\documentclass[aspectratio=169]{beamer}

\usepackage{microtype}
\usepackage{tikz}
\usetikzlibrary{fit}
\usepackage[style=verbose-ibid,url=false,natbib=true]{biblatex}
\addbibresource{references.bib}
\renewcommand*{\footnotesize}{\Tiny}
\setlength{\footnotesep}{3pt}

\definecolor{bngreen}{HTML}{3c8e64}
\definecolor{bnorange}{HTML}{e08919}
%\setbeamercolor*{structure}{bg=white,fg=bngreen}
\usecolortheme[named=bngreen]{structure}
\setbeamertemplate{navigation symbols}{}
\setbeamertemplate{headline}{\hfill\includegraphics[width=.7cm]{logo-running}\hspace{0.1cm}\vspace{-.7cm}}

\author{Justin Bed\H{o}\\WEHI}
\title{\includegraphics[width=.7\linewidth]{logo}\\functional, reproducible bioinformatics workflows}
\date{November 10, 2020}

\begin{document}

{
  \setbeamertemplate{headline}{}
  \begin{frame}
    \maketitle
  \end{frame}
}

\begin{frame}
  \frametitle{Core problems}
  \begin{enumerate}
    \item \emph{Managing software versions and dependencies}.
      \begin{itemize}
        \item Conda
        \item BioConda~\autocite{Grning2018}
        \item apt-get
      \end{itemize}

    \item \emph{Managing computational environments}.
      \begin{itemize}
        \item Docker
        \item Singularity
        \item \emph{virtual machines}
      \end{itemize}

    \item \emph{Managing workflows}.
      \begin{itemize}
        \item Toil~\autocite{toil}
        \item SnakeMake~\autocite{Koster2012}
        \item NextFlow~\autocite{di_tommaso_nextflow_2017}
      \end{itemize}
  \end{enumerate}
\end{frame}

\begin{frame}
  \begin{center}
    \begin{tikzpicture}[->,>=stealth,shorten >=1pt,auto,node distance=2cm,thick]
      \node (a) {align};
      \node (s) [below of=a] {sort};
      \node (c) [below of=s] {calling};

      \path (a) edge node {} (s);
      \path (s) edge node {} (c);

      \pause

      \node (input) [above of=a] {input};
      \path (input) edge node {} (a);
      \node (ref) [right of=a] {reference};
      \path (ref) edge node {} (a);
      \node (db) [right of=c] {dbNSFP};
      \path (db) edge node {} (c);

      \pause

      \node (bwa) [left of=a] {BWA};
      \path (bwa) edge node {} (a);
      \node (samtools) [left of=s] {samtools};
      \path (samtools) edge node {} (s);
      \node (platypus) [left of=c] {platypus};
      \path (platypus) edge node {} (c);

      \pause

      \node (glib) [left of=samtools] {glibc,$\cdots$};
      \node (python) [left of=platypus] {python};
      \path (glib) edge node {} (bwa);
      \path (glib) edge node {} (samtools);
      \path (python) edge node {} (platypus);
      \path (glib) edge node {} (python);

      \pause

      \node[draw=bngreen, fit=(bwa) (samtools) (platypus) (glib) (python),label=containers](cont){};
      \node[draw=bnorange, fit=(ref) (db),label=tarball](tar){};
    \end{tikzpicture}
  \end{center}
\end{frame}

\begin{frame}
  \frametitle{BioNix contributions}
  \begin{enumerate}
    \item Builds on Nix, a robust functional package manager
    \item Manages both software and workflows within the one system
    \item Implicitly specifies its entire computational environment
    \item Simple, purely functional domain-specific language, simplifying specifying workflows
      to function composition
    \item Typing to reduce errors~\autocite{Bed2019}
  \end{enumerate}
\end{frame}  

\end{document}
