From 5a9de3b5a3b263f1042148b84f8e9adedc652396 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Thu, 2 Dec 2021 05:00:33 +0100
Subject: Updated slides for talk at Paris Observatory

---
 slides-intro.tex | 273 +++++++++++++++++++++++++++++++------------------------
 1 file changed, 152 insertions(+), 121 deletions(-)

(limited to 'slides-intro.tex')

diff --git a/slides-intro.tex b/slides-intro.tex
index 8a22ccb..35d71cc 100644
--- a/slides-intro.tex
+++ b/slides-intro.tex
@@ -35,7 +35,7 @@
 
 %% Set the title
 \title{\huge\textbf{BIG} Data, \textbf{BIG} responsibility
-  \\\vspace{2mm} \large Maneage: \emph{Man}aging data lin\emph{eage} for long-term and archivable reproducibility \\\vspace{1mm} \footnotesize (\href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}, \href{https://doi.org/10.1109/MCSE.2021.3072860}{DOI:10.1109/MCSE.2021.3072860})}
+  \\\vspace{2mm} \large Maneage: \emph{Man}aging data lin\emph{eage} for long-term and archivable reproducibility \\\vspace{1mm} \footnotesize (Published in CiSE 23 (3), pp 82-91: \textcolor{blue}{\href{https://doi.org/10.1109/MCSE.2021.3072860}{DOI:10.1109/MCSE.2021.3072860}}, \textcolor{blue}{\href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}})}
 
 %% Set the author
 \author{\\
@@ -46,8 +46,8 @@
 
 %% Set the date and insitutional logos.
 \date{\footnotesize\vspace{-5mm}\\
-  \textcolor{black}{SoftwareHeritage 5th Anniversary}\\
-  \textcolor{black}{November 30th, 2021 (Inria, Paris)} \\
+  \textcolor{black}{S\'eminaires LERMA}\\
+  \textcolor{black}{December 2nd, 2021 (Paris Observatory)} \\
   \tiny\vspace{9mm}
   Most recent slides available in link below (this PDF is built from \href{http://git.maneage.org/slides-intro.git}{Git commit} \gitcommit):\\
   \footnotesize\textcolor{blue}{