From 1f063ee8276a5653ec59939d79f1a999bf7c529d Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Tue, 13 Mar 2018 11:45:40 +0100
Subject: Renamed main file to reproducible-paper.tex

The name of the repository and the various links to it are
`reproducibile-paper', so its better that the slides also have a
similar name.
---
 reproducible-paper.tex | 258 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 258 insertions(+)
 create mode 100644 reproducible-paper.tex

(limited to 'reproducible-paper.tex')

diff --git a/reproducible-paper.tex b/reproducible-paper.tex
new file mode 100644
index 0000000..d9ce898
--- /dev/null
+++ b/reproducible-paper.tex
@@ -0,0 +1,258 @@
+\documentclass[9pt]{beamer}
+
+
+%% Beamer settings.
+\setbeamertemplate{footline}[frame number]
+
+
+%% Packages to import.
+\usepackage{tcolorbox}          %For a color-box.
+\usepackage{textcomp}           %For a copyright sign.
+
+
+%% To simplify arXiv links
+\newcommand{\arxivlink}[1]{{\footnotesize
+  (\textcolor{blue}{\href{https://arxiv.org/abs/#1}{arXiv:#1}})}}
+
+
+
+%% Set the title
+\title{Reproducible scientific research in the era of big data}
+
+
+%% Set the author
+\author{Mohammad Akhlaghi\\\vspace{2mm}\footnotesize Centre de
+  Recherche Astrophysique de Lyon({\scriptsize CRAL}),\\Universit\'e de
+  Lyon, France.\\
+  \vspace{1.5cm}
+  \includegraphics[width=3.5cm]{img/muse.png}\\
+  \includegraphics[width=1.4cm]{img/cral.png}
+  \includegraphics[width=1.9cm]{img/univ-lyon.png}
+  \includegraphics[width=1cm]{img/cnrs.png}
+  \includegraphics[width=1cm]{img/erc.png}\\
+}
+
+
+%% Set the date and insitutional logos.
+\date{}
+
+
+
+
+
+
+
+
+
+
+\begin{document}
+
+  \begin{frame}
+    \titlepage
+  \end{frame}
+
+
+  \begin{frame}{Necessity of (exactly) reproducible research}
+    \begin{itemize}
+      \setlength\itemsep{0.3cm}
+    \item To be considered \alert{scientific}, any result has to be
+      reproducible.
+    \item The tsunami of data, fast internet, and high processing
+      power have made it very easy to \alert{promptly arrive at a
+        result}.
+    \item But these factors have also greatly increased the
+      \alert{complexity} of an analysis. Making it impossible to
+      exactly descibe all steps in a published paper.
+    \item Most scientific papers thus ignore the ``details'' (as they
+      interpret it).
+    \item But due to the complexity, even a small deviation from the
+      exact result, can be due to many different parts of the
+      analysis. Hence, its \alert{critical to exactly reproduce} a
+      result.
+     \item The software(s) used, configuration file(s), the order of
+       steps taken, along with the input data are necessary for
+       reproducibility.
+     \item \alert{A solution} is proposed here, which if adopted from
+       the start, can greatly \alert{simplify a scientific research
+         project} and \alert{allow full/exact reproducibility} once it
+       is published.
+    \end{itemize}
+  \end{frame}
+
+
+
+  \begin{frame}{Values in final report/paper}
+    All necessary analysis/processing \alert{input} and \alert{output}
+    values are writen into the final report as \LaTeX{} macros. Shown
+    here is a portion of the \textsf{NoiseChisel} paper and its source
+    (\textcolor{blue}{\small\href{https://arxiv.org/abs/1505.01664}{arXiv:1505.01664}}).
+
+    \vspace{1.2cm}
+    \includegraphics[width=\linewidth]{img/reproducible-latex.png}
+  \end{frame}
+
+  \begin{frame}{Values in final report/paper}
+    All necessary analysis/processing \alert{input} and \alert{output}
+    values are writen into the final report as \LaTeX{} macros. Shown
+    here is a portion of the \textsf{NoiseChisel} paper and its source
+    (\textcolor{blue}{\small\href{https://arxiv.org/abs/1505.01664}{arXiv:1505.01664}}).
+
+    \vspace{1.2cm}
+    \includegraphics[width=\linewidth]{img/reproducible-latex-highlighted.png}
+  \end{frame}
+
+
+  \begin{frame}{Values are the pipeline's final product}
+    All the \LaTeX{} macros (processing inputs and outputs) come from
+    a \alert{single file}. This file is the \alert{final product} of
+    the \emph{reproduction pipeline}.
+
+    \begin{center}
+    \includegraphics[width=0.8\linewidth]{img/reproducible-macros.png}
+    \end{center}
+  \end{frame}
+
+
+
+  \begin{frame}{Values are the pipeline's final product}
+    All the \LaTeX{} macros (processing inputs and outputs) come from
+    a \alert{single file}. This file is the \alert{final product} of
+    the \emph{reproduction pipeline}.
+
+    \begin{center}
+    \includegraphics[width=0.8\linewidth]{img/reproducible-macros-highlighted.png}
+    \end{center}
+  \end{frame}
+
+
+  \begin{frame}{Values written during analysis}
+    Various steps of the analysis pipeline write the macro values as
+    soon as they are calculated internally.
+
+    \begin{center}
+    \includegraphics[width=0.8\linewidth]{img/reproducible-write-macro.png}
+    \end{center}
+  \end{frame}
+
+
+  \begin{frame}{Values written during analysis}
