Commit 612f85c4 authored by Laros's avatar Laros
Browse files

Updated RSE lecture.

parent 846a91c9
......@@ -440,37 +440,37 @@
\end{figure}
\end{pframe}
\subsection{Interactive computational environments}
\begin{pframe}
Combine code execution, text, mathematics, plots and rich media into a single
document.
\bigskip
Ideal for exploration of data.
\begin{itemize}
\item Documentation and code are interwoven.
\item Results are displayed inline.
\item Web based.
\item Versions.
\end{itemize}
\bigskip
\pause
Integration with GitLab.
\vfill
\permfoot{\url{http://ipython.org/notebook.html}}
\end{pframe}
\subsection{iPython notebook}
\begin{pframe}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.85\textheight]{ipynb}
\end{center}
\caption{iPython notebook.}
\end{figure}
\end{pframe}
%\subsection{Interactive computational environments}
%\begin{pframe}
% Combine code execution, text, mathematics, plots and rich media into a single
% document.
% \bigskip
%
% Ideal for exploration of data.
% \begin{itemize}
% \item Documentation and code are interwoven.
% \item Results are displayed inline.
% \item Web based.
% \item Versions.
% \end{itemize}
% \bigskip
% \pause
%
% Integration with GitLab.
% \vfill
%
% \permfoot{\url{http://ipython.org/notebook.html}}
%\end{pframe}
%
%\subsection{iPython notebook}
%\begin{pframe}
% \begin{figure}[]
% \begin{center}
% \includegraphics[height=0.85\textheight]{ipynb}
% \end{center}
% \caption{iPython notebook.}
% \end{figure}
%\end{pframe}
\section{Education}
\subsection{Overview}
......@@ -544,20 +544,15 @@
Full day course, given twice a year.
\bigskip
Everyone in the Bioinformatics field:
\begin{itemize}
\item Software development.
\item Project management.
\item Collaboration.
\end{itemize}
Version control for developers and data analysts.
\bigskip
\pause
Topics:
\begin{itemize}
\item Git Basics
\item Remotes
\item Writing Markdown files.
\item Project management and collaboration.
\end{itemize}
\vfill
......@@ -589,6 +584,29 @@
\section{Production data analysis}
\subsection{Computational infrastructure}
\begin{pframe}
Observation:
\begin{itemize}
\item Much of the automated data analysis is extremely complex.
\begin{itemize}
\item Many implicit dependencies and workflows.
\end{itemize}
\item Virtually impossible to transfer to other people.
\begin{itemize}
\item Problematic in diagnostics.
\end{itemize}
\end{itemize}
\bigskip
Our approach:
\begin{itemize}
\item Highly specialised microservices.
\begin{itemize}
\item Do only one thing and do it well.
\end{itemize}
\end{itemize}
\end{pframe}
\begin{pframe}
Reproducibility and automation.
\bigskip
......@@ -622,12 +640,12 @@
\begin{itemize}
\item The \emph{consumer} of the data decides what is to be sent.
\begin{itemize}
\item Sample IDs and grouping.
\item QC metrics.
\item Sample IDs and grouping, QC metrics, \ldots
\end{itemize}
\item The data is only accepted when this metadata is valid.
\end{itemize}
\bigskip
\pause
Some statistics:
\begin{itemize}
......@@ -646,6 +664,13 @@
\end{itemize}
\bigskip
About the metadata:
\begin{itemize}
\item The order is not relevant.
\item The data can come from any (authorised) source.
\end{itemize}
\bigskip
When all data is available, a signal is sent to an actor that runs the
analysis.
\end{pframe}
......@@ -656,8 +681,8 @@
\begin{itemize}
\item Get the pipeline configuration from our GitLab system.
\item Start the pipeline.
\item Monitor.
\item Keep track of the status.
\item Monitor the pipeline progress.
\item Keep track of the status (query via the API).
\end{itemize}
\end{pframe}
......@@ -676,6 +701,9 @@
\item Only open standards.
\end{itemize}
\end{itemize}
\bigskip
All actions are stored in a database that can be queried via the API.
\end{pframe}
\subsection{Use case: NIPT}
......@@ -704,6 +732,7 @@
\begin{pframe}
Our first run using the API system.
\medskip
\begin{tabular}{l@{:}l@{:}ll}
16 & 30 & 54 & Data transfer is initiated.\\
......@@ -722,6 +751,7 @@
% Make the acknowledgements slide.
\makeAcknowledgementsSlide{
\begin{tabular}{l}
Guy Allard\\
Jonathan Vis\\
Mark Santcroos\\
Martijn Vermaat\\
......
Subproject commit d9bfb3518b162006000138cc646b614a7bdc60b4
Subproject commit e8f15b637cab7194573357c7a09b0efb709c7c1c
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