Updated and slightly modernized slides prior to the RDA Webinar

Several figures were added to highlight the major points and add
better examples.

10 files changed, 154 insertions, 72 deletions

diff --git a/img/firstpage-190911230-highlighted.png b/img/firstpage-190911230-highlighted.png
new file mode 100644
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+++ b/img/firstpage-190911230-highlighted.png
diff --git a/img/firstpage-190911230.png b/img/firstpage-190911230.png
new file mode 100644
index 0000000..ed16f38
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+++ b/img/firstpage-190911230.png
diff --git a/img/firstpage-191101430-highlighted.png b/img/firstpage-191101430-highlighted.png
new file mode 100644
index 0000000..e700e8e
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+++ b/img/firstpage-191101430-highlighted.png
diff --git a/img/firstpage-191101430.png b/img/firstpage-191101430.png
new file mode 100644
index 0000000..abadde2
--- /dev/null
+++ b/img/firstpage-191101430.png
diff --git a/img/inputs-highlighted.png b/img/inputs-highlighted.png
index f2a24f4..f1f6b9b 100644
--- a/img/inputs-highlighted.png
+++ b/img/inputs-highlighted.png
diff --git a/img/inputs.png b/img/inputs.png
index 9ecbbf5..8651c10 100644
--- a/img/inputs.png
+++ b/img/inputs.png
diff --git a/img/m51-amateur.jpg b/img/m51-amateur.jpg
new file mode 100644
index 0000000..46bb2fe
--- /dev/null
+++ b/img/m51-amateur.jpg
diff --git a/img/rda-europe.png b/img/rda-europe.png
new file mode 100644
index 0000000..d6e0f9c
--- /dev/null
+++ b/img/rda-europe.png
diff --git a/img/reproducibility-crisis.jpg b/img/reproducibility-crisis.jpg
new file mode 100644
index 0000000..362576a
--- /dev/null
+++ b/img/reproducibility-crisis.jpg
diff --git a/reproducible-paper.tex b/reproducible-paper.tex
index 1820456..e85dad7 100644
--- a/reproducible-paper.tex
+++ b/reproducible-paper.tex
@@ -30,10 +30,9 @@
   \includegraphics[width=1.5cm]{img/iac.png}
   \raisebox{0.13\height}{\includegraphics[width=1cm]{img/eu-regional.png}}
   \raisebox{+1.3\height}{\includegraphics[width=1.4cm]{img/ull.png}}\\
-  \raisebox{+0.2\height}{\includegraphics[width=2cm]{img/gobierno-canarias.png}}
-  \includegraphics[width=1.4cm]{img/rda.png}
-  { }\raisebox{+0.3\height}{\includegraphics[width=2cm]{img/ministerio-ciencia.png}}\\
-  \vspace{4mm}
+  \raisebox{+1.2\height}{\includegraphics[width=2cm]{img/ministerio-ciencia.png}}
+  \raisebox{+0.1\height}{\includegraphics[width=1.5cm]{img/rda-europe.png}}
+  { }\raisebox{+0.9\height}{\includegraphics[width=2cm]{img/gobierno-canarias.png}}\\
   \scriptsize \href{https://www.rd-alliance.org/groups/early-career-and-engagement-ig}{RDA Early Career and Engagement Interest Group},\\ \href{https://www.rd-alliance.org/group/early-career-and-engagement-ig-early-career-networking-group/event/november-ama-call}{AMA Webinar}, November 20th, 2019 \\
   \vspace{0.1cm} Slides available at\\
   \textcolor{blue}{\url{http://akhlaghi.org/pdf/reproducible-paper.pdf}}}
@@ -104,38 +103,49 @@
 
 
 
+  \begin{frame}{Let's start with this nice image of the Wirlpool galaxy (M51): \small{\url{https://i.redd.it/jfqgpqg0hfk11.jpg}}}
+    \begin{center}
+      \includegraphics[width=0.8\linewidth]{img/m51-amateur.jpg}
+    \end{center}
+  \end{frame}
+
+
+
+
 
   \begin{frame}{Reproducibility is critically important in the sciences (example from astronomy)}
-    \small
+    \footnotesize
     \begin{columns}
-      \column{6cm} Example: Detecting outer regions of M51 in a
-      \alert{single exposure} SDSS image, using NoiseChisel, with
-      default and optimized parameters.
+      \column{6cm} Example: Detecting outer regions of the M51 galaxy
+      in a \alert{single exposure} SDSS image, using the NoiseChisel
+      (part of `GNU Astronomy Utilities' software package).
 
