From ddd1690dacaecdfa9bfe982935a1365c27b7491b Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Thu, 20 Jun 2019 02:18:40 +0100
Subject: Reordered slides describing template

After the previous experience of presenting the slides in Ghent, they
are reordered to be more clear and cause less confusion. In
particular, until this commit, I was describing the software build
steps in the end, so the audience mainly forgot about the analysis
steps and thought this template is just something like Docker or a
virtual machine.

With this commit, the steps are described in the same step that occur:
first how the software are built, then how the input data are
downloaded and finally how the software are run on the data and the
values are written into the paper.
---
 reproducible-paper.tex | 530 +++++++++++++++++++++++++++++--------------------
 1 file changed, 310 insertions(+), 220 deletions(-)

(limited to 'reproducible-paper.tex')

diff --git a/reproducible-paper.tex b/reproducible-paper.tex
index d9f7d52..b0603de 100644
--- a/reproducible-paper.tex
+++ b/reproducible-paper.tex
@@ -1,4 +1,4 @@
-\documentclass[9pt]{beamer}
+\documentclass[9pt,usenames,dvipsnames]{beamer}
 
 %% Beamer settings.
 %\setbeamertemplate{footline}[frame number]
@@ -24,7 +24,7 @@
 }
 
 %% Set the date and insitutional logos.
-\date{\scriptsize \href{https://www.astro.rug.nl/~sundial/MidtermMeeting.html}{SUNDIAL Midterm meeting}, June 5th, 2019\\ Ghent, Belgium}
+\date{\scriptsize \href{https://eas.unige.ch/EWASS2019/session.jsp?id=SS34}{EWASS 2019, Special Session 34}, June 25th, 2019\\ Lyon, France}
 
 %% For a wider writing width.
 \newcommand\Wider[2][3em]{%
@@ -93,26 +93,6 @@
 
 
 
-%  \begin{frame}{Necessity of (exactly) reproducible research}
-%    \begin{itemize}
-%      \setlength\itemsep{0.7cm}
-%    \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 describe all steps in a traditional published paper.
-%    \item Most scientific papers thus \alert{ignore some ``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.
-%    \end{itemize}
-%  \end{frame}
-
   \begin{frame}{Reproducibility crisis in the sciences/astronomy}
     \begin{tcolorbox}[title=Snakes on a Spaceship -- An Overview of Python in Heliophysics]
       \small ``...\alert{inadequate analysis descriptions} and loss of
@@ -145,8 +125,13 @@
 
 
 
+  %% Initially in full opacity:
+  \newcommand{\allopacity}{1}
+
+
 
-  \newcommand{\nodeopacity}{1}
+
+  %% Step-by-step slides.
   \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
   \newcommand{\paperinit}{}
   \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
@@ -162,6 +147,19 @@
   \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
   \newcommand{\confenv}{}
   \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
+  \begin{frame}{Example: Matplotlib (a Python visualization library) build dependencies}
+    \Wider[5em]{
+      \vspace{5mm}
+      \includegraphics[width=\linewidth]{img/matplotlib.pdf}
+
+      \vspace{7mm}\tiny From ``Attributing and Referencing (Research)
+      Software: Best Practices and Outlook from Inria'' (Alliez et
+      al. 2019,
+      \textcolor{blue}{\href{https://hal.archives-ouvertes.fr/hal-02135891}{hal-02135891}})
+    }
+  \end{frame}
+  \newcommand{\containers}{}
+  \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
   \newcommand{\db}{}
   \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
   \newcommand{\calib}{}
@@ -189,9 +187,11 @@
   \newcommand{\paperfinal}{}
   \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
 
-  %% Don't show the happy scientist any more.
-  \let\paperfinal\undefined
+  %% Don't show the happy scientist or the existing containers box.
   \let\paperinit\undefined
+  \let\allopacity\undefined
+  \let\paperfinal\undefined
+  \let\containers\undefined
 
 
 
@@ -208,10 +208,10 @@
 
     \vspace{0.2cm}
     \begin{tcolorbox}
-      \small Data analysis [...] is a human behaviour. Researchers
-      who hunt hard enough will turn up a result that fits
-      statistical criteria, but their \alert{discovery} will
-      probably be a \alert{false positive}.
+      \small Data analysis [...] is a \alert{human
+        behaviour}. Researchers who hunt hard enough will turn up a
+      result that fits statistical criteria, but their
+      \alert{discovery} will probably be a \alert{false positive}.
 
