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authorJustin Bedo <cu@cua0.org>2020-12-08 10:01:39 +1100
committerJustin Bedo <cu@cua0.org>2020-12-08 10:01:39 +1100
commitba248122fe57add929046f304844a7fa14b47207 (patch)
tree8646ea4190c5e5f1e0aaece5deb017f7dba026ba
parent5cf9dcf15c3e384d02b81e81cb3e2c4a1de0efa4 (diff)
add reference to bionix paper and repowehi-talk
-rw-r--r--references.bib14
-rw-r--r--slides.tex18
2 files changed, 14 insertions, 18 deletions
diff --git a/references.bib b/references.bib
index 2ec514c..3d4075f 100644
--- a/references.bib
+++ b/references.bib
@@ -561,4 +561,16 @@ title = {Supporting data for "Unifying package managers, workflow engines, and
publisher = {GigaScience Database},
year = {2020},
copyright = {Creative Commons Zero v1.0 Universal}
-} \ No newline at end of file
+}
+@article{Bed2020,
+ doi = {10.1093/gigascience/giaa121},
+ url = {https://doi.org/10.1093/gigascience/giaa121},
+ year = {2020},
+ month = nov,
+ publisher = {Oxford University Press ({OUP})},
+ volume = {9},
+ number = {11},
+ author = {Justin Bed{\H{o}} and Leon Di~Stefano and Anthony T Papenfuss},
+ title = {Unifying package managers, workflow engines, and containers: Computational reproducibility with {BioNix}},
+ journal = {{GigaScience}}
+}
diff --git a/slides.tex b/slides.tex
index 04ed327..fa94707 100644
--- a/slides.tex
+++ b/slides.tex
@@ -180,23 +180,6 @@
\end{frame}
\begin{frame}
- \frametitle{HPC execution}
- \begin{minipage}{.3\textwidth}
- \begin{overprint}
- \onslide<1>\includegraphics[width=\linewidth]{slurm}
- \onslide<2>\includegraphics[width=\linewidth]{cluster}
- \end{overprint}
- \end{minipage}
- \begin{minipage}{.68\textwidth}
- \begin{enumerate}
- \item Easy implementation due to derivation overriding pattern from Nix
- \item Call \Verb|(bionix.slurm \{ ... \}).samtools.sort| instead of \Verb|bionix.samtools.sort|
- \onslide<2>\item Easy to shift previous example to HPC execution
- \end{enumerate}
- \end{minipage}
-\end{frame}
-
-\begin{frame}
\frametitle{Stafford Fox Rare Cancer Project}
\begin{enumerate}
\item $\geq100$ WGS/WES samples totalling 20 TiB of primary data
@@ -290,6 +273,7 @@
\item BioNix provides a high degree of reproducibility
\item Obviates the need for multiple technologies (i.e., package managers and containers)
\item Workflows as function composition, simplifying specification
+ \item BioNix~\autocite{Bed2020} available at \url{https://github.com/PapenfussLab/BioNix}
\end{enumerate}
\end{frame}