From 5cf9dcf15c3e384d02b81e81cb3e2c4a1de0efa4 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 7 Dec 2020 16:30:53 +1100
Subject: first draft

---
 slides.tex | 101 ++++++++++++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 80 insertions(+), 21 deletions(-)

(limited to 'slides.tex')

diff --git a/slides.tex b/slides.tex
index c51f1e5..04ed327 100644
--- a/slides.tex
+++ b/slides.tex
@@ -20,7 +20,7 @@
 
 \author{Justin Bed\H{o}\\WEHI}
 \title{\includegraphics[width=.7\linewidth]{logo}\\functional, reproducible bioinformatics workflows}
-\date{November 10, 2020}
+\date{December 8th, 2020}
 
 \begin{document}
 
@@ -40,7 +40,7 @@
     \item More complex than a straight chain
   \end{enumerate}
   \begin{center}
-    $\Rightarrow$ tooling needed for reproducibility
+    $\Rightarrow$ tooling needed for reproducibility\footnote{generate bit-identical output from an analysis specification on any machine with sufficient resources}
   \end{center}
 \end{frame}
 
@@ -169,8 +169,6 @@
   \begin{minipage}{.55\textwidth}
   \begin{overprint}
   \onslide<1>\includegraphics[width=\linewidth]{pipeline}
-  \onslide<2>\includegraphics[width=.75\linewidth]{bwa-stage}
-  \onslide<3>\includegraphics[width=\linewidth]{bwa-drv}
   \end{overprint}
   \end{minipage}
 \end{frame}
@@ -199,30 +197,91 @@
 \end{frame}
 
 \begin{frame}
-  \frametitle{NextFlow example translation}
-  \begin{minipage}{.5\textwidth}
-  \begin{block}{BioNix}
-  \vspace{.25cm}
-  \includegraphics[height=.65\textheight]{nextflow-nix}
-  \end{block}
-  \end{minipage}
-  \begin{minipage}{.4\textwidth}
-  \begin{block}{NextFlow}
-  \vspace{.25cm}
-  \includegraphics[height=.65\textheight]{nextflow}
-  \end{block}
-  \end{minipage}
+  \frametitle{Stafford Fox Rare Cancer Project}
+  \begin{enumerate}
+    \item $\geq100$ WGS/WES samples totalling 20 TiB of primary data
+    \item Clinical \& research driven
+    \item Timely reporting to requesting clinicians
+    \item Flexibility required to respond to research questions
+    \item Cohort requires consistent processing
+    \item Reproducibility throughout time
+  \end{enumerate}
 \end{frame}
 
 \begin{frame}
-  \frametitle{Real-world usage at WEHI}
+  \frametitle{Stafford Fox Rare Cancer Project}
   \begin{enumerate}
-    \item Stafford Fox Rare Cancer Project
-    \item $\geq100$ WGS/WES samples totalling 20 TiB of primary data
+    \item Reproducible workflow via BioNix, with version control provided by git
     \item SNV calling, neoantigen prediction, structural variants, copy number, mutational signatures, and report generation with embedded revision hash
-    \item CI ensures reports are always up to date and consistent across the cohort
+    \item Handles WES, WGS, comprehensive cancer panel, PDX
+    \item Continuous integration ensures reports are always up to date and consistent across the cohort
     \item Processed at Pawsey (Slurm) and WEHI (PBS \& Slurm)
+    \item Almost completely automated handling of new data
+  \end{enumerate}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Example report}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Stafford Fox Rare Cancer Workflow}
+  \includegraphics[width=\linewidth]{sfrc01042}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Stafford Fox Rare Cancer Workflow}
+  \includegraphics[width=\linewidth]{sfrc01042-gridss}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Generating expressions for new data}
+  \includegraphics[width=.9\linewidth]{autogen}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Integrating RedCap information reproducibly}
+  \begin{minipage}{.3\textwidth}
+    \includegraphics[width=\linewidth]{redcap}
+  \end{minipage}
+  \begin{minipage}{.68\textwidth}
+    \begin{enumerate}
+    \item Difficult, live database without a release schedule
+    \item Solution: store the relevant annotations in the expressions
+    \item Git version control then also applies to the DB content
+    \item Sync script to update annotations
   \end{enumerate}
+  \end{minipage}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Benefits from using BioNix}
+  \begin{enumerate}
+    \item Guarantees a high degree of reproducibility and portability
+    \item Easy to modify workflow and add components
+    \item Small continuous integration implementation
+    \item Inbuilt consistency checking via hash verification
+  \end{enumerate}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Issues with BioNix}
+  \begin{enumerate}
+    \item Steep learning curve
+      \begin{enumerate}
+        \item Nix the language
+        \item BioNix/nixpkgs abstractions
+        \item Stafford Fox workflow particulars
+      \end{enumerate}
+    \item Low discoverability
+    \item Modest collection of bioinformatics software in nixpkgs
+    \item Nix evaluation isn't hermetic (fixed with flakes)
+  \end{enumerate}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Alternative configuration structure}
+  \includegraphics[width=\linewidth]{config}
 \end{frame}
 
 \begin{frame}
-- 
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