       \hfill Five ways to fix statistics, Nature, 551, Nov 2017.
     \end{tcolorbox}
@@ -245,111 +245,10 @@
 
 
 
-  \renewcommand{\nodeopacity}{0.3}
-  \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
-
-
-
-
-
-  \begin{frame}{Values in final report/paper}
-    All necessary analysis/processing \alert{input} and \alert{output}
-    values are written 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 written 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 come from a single file}
-    All the \LaTeX{} macros (processing inputs and outputs) come from
-    a \alert{single file}. This file is the \alert{final product} of
-    the analysis steps.
-
-    \begin{center}
-      \includegraphics[width=0.8\linewidth]{img/reproducible-macros.png}
-    \end{center}
-  \end{frame}
-
-
-
-  \begin{frame}{Values come from a single file}
-    All the \LaTeX{} macros (processing inputs and outputs) come from
-    a \alert{single file}. This file is the \alert{final product} of
-    the analysis steps.
-
-    \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 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 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: Template is managed through a Makefile}
-    \small
-    \begin{columns}
-      \column{5.5cm}
-
-      All steps (downloading and analysis) 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}
+  \newcommand{\focusonpackages}{}
+  \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
+  \let\focusonpackages\undefined
 
 
 
@@ -368,17 +267,15 @@
         reproducibility.
       \end{tcolorbox}
 
+      \vspace{1cm}
+
       \begin{itemize}
         \setlength\itemsep{0.4cm}
       \item \emph{Containers} or \emph{Virtual Machines} are a
-        \alert{binary black box}: just contain the environment, not
-        how to set it up, or its history. They are also an overhead.
+        \alert{binary black box}.
 
       \item This template \alert{installs fixed versions} of all
-        necessary research software and their dependencies, down to
-        the command-line shell, C compiler, POSIX tools and Python
-        interpreter. It just avoids very low-level OS elements like
-        the kernel or linker.
+        necessary research software and their dependencies.
 
       \item Installs similar environment on \alert{GNU/Linux}, or
         \alert{macOS} systems.
@@ -388,7 +285,7 @@
       \end{itemize}
 
       \column{5.5cm}
-      \includegraphics[width=\linewidth]{img/software.png}
+      \includegraphics[width=\linewidth]{img/version.png}
     \end{columns}
   \end{frame}
 
@@ -409,17 +306,15 @@
         reproducibility.
       \end{tcolorbox}
 
+      \vspace{1cm}
+
       \begin{itemize}
         \setlength\itemsep{0.4cm}
       \item \emph{Containers} or \emph{Virtual Machines} are a
-        \alert{binary black box}: just contain the environment, not
-        how to set it up, or its history. They are also an overhead.
+        \alert{binary black box}.
 
       \item This template \alert{installs fixed versions} of all
-        necessary research software and their dependencies, down to
-        the command-line shell, C compiler, POSIX tools and Python
-        interpreter. It just avoids very low-level OS elements like
-        the kernel or linker.
+        necessary research software and their dependencies.
 