-      \vspace{2mm}
       \begin{itemize}
-        \setlength\itemsep{2mm}
-      \item When optimized, outer wing detected to
-        $\rm{S/N}=$\alert{$1/4$}, or \alert{$28.3$} mag/arcsec$^2$.
+        \setlength\itemsep{1.5mm}
+      \item When optimized, outskirts detected down to
+        $\rm{S/N}=$\alert{$1/4$}, or \alert{$28.3$} mag/arcsec$^2$. By
+        default, it only reaches $\rm{S/N}>1/5$.
       \item
-        \textcolor{blue}{\href{https://www.gnu.org/software/gnuastro/manual/html_node/Detecting-large-extended-targets.html}{Complete
-            tutorial}} in manual fully describes how to
-        derive/reproduce optimized result:
+        Akhlaghi 2019
+        (\textcolor{blue}{\href{https://arxiv.org/abs/1909.11230}{arXiv:1909.11230}})
+        describes optimized result:
         \begin{itemize}
+          \footnotesize
         \item \alert{Run-time} options/configuration.
         \item Steps \alert{before/after} NoiseChisel.
         \end{itemize}
       \item Deep/orange image from Watkins+2015
-        (\textcolor{blue}{\href{https://arxiv.org/abs/1501.04599}{arXiv:1501.04599}}).
+        (\textcolor{blue}{\href{https://arxiv.org/abs/1501.04599}{arXiv:1501.04599}}) shown for reference.
       \item Therefore:
         \begin{itemize}
+          \footnotesize
         \item Default settings not enough.
         \item Final number not just from NoiseChisel (more software
           involved).
         \end{itemize}
       \end{itemize}
 
-      \vspace{0.5mm}
+      \vspace{2mm}
       \begin{tcolorbox}[boxsep=0pt,left=1mm,right=1mm,top=1mm,bottom=1mm]
         Simply reporting in your paper that ``\emph{\alert{we used
             NoiseChisel}}'' is \alert{not enough} to reproduce,
@@ -211,6 +221,63 @@
   \end{frame}
 
 
+  \begin{frame}{``Reproducibility crisis'' in the sciences? (Baker 2016, Nature 533, 452)}
+    \centering
+    \includegraphics[width=0.85\linewidth]{img/reproducibility-crisis.jpg}
+  \end{frame}
+
+
+
+
+
+  \begin{frame}[t]{Types of reproducibility}
+    \vspace{-5mm}
+    \begin{columns}[t]
+      \column{0.5\linewidth}
+      \begin{center}
+        \large\textbf{Hardware/Statistical reproducibility}
+        \rule{0.5\linewidth}{1pt}
+      \end{center}
+      \begin{itemize}
+        \setlength\itemsep{0.5em}
+      \item Involves data \alert{collection}.
+      \item Inherently includes \alert{measurements errors}\\(can
+        never be exactly reproduced).
+      \item Example: Raw telescope image/spectra.
+      \item \alert{\textbf{NOT DISCUSSED HERE.}}
+      \end{itemize}
+
+      \vspace{3.5mm}
+      \begin{center}
+        \vspace{-5mm}
+        \includegraphics[width=0.7\linewidth]{img/hale-prime-focus.jpg}\\
+        \vspace{-0.6mm}
+        \tiny \href{http://slittlefair.staff.shef.ac.uk/teaching/phy217/lectures/telescopes/L07/index.html}{http://slittlefair.staff.shef.ac.uk}
+      \end{center}
+
+      \column{0.5\linewidth}
+      \begin{center}
+        \large\textbf{Software/Deterministic reproducibility}
+        \rule{0.5\linewidth}{1pt}
+      \end{center}
+      \begin{itemize}
+        \setlength\itemsep{1em}
+      \item Involves data \alert{analysis}, or simulations.
+      \item Starts \alert{after} data is collected/digitized.
+      \item Example: $2+2=4$ (i.e., sum of datasets).
+      \item \textbf{\textcolor{green!50!black}{DISCUSSED HERE.}}
+      \end{itemize}
+
+      \centering
+      \vspace{3mm}
+      \includegraphics[width=0.8\linewidth]{img/digital-tunnel.jpg}\\
+      \vspace{-0.6mm}
+      \tiny \href{https://tsongas.com/newsletter_articles/the-new-electronic-version-of-the-advantage/digital-tunnel-wallpaper/}{https://tsongas.com}
+    \end{columns}
+  \end{frame}
+
+
+
 
