Updated some typos and statistics.

lectures/nipt_dataanalysis/nipt_dataanalysis.tex

@@ -109,7 +109,7 @@
 \end{pframe}
 
 \begin{pframe}
-  Standard score ($z$-score):
+  Standard score ($z$-score) of a raw score $x$:
   \begin{displaymath}
     z = \frac{x - \mu}{\sigma}
   \end{displaymath}
@@ -184,19 +184,24 @@
 \begin{pframe}
   The pipeline is straightforward:
   \begin{itemize}
-    \item Alignment to the reference genomen (GRCh37, hg19).
+    \item Alignment to the reference genome (GRCh37, hg19).
     \item Deduplication.
     \item CNV calling.
   \end{itemize}
   \bigskip
 
-  Original run time: $5$ to $6$ hours.
+  Original run time: $6$ hours, but with up to $500$ samples per week.
+  \begin{itemize}
+    \item $20$ minutes per sample.
+  \end{itemize}
   \bigskip
+  \pause
 
-  We expect up to $500$ samples per week.
+  Additional constraint: $8$ (office) hours turnaround time.
   \begin{itemize}
-    \item $20$ minutes per sample.
-    \item No room for delays.
+    \item $2.5$ minutes per sample ($2$ batches of $96$ samples).
+    \pause
+    \item Implementation time of two months.
   \end{itemize}
 \end{pframe}
 
@@ -207,8 +212,11 @@
     \item Other aligner (\lstinline{BWA mem}).
     \item Other computational framework (\lstinline{Snakemake}).
   \end{itemize}
+  \bigskip
+
   These improvements brought the runtime back to around $40$ minutes per sample.
   \bigskip
+  \pause
 
   Parallel processing on the LUMC cluster.
   \begin{itemize}
@@ -216,6 +224,8 @@
     \item Between $90$ and $180$ minutes per batch.
     \begin{itemize}
       \item Depending on the number of batches per flowcell.
+      \pause
+      \item Around $56$ seconds per sample.
     \end{itemize}
   \end{itemize}
 \end{pframe}
@@ -256,13 +266,6 @@
     \item Florea: API adapter for the HPC cluster.
     \item Amegilla: API adapter for legacy / proprietary systems.
   \end{itemize}
-  %\bigskip
-
-  %Common framework:
-  %\begin{itemize}
-  %  \item Nginx, REST.
-  %  \item X.509 certificates.
-  %\end{itemize}
 
   \vfill
   \permfoot{\url{https://git.lumc.nl/groups/apis}}
@@ -324,6 +327,10 @@
     \item Monitor the pipeline progress.
     \item Keep track of the status (query via the API).
   \end{itemize}
+  \bigskip
+
+  Once the pipeline is finished, a status update is reported back to the
+  submitter of the pipeline run.
 \end{pframe}
 
 \subsection{Underlying infrastructure}

presentation-pics @ 49bd4b89

-Subproject commit e8f15b637cab7194573357c7a09b0efb709c7c1c
+Subproject commit 49bd4b899df12078e4c9e93e766960bb0d5bf951