       \item Installs similar environment on \alert{GNU/Linux}, or
         \alert{macOS} systems.
@@ -429,61 +324,105 @@
       \end{itemize}
 
       \column{5.5cm}
-      \includegraphics[width=\linewidth]{img/software-highlighted.png}
+      \includegraphics[width=\linewidth]{img/version-highlighted.png}
     \end{columns}
   \end{frame}
 
 
-  \newcommand{\redbdir}{\textcolor{green!80!black}{/TEMPLATE/BUILD/DIRECTORY/software/installed/lib}}
-  \begin{frame}{Dependencies are cleanly managed}
 
-    \begin{itemize}
-    \item All the software are configured and built to use the
-      \alert{template's own builds}: indepenent of host system
-      (\textcolor{green!80!black}{in green}).
-    \item Template even builds a fixed GNU C Compiler (\alert{GCC}).
-    \item Only extremely low-level dependencies (for example C library
-      and Kernel) not built.
-      \begin{itemize}
-      \item GNU C library will also be added later (\alert{in red}).
-      \end{itemize}
-    \end{itemize}
 
+
+  \begin{frame}{Controlled environment and build instructions}
+    \small
+    \begin{columns}
+      \column{5.5cm}
+      \includegraphics[width=\linewidth]{img/env.png}
+      \column{5.5cm}
+      \includegraphics[width=\linewidth]{img/build.png}
+    \end{columns}
+  \end{frame}
+
+  \begin{frame}{Controlled environment and build instructions}
+    \small
+    \begin{columns}
+      \column{5.5cm}
+      \includegraphics[width=\linewidth]{img/env-highlighted.png}
+      \column{5.5cm}
+      \includegraphics[width=\linewidth]{img/build-highlighted.png}
+    \end{columns}
+  \end{frame}
+
+
+
+
+
+  \newcommand{\redbdir}{\textcolor{green!80!black}{/PROJECT/PATH/software/installed/lib}}
+  \begin{frame}{All dependencies (except C library and linker) built in project\\
+                Linked libraries to NoiseChisel executable on GNU/Linux}
     \vspace{0.5cm}
     \tiny\texttt{
       \$ ldd .local/bin/astnoisechisel\\
-      \hspace{0.5cm}libgit2.so.26 => \redbdir/libgit2.so.26 (0x00007febb5232000)\\
-      \hspace{0.5cm}libtiff.so.5 => \redbdir/libtiff.so.5 (0x00007febb51b8000)\\
-      \hspace{0.5cm}liblzma.so.5 => \redbdir/liblzma.so.5 (0x00007febb5190000)\\
-      \hspace{0.5cm}libjpeg.so.9 => \redbdir/libjpeg.so.9 (0x00007febb5153000)\\
-      \hspace{0.5cm}z.so.1 => \redbdir/libz.so.1 (0x00007febb5136000)\\
