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.
---
 reproduction-pipeline.tex | 258 ----------------------------------------------
 1 file changed, 258 deletions(-)
 delete mode 100644 reproduction-pipeline.tex

(limited to 'reproduction-pipeline.tex')

diff --git a/reproduction-pipeline.tex b/reproduction-pipeline.tex
deleted file mode 100644
index d9ce898..0000000
--- a/reproduction-pipeline.tex
+++ /dev/null
@@ -1,258 +0,0 @@
-\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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