 
 
@@ -357,56 +424,6 @@
 
 
 
-  \begin{frame}[t]{Types of reproducibility}
-    \vspace{-5mm}
-    \begin{columns}[t]
-      \column{0.5\linewidth}
-      \begin{center}
-        \large\textbf{Hardware/Statistical reproducibility}
-        \rule{0.5\linewidth}{1pt}
-      \end{center}
-      \begin{itemize}
-        \setlength\itemsep{0.5em}
-      \item Involves data \alert{collection}.
-      \item Inherently includes \alert{measurements errors}\\(can
-        never be exactly reproduced).
-      \item Example: Raw telescope image/spectra.
-      \item \alert{\textbf{NOT DISCUSSED HERE.}}
-      \end{itemize}
-
-      \vspace{3.5mm}
-      \begin{center}
-        \vspace{-5mm}
-        \includegraphics[width=0.7\linewidth]{img/hale-prime-focus.jpg}\\
-        \vspace{-0.6mm}
-        \tiny \href{http://slittlefair.staff.shef.ac.uk/teaching/phy217/lectures/telescopes/L07/index.html}{http://slittlefair.staff.shef.ac.uk}
-      \end{center}
-
-      \column{0.5\linewidth}
-      \begin{center}
-        \large\textbf{Software/Deterministic reproducibility}
-        \rule{0.5\linewidth}{1pt}
-      \end{center}
-      \begin{itemize}
-        \setlength\itemsep{1em}
-      \item Involves data \alert{analysis}, or simulations.
-      \item Starts \alert{after} data is collected/digitized.
-      \item Example: $2+2=4$ (i.e., sum of datasets).
-      \item \textbf{\textcolor{green!50!black}{DISCUSSED HERE.}}
-      \end{itemize}
-
-      \centering
-      \vspace{3mm}
-      \includegraphics[width=0.8\linewidth]{img/digital-tunnel.jpg}\\
-      \vspace{-0.6mm}
-      \tiny \href{https://tsongas.com/newsletter_articles/the-new-electronic-version-of-the-advantage/digital-tunnel-wallpaper/}{https://tsongas.com}
-    \end{columns}
-  \end{frame}
-
-
-
-
-
   \newcommand{\focusonpackages}{}
   \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
   \let\focusonpackages\undefined
@@ -675,13 +692,16 @@
       \item \alert{MD5}-sum to check integrity.
       \end{itemize}
 
-      \vspace{1cm} All inputs are \alert{downloaded} from the given
+      \vspace{0.75cm} All inputs are \alert{downloaded} from the given
       PID/URL when necessary\\(during the analysis).
 
-      \vspace{1cm} MD5-sums are \alert{checked} to make sure the
+      \vspace{0.75cm} MD5-sums are \alert{checked} to make sure the
       download was done properly or the file is the same (hasn't
       changed on the server/source).
 
+      \vspace{0.75cm}Example from the reproducible paper \textcolor{blue}{\href{https://arxiv.org/abs/1909.11230}{arXiv:1909.11230}}.\\
+      This paper needs three input files (two images, one catalog).
+
       \column{5cm}
       \includegraphics[width=\linewidth]{img/inputs.png}
     \end{columns}
@@ -698,13 +718,16 @@
       \item \alert{MD5}-sum to check integrity.
       \end{itemize}
 
-      \vspace{1cm} All inputs are \alert{downloaded} from the given
+      \vspace{0.75cm} All inputs are \alert{downloaded} from the given
       PID/URL when necessary\\(during the analysis).
 