-      \hspace{0.5cm}wcs.so.6 => \redbdir/libwcs.so.6 (0x00007febb4fcc000)\\
-      \hspace{0.5cm}cfitsio.so.8 => \redbdir/libcfitsio.so.8 (0x00007febb4caf000)\\
-      \hspace{0.5cm}curl.so.4 => \redbdir/libcurl.so.4 (0x00007febb4c35000)\\
-      \hspace{0.5cm}ssl.so.1.1 => \redbdir/libssl.so.1.1 (0x00007febb4b9b000)\\
-      \hspace{0.5cm}crypto.so.1.1 => \redbdir/libcrypto.so.1.1 (0x00007febb48b5000)\\
-      \hspace{0.5cm}gsl.so.23 => \redbdir/libgsl.so.23 (0x00007febb4626000)\\
-      \hspace{0.5cm}gslcblas.so.0 => \redbdir/libgslcblas.so.0 (0x00007febb45e2000)\\
-      \hspace{0.5cm}gnuastro.so.8 => \redbdir/libgnuastro.so.8 (0x00007febb419e000)\\
-      \hspace{0.5cm}bz2.so.1.0 => \redbdir/libbz2.so.1.0 (0x00007febb3e20000)\\
-      \hspace{0.5cm}\alert{m.so.6} => /usr/lib/libm.so.6 (0x00007febb4025000)\\
-      \hspace{0.5cm}\alert{pthread.so.0} => /usr/lib/libpthread.so.0 (0x00007febb4004000)\\
-      \hspace{0.5cm}\alert{c.so.6} => /usr/lib/libc.so.6 (0x00007febb3e3f000)\\
-      \hspace{0.5cm}rt.so.1 => /usr/lib/librt.so.1 (0x00007febb3e35000)\\
-      \hspace{0.5cm}dl.so.2 => /usr/lib/libdl.so.2 (0x00007febb3e1b000)\\
-      \hspace{0.5cm}linux-vdso.so.1 (0x00007ffcf2497000)\\
-      \hspace{0.5cm}/lib64/ld-linux-x86-64.so.2 => /usr/lib64/ld-linux-x86-64.so.2 (0x00007febb53c6000)
+      \hspace{0.5cm}linux-vdso.so.1 (0x00007fffdcbf7000)\\
+      \hspace{0.5cm}libgnuastro.so.7 => \redbdir/libgnuastro.so.7 (0x00007f6745f39000)\\
+      \hspace{0.5cm}libgit2.so.26 => \redbdir/libgit2.so.26 (0x00007f6745df1000)\\
+      \hspace{0.5cm}libtiff.so.5 => \redbdir/libtiff.so.5 (0x00007f6745d77000)\\
+      \hspace{0.5cm}liblzma.so.5 => \redbdir/liblzma.so.5 (0x00007f6745d4f000)\\
+      \hspace{0.5cm}libjpeg.so.9 => \redbdir/libjpeg.so.9 (0x00007f6745d12000)\\
+      \hspace{0.5cm}libwcs.so.6 => \redbdir/libwcs.so.6 (0x00007f6745ba8000)\\
+      \hspace{0.5cm}libcfitsio.so.8 => \redbdir/libcfitsio.so.8 (0x00007f674588b000)\\
+      \hspace{0.5cm}libcurl.so.4 => \redbdir/libcurl.so.4 (0x00007f6745811000)\\
+      \hspace{0.5cm}libssl.so.1.1 => \redbdir/libssl.so.1.1 (0x00007f6745777000)\\
+      \hspace{0.5cm}libcrypto.so.1.1 => \redbdir/libcrypto.so.1.1 (0x00007f6745491000)\\
+      \hspace{0.5cm}libz.so.1 => \redbdir/libz.so.1 (0x00007f6745474000)\\
+      \hspace{0.5cm}libgsl.so.23 => \redbdir/libgsl.so.23 (0x00007f67451e3000)\\