+    Various steps of the analysis pipeline write the macro values as
+    soon as they are calculated internally.
+
+    \begin{center}
+    \includegraphics[width=0.8\linewidth]{img/reproducible-write-macro-highlight.png}
+    \end{center}
+  \end{frame}
+
+
+  \begin{frame}{Reproducible science: Pipeline is managed through a Makefile}
+    \small
+    \begin{columns}
+      \column{5.5cm}
+
+      The whole pipeline is managed by Makefiles (example from
+      \textcolor{blue}{\small\href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}}):
+
+      \begin{itemize}
+        \setlength\itemsep{0.2cm}
+      \item Unlike a script which always starts from the top, a
+        Makefile \alert{starts from the end} and steps that don't
+        change will be left untouched (not remade).
+      \item A single \emph{rule} can \alert{manage any number of
+        files}. See the examples here where \textsf{NoiseChisel} and
+        \textsf{MakeCatalog} are run separately on \alert{$\sim20$
+          files} (different filters/fields) with a single rule.
+      \item Make can identify independent steps internally and do them
+        in \alert{parallel}.
+      \item Make was \alert{designed for complex problems} with
+        thousands of files (all major Unix-like components), so it is
+        highly evolved and efficient.
+      \item Make is a very \alert{simple} and \alert{small} language,
+        thus easy to learn with great and free documentation (for
+        example
+        \textcolor{blue}{\href{https://www.gnu.org/software/make/manual/}{GNU
+            Make's manual}}, usable to learn all implementations).
+      \end{itemize}
+
+      \column{5.5cm}
+      \includegraphics[width=\linewidth]{img/reproducible-makefile.png}
+    \end{columns}
+  \end{frame}
+
+
+  \begin{frame}{Reproducing the result and report/paper}
+    Once software dependencies are installed, the two \alert{simple}
+    and \alert{familiar} commands below are enough to exactly
+    reproduce the results at any time (as in
+    \textcolor{blue}{\small\href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}}):
+
+    \begin{itemize}
+    \item[] \texttt{\$ ./configure{ }{ }{ }{ }{ }{ }\# To
+      define top-level local directories.}
+    \item[] \texttt{\$ make{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }\# To reproduce the analysis and paper.}
+    \end{itemize}
+
+    \vspace{0.5cm} Enabling version control (e.g. \alert{Git}) will
+    make it very easy to test different ideas while not harming the
+    initial/base result (thus encouraging \alert{creativity} and
+    brainstorming during the project).
+
+    \vspace{0.5cm} The pipeline can also \alert{download input} data
+    from online archives (databases) if not locally available (as in
+    \textcolor{blue}{\small\href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}}
+    and
+    \textcolor{blue}{\href{https://gitlab.com/makhlaghi/reproduction-pipeline-template}{template}}).
+
+    \vspace{0.5cm} After publication, \alert{readers} can
+    \alert{change} the input configurations and the numbers and
+    figures of the reproduced paper will respectively change. This
+    encourages creativity and brainstorming after the project as well
+    as sharing of (the hardly gained) experiences with the whole
+    community.
+  \end{frame}
+
+
+
+  \begin{frame}{Publication of the pipeline}
+
+    A reproduction pipeline like this will have the following
+    (\alert{plain text}) components:
+    \begin{itemize}
+    \item Makefiles.
+    \item \LaTeX{} source files.
+    \item Configuration files.
+    \item Scripts/programming files (e.g., Python, Shell, AWK, C).
+    \end{itemize}
+    The \alert{volume} of the reproduction pipeline will thus be
+    \alert{negligible} compared to a single figure in a paper
+    (especially after compression).
+
+    \vspace{1.5cm} The reproduction pipeline can be \alert{published} in
+    \begin{itemize}
+    \item \alert{arXiv}: uploaded with the \TeX{} source to always
+      stay with the paper \\(for example
+      \textcolor{blue}{\small\href{https://arxiv.org/abs/1505.01664}{arXiv:1505.01664}}). The
+      file containing all macros must also be uploaded so arXiv's
+      server can easily build the \LaTeX{} source.
+    \item \alert{Zenodo}: Along with all the input datasets (many
+      Gigabytes) and software \\(for example
+      \textcolor{blue}{\small\href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}}) and given a unique DOI.
+    \end{itemize}
+
+  \end{frame}
+
+
+
+  \begin{frame}
+    A template/blank pipeline has been written and is ready to use,
+    with implementation guidelines and practical tips and
+    recommendations:
+
+    \textcolor{blue}{\url{https://gitlab.com/makhlaghi/reproducible-paper}}
+
+    \vspace{2.5cm}
+    Please see this page for more:
+
+    \textcolor{blue}{\url{http://akhlaghi.org/reproducible-science.html}}
+  \end{frame}
+\end{document}
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