From 823a2a6cd2f10710cb9ea7d5958e66da2e34bafd Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Thu, 21 Mar 2019 23:51:23 +0000
Subject: Updated with new affiliation and describing installing of software

It was a long time since the last work on these slides. So the recent
changes (and in particular the installation of software) are now
described and my affiliation is also corrected).
---
 reproducible-paper.tex | 84 ++++++++++++++++++++++++++------------------------
 1 file changed, 43 insertions(+), 41 deletions(-)

(limited to 'reproducible-paper.tex')

diff --git a/reproducible-paper.tex b/reproducible-paper.tex
index c4cf260..b188711 100644
--- a/reproducible-paper.tex
+++ b/reproducible-paper.tex
@@ -21,20 +21,13 @@
 
 
 %% 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}\\
+\author{Mohammad Akhlaghi\\\vspace{2mm}\footnotesize Instituto de
+  Astrof\'isica de Canarias ({\scriptsize IAC}),\\Tenerife, Spain
 }
 
 
 %% Set the date and insitutional logos.
-\date{}
+\date{\includegraphics[width=2cm]{img/iac.png}}
 
 
 
@@ -62,7 +55,7 @@
         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.
+      exactly describe 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
@@ -83,7 +76,7 @@
 
   \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
+    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}}).
 
@@ -93,7 +86,7 @@
 
   \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
+    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}}).
 
@@ -181,29 +174,33 @@
 
 
   \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}}):
+    The two \alert{simple} and \alert{familiar} commands below are
+    enough to exactly reproduce the results at any time.
 
     \begin{itemize}
-    \item[] \texttt{\$ ./configure{ }{ }{ }{ }{ }{ }\# To
-      define top-level local directories.}
-    \item[] \texttt{\$ make{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }\# To reproduce the analysis and paper.}
+    \item[] \texttt{\$ ./configure}
+    \item[] \texttt{\$ make}
     \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).
+    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{0.5cm} The pipeline can also \alert{download input} data
-    from online archives (databases) if not locally available (as in
+    \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}}
-    and
-    \textcolor{blue}{\href{https://gitlab.com/makhlaghi/reproducible-paper}{template}}).
+    or
+    \textcolor{blue}{\small\href{https://gitlab.com/makhlaghi/reproducible-paper-output/raw/master/paper.pdf}{template's
+        output}}).
 
-    \vspace{0.5cm} After publication, \alert{readers} can
+    \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
@@ -215,19 +212,19 @@
 
   \begin{frame}{Publication of the pipeline}
 
-    A reproduction pipeline like this will have the following
+    A reproducible project using this template will have the following
     (\alert{plain text}) components:
     \begin{itemize}
     \item Makefiles.
     \item \LaTeX{} source files.
-    \item Configuration files.
+    \item Configuration files for software used in analysis.
     \item Scripts/programming files (e.g., Python, Shell, AWK, C).
     \end{itemize}
-    The \alert{volume} of the reproduction pipeline will thus be
+    The \alert{volume} of the project's source will thus be
     \alert{negligible} compared to a single figure in a paper
-    (especially after compression).
+    (usually $\sim100$ kilo-bytes).
 
-    \vspace{1.5cm} The reproduction pipeline can be \alert{published} in
+    \vspace{1cm} 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
@@ -244,16 +241,21 @@
 
 
   \begin{frame}
-    A template/blank pipeline has been written and is ready to use,
-    with implementation guidelines and practical tips and
-    recommendations (see the template's
+    A template/blank pipeline has been written and is ready to use
+    (see the template's
     \textcolor{blue}{\href{https://gitlab.com/makhlaghi/reproducible-paper-output/raw/master/paper.pdf}{output}}):
 
-    \textcolor{blue}{\url{https://gitlab.com/makhlaghi/reproducible-paper}}
+    \textcolor{blue}{\footnotesize\url{https://gitlab.com/makhlaghi/reproducible-paper}}
+
+    \vspace{1.5cm} For a technical description of the template's
+    implementation, as well as a checklist to customize it, and tips
+    on good practices, please see this page:
+
+    \textcolor{blue}{\footnotesize\url{https://gitlab.com/makhlaghi/reproducible-paper/blob/pipeline/README-hacking.md}}
 
-    \vspace{2.5cm}
-    Please see this page for more:
+    \vspace{1.5cm} For more on the necessity of reproducible research,
+    please see:
 
-    \textcolor{blue}{\url{http://akhlaghi.org/reproducible-science.html}}
+    \textcolor{blue}{\footnotesize\url{http://akhlaghi.org/reproducible-science.html}}
   \end{frame}
 \end{document}
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