+      \hspace{0.5cm}libgslcblas.so.0 => \redbdir/libgslcblas.so.0 (0x00007f67451a1000)\\
+      \hspace{0.5cm}libbz2.so.1.0 => \redbdir/libbz2.so.1.0 (0x00007f6744e23000)\\
+      \hspace{0.5cm}\alert{libpthread.so.0} => /usr/lib/libpthread.so.0 (0x00007f6745006000)\\
+      \hspace{0.5cm}\alert{libm.so.6} => /usr/lib/libm.so.6 (0x00007f6745027000)\\
+      \hspace{0.5cm}\alert{libc.so.6} => /usr/lib/libc.so.6 (0x00007f6744e43000)\\
+      \hspace{0.5cm}libdl.so.2 => /usr/lib/libdl.so.2 (0x00007f6744e1e000)\\
+      \hspace{0.5cm}librt.so.1 => /usr/lib/librt.so.1 (0x00007f6744e36000)\\
+      \hspace{0.5cm}/lib64/ld-linux-x86-64.so.2 => /usr/lib64/ld-linux-x86-64.so.2 (0x00007f67463c7000)
+   }
+  \end{frame}
+
+
+  \begin{frame}{All dependencies (except C library and linker) built in project\\
+                Linked libraries to NoiseChisel executable on macOS}
+    \vspace{0.5cm}
+    \tiny\texttt{
+      \$ otool -L .local/bin/astnoisechisel\\
+      \hspace{0.5cm}.local/bin/astnoisechisel:\\
+      \hspace{0.5cm}\redbdir/libgnuastro.7.dylib (compatibility ver 8.0.0, current ver 8.0.0)\\
+      \hspace{0.5cm}\redbdir/libgit2.26.dylib (compatibility ver 26.0.0, current ver 0.26.0)\\
+      \hspace{0.5cm}\redbdir/libtiff.5.dylib (compatibility ver 10.0.0, current ver 10.0.0)\\
+      \hspace{0.5cm}\redbdir/liblzma.5.dylib (compatibility ver 8.0.0, current ver 8.4.0)\\
+      \hspace{0.5cm}\redbdir/libjpeg.9.dylib (compatibility ver 12.0.0, current ver 12.0.0)\\
+      \hspace{0.5cm}\redbdir/libwcs.6.2.dylib (compatibility ver 6.0.0, current ver 6.2.0)\\
+      \hspace{0.5cm}\redbdir/libcfitsio.8.dylib (compatibility ver 8.0.0, current ver 8.3.47)\\
+      \hspace{0.5cm}\redbdir/libcurl.4.dylib (compatibility ver 10.0.0, current ver 10.0.0)\\
+      \hspace{0.5cm}\redbdir/libssl.1.1.dylib (compatibility ver 1.1.0, current ver 1.1.0)\\
+      \hspace{0.5cm}\redbdir/libcrypto.1.1.dylib (compatibility ver 1.1.0, current ver 1.1.0)\\
+      \hspace{0.5cm}\redbdir/libz.1.dylib (compatibility ver 1.0.0, current ver 1.2.11)\\
+      \hspace{0.5cm}\redbdir/libgsl.23.dylib (compatibility ver 25.0.0, current ver 25.0.0)\\
+      \hspace{0.5cm}\redbdir/libgslcblas.0.dylib (compatibility ver 1.0.0, current ver 1.0.0)\\
+      \hspace{0.5cm}/usr/lib/libSystem.B.dylib (compatibility ver 1.0.0, current ver 1252.50.4)
    }
   \end{frame}
 
