $\times$ & & number of flowcells\\ \cline{1-2}
\euro & $41,200$ & & & total
\end{tabular}
\end{frame}
\section{PacBio sequencing}
\begin{frame}
\frametitle{Pacific Biosciences Single Molecule, Real-Time}
\begin{figure}
\includegraphics[height=0.9\textheight]{pacbio}
\caption{PacBio RS.}
\end{figure}
\end{frame}
\begin{frame}
\frametitle{Base calling}
\begin{figure}[]
\begin{center}
\includegraphics[width=\textwidth]{base-pacbio}
\end{center}
\caption{PacBio trace.}
\label{}
\end{figure}
\end{frame}
\begin{frame}
\frametitle{Some figures}
Runtime $90$ minutes.
\bigskip
\pause
Per cell:
\begin{itemize}
\item $3$G/sec.
\begin{itemize}
\item $4$ cameras.
\item $72$ fps.
\item $10$M pictures.
\end{itemize}
\item $16$T of raw data.
\item $4$G after base calling.
\end{itemize}
\bigskip
\pause
There are $16$ cells in this machine:
\begin{itemize}
\item $256$T per run.
\item $64$G after base calling.
\end{itemize}
\end{frame}
\begin{frame}
\frametitle{Some figures}
Cost:
\bigskip
\begin{tabular}{lr@{\,}l@{\,}ll}
\euro & $6,912$ & & & sequencing\\
\euro & $2,284$ & & & sample preparation\\
\euro & $1,200$ & $+$ & & personnel\\ \cline{1-2}
\euro & $10,560$ & & & total\\
\end{tabular}
\end{frame}
\section{Secondary data analysis}
\begin{frame}
\frametitle{Alignment}
\begin{figure}[]
\begin{center}
\includegraphics[width=0.9\textwidth]{varcall}
\end{center}
\caption{Result of an alignment.}
\label{}
\end{figure}
\end{frame}
\section{Facilities}
\begin{frame}
\frametitle{Clusters}
\begin{figure}
\includegraphics[width=0.95\textwidth]{DellBlade4}
\caption{Dell M610 blade server}
\end{figure}
\end{frame}
\begin{frame}
\frametitle{Local cluster}
Some figures:
\begin{itemize}
\item $29$ nodes.
\item $368$ cores.
\item $94$ users.
\end{itemize}
\bigskip
\pause
Funded by four departements:
\begin{itemize}
\item Molecular Epidemiology.
\item Clinical Genetics.
\item Human Genetics.
\item Parasitology.
\end{itemize}
\end{frame}
\begin{frame}
\frametitle{Storage}
Funded by the same four departements.
\begin{table}[]
\begin{center}
\begin{tabular}{l|rr}
Share & Size (TB)& Used\\
\hline
MolEpi & $65$ & $51$\\
KG & $27$ & $13$\\
HumGen & $37$ & $18$\\
BMS & $15$ & $0$\\ % Parasitology
LGTC & $105$ & $89$\\
SASC & $5$ & $0$\\
GoNL & $140$ & $105$\\
UCSC-bam & $1$ & $1$\\
total & $520$ & $372$\\
\end{tabular}
\end{center}
\caption{Usage of the storage.}
\label{}
\end{table}
\end{frame}
\section{Common analyses}
\begin{frame}
\frametitle{Resequencing}
Exome:
\begin{itemize}
\item Only look at the genes.
\item Will not detect everything.
\end{itemize}
\bigskip
\pause
Full genome:
\begin{itemize}
\item Analyse everything.
\end{itemize}
\bigskip
\pause
\begin{table}[]
\begin{center}
\begin{tabular}{l|rr}
type & desktop & cluster\\
\hline
exome & $4$ days & $5$ hours\\
genome & one year & $3$ days\\
\end{tabular}
\end{center}
\caption{Gain of using a cluster.}
\label{}
\end{table}
\end{frame}
\begin{frame}
\frametitle{Large projects}
Genome of the Netherlands:
\begin{itemize}
\item $750$ full genomes.
\end{itemize}
\bigskip
\pause
Centre for Genome Diagnostics:
\begin{itemize}
\item $10$ full genomes.
\end{itemize}
\bigskip
\pause
Geuvadis:
\begin{itemize}
\item QC for $667$ samples done in two days.
\end{itemize}
\bigskip
These types of analysis would be impossible without the cluster.
\end{frame}
\begin{frame}
\frametitle{Future}
Sequencing in diagnostics (figures from Rotterdam):
\begin{itemize}
\item $100$ exomes per week.
\item $100 \times 2$G.
\end{itemize}
\bigskip
\pause
We will switch to full genome sequencing soon:
\begin{itemize}
\item $\pm 40$G per genome.
\item $4$T of data per week.
\end{itemize}
\bigskip
\pause
Needs to be more reliable.
\end{frame}
\section{Questions?}
\lastpagetemplate
\begin{frame}
\begin{center}
Acknowledgements:
\bigskip
\bigskip
Michiel van Galen
Martijn Vermaat
Michel Villerius
Johan den Dunnen
\end{center}
\end{frame}
\end{document}
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