-      \vspace{1cm} MD5-sums are \alert{checked} to make sure the
+      \vspace{0.75cm} MD5-sums are \alert{checked} to make sure the
       download was done properly or the file is the same (hasn't
       changed on the server/source).
 
+      \vspace{0.75cm}Example from the reproducible paper \textcolor{blue}{\href{https://arxiv.org/abs/1909.11230}{arXiv:1909.11230}}.\\
+      This paper needs three input files (two images, one catalog).
+
       \column{5cm}
       \includegraphics[width=\linewidth]{img/inputs-highlighted.png}
     \end{columns}
@@ -897,6 +920,28 @@
   \newcommand{\gitverified}{}
   \begin{frame}{New projects branch from template} \include{tex/git-branch} \end{frame}
 
+  \begin{frame}{Two recent examples (publishing Git checksum in abstract)}
+    \begin{columns}
+      \column{0.5\linewidth}
+      \centering
+      \includegraphics[width=0.8\linewidth]{img/firstpage-190911230.png}
+      \column{0.5\linewidth}
+      \centering
+      \includegraphics[width=0.8\linewidth]{img/firstpage-191101430.png}
+    \end{columns}
+  \end{frame}
+
+  \begin{frame}{Two recent examples (publishing Git checksum in abstract)}
+    \begin{columns}
+      \column{0.5\linewidth}
+      \centering
+      \includegraphics[width=0.8\linewidth]{img/firstpage-190911230-highlighted.png}
+      \column{0.5\linewidth}
+      \centering
+      \includegraphics[width=0.8\linewidth]{img/firstpage-191101430-highlighted.png}
+    \end{columns}
+  \end{frame}
+
 
 
 
@@ -988,7 +1033,7 @@
 
 
 
-  \begin{frame}{GOOD NEWS: RDA adoption grant to IAC for this template}
+  \begin{frame}{RDA adoption grant (2019) to IAC for this template}
       \begin{center}
         \includegraphics[width=3cm]{img/rda.png}\hspace{1cm}
         \includegraphics[width=1.8cm]{img/iac.png}
@@ -1057,4 +1102,41 @@
     \textcolor{blue}{\footnotesize\url{https://gitlab.com/makhlaghi/reproducible-paper/blob/master/README-hacking.md}}
     \end{tcolorbox}
   \end{frame}
+
+
+
+
+
+  \begin{frame}{Funding to help adoption of template}
+    \begin{itemize}
+      \setlength\itemsep{5mm}
+    \item With the RDA grant, \alert{we have funding} to support the
+      travel and stay of several researchers from outside of
+      astronomy/astrophysics to the IAC \alert{for one week} to help
+      in adopting the template in their research.
+    \item Conditions:
+      \begin{itemize}
+        \setlength\itemsep{3mm}
+      \item The exact date will be set in coordination with the
+        selected researchers.
+      \item \alert{Early Career Researchers} (PhD students or Postdocs) will
+        be preferred.
+      \item Your project can be done with \alert{Free
+        Sofware} [1].\\ {\footnotesize (Note that non-free software are
+        by definition non-reproducible:\\ A random researcher can't
+        run and redistribute them as they wish, or study and modify
+        their source.)}
+      \item Your project can be run in \alert{Unix-like operating
+        systems}, ideally GNU/Linux distributions [2].\\(but other Unix-like OSs are also fine, for example BSD-based distributions, or macOS).
+      \end{itemize}
+    \item Please contact me by the end of November 2019 if you are
+      interested
+      (\textcolor{blue}{\href{mailto:mohammad@akhlaghi.org}{mohammad@akhlaghi.org}}).\\ {\footnotesize (If positions aren't filled by then, we will still accept letters of interest, and generally, we would be happy to help in adoption remotely. So if you are interested, please get in touch any way!)}
+    \end{itemize}
+
+    \vspace{3mm}
+    \footnotesize
+    1. \url{https://www.gnu.org/philosophy/free-sw.en.html}\\
+    2. For example: Mint, Debian, Ubuntu, OpenSUSE, Manjaro, Fedora, CentOS, Redhat, and many others.
+  \end{frame}
 \end{document}