 
 
 
+
   \begin{frame}{Advantages of this build system}
     \begin{columns}
       \column{7cm}
       \begin{itemize}
-        \setlength\itemsep{1cm}
+        \setlength\itemsep{0.7cm}
+      \item Project runs in fixed/controlled environment: custom build
+        of \alert{Bash}, GNU Coreutils (\alert{\texttt{ls}},
+        \alert{\texttt{cp}}, \alert{\texttt{mkdir}} and etc),
+        \alert{AWK}, or \alert{SED}, \alert{\LaTeX}, etc.
       \item No need for \alert{root}/administrator \alert{permissions}
         (on servers or super computers).
       \item Whole system is built \alert{automatically} on any
@@ -511,44 +450,195 @@
 
 
 
-%  \begin{frame}{Reproducing the result and report/paper}
-%    The two \alert{simple} and \alert{familiar} commands below are
-%    enough to exactly reproduce the results at any time.
-%
-%    \begin{itemize}
-%    \item[] \texttt{\$ ./configure}
-%    \item[] \texttt{\$ make}
-%    \end{itemize}
-%
-%    With \texttt{./configure}, you specify the local directories to
-%    use. All necessary \alert{software} are then \alert{downloaded}
-%    and installed there (independent of your OS or other projects).
-%
-%    \vspace{0.3cm} With \texttt{make}, input \alert{data} from online
-%    archives (databases) are \alert{downloaded}, if not locally
-%    available, the processing is done, and the \LaTeX{} paper is built
-%    as a PDF (e.g., see
-%    \textcolor{blue}{\small\href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}}
-%    or
-%    \textcolor{blue}{\small\href{https://gitlab.com/makhlaghi/reproducible-paper-output/raw/master/paper.pdf}{template's
-%        output}}).
-%
-%   \vspace{0.3cm} Enabling version control (e.g., with \alert{Git})
-%    encourages testing different ideas while not harming the
-%    initial/base result (thus encouraging \alert{creativity} and
-%    brainstorming during the project).
-%
-%    \vspace{0.3cm} 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}
-
-
-
-  \renewcommand{\nodeopacity}{1}
+
+
+
+
+
+  %% Hardware/data
+  \newcommand{\focusonhardware}{}
+  \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
+  \let\focusonhardware\undefined
+
+  \begin{frame}{Input data source and integrity is documented and checked}
+    \small
+    \begin{columns}
+      \column{5.5cm}
+      Stored information about each input file:
+      \begin{itemize}
+      \item \alert{PID} (where available).
+      \item Download \alert{URL}.
+      \item \alert{MD5}-sum to check integrity.
+      \end{itemize}
+
+      \vspace{1cm} All inputs are downloaded from the given PID/URL.
+
+      \vspace{1cm} Their MD5-sum is checked to make sure the download
+      was done properly or the file is the same (hasn't changed on the
+      server/source).
+
+      \column{5.5cm}
+      \includegraphics[width=\linewidth]{img/inputs.png}
+    \end{columns}
+  \end{frame}
+
+  \begin{frame}{Input data source and integrity is documented and checked}
+    \small
+    \begin{columns}
+      \column{5.5cm}
+      Stored information about each input file:
+      \begin{itemize}
+      \item \alert{PID} (where available).
+      \item Download \alert{URL}.
+      \item \alert{MD5}-sum to check integrity.
+      \end{itemize}
+
+      \vspace{1cm} All inputs are downloaded from the given PID/URL.
+
+      \vspace{1cm} Their MD5-sum is checked to make sure the download
+      was done properly or the file is the same (hasn't changed on the
+      server/source).
+
+      \column{5.5cm}
+      \includegraphics[width=\linewidth]{img/inputs-highlighted.png}
+    \end{columns}
+  \end{frame}
+
+
+
+
+
+
+
+
+
+
+  %% Analysis
+  \newcommand{\focusonrun}{}
+  \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
+  \let\focusonrun\undefined
+
+
+
+
+
+  \begin{frame}{Reproducible science: Template is managed through a Makefile}
+    \small
+    \begin{columns}
+      \column{5.5cm}
+
+      All steps (downloading and analysis) is managed by Makefiles
+      (example from
+      \textcolor{blue}{\small\href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}}):
+
+      \begin{itemize}
+        \setlength\itemsep{0.3cm}
+      \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}.
+      \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}}).
+      \end{itemize}
+
+      \column{5.5cm}
+      \includegraphics[width=\linewidth]{img/reproducible-makefile.png}
+    \end{columns}
+  \end{frame}
+
+
+
+
+
+
+
+  \newcommand{\focusonpaper}{}
+  \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
+  \let\focusonpaper\undefined
+
+  \begin{frame}{Values in final report/paper}
+    All necessary analysis/processing \alert{input} and \alert{output}
+    values are written 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 written 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 come from a single file}
+    All the \LaTeX{} macros (processing inputs and outputs) come from
+    a \alert{single file}. This file is the \alert{final product} of
+    the analysis steps.
+
+    \begin{center}
+      \includegraphics[width=0.8\linewidth]{img/reproducible-macros.png}
+    \end{center}
+  \end{frame}
+
+
+
+  \begin{frame}{Values come from a single file}
+    All the \LaTeX{} macros (processing inputs and outputs) come from
+    a \alert{single file}. This file is the \alert{final product} of
+    the analysis steps.
+
+    \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 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 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}
+
+
+
+
+
+
+
+
+
+
+  \newcommand{\allopacity}{1}
   \begin{frame}{Everything in plain text (machine and human readable)}
     \include{tex/project-graph} \end{frame}
   \newcommand{\gitlogo}{}
-- 
cgit v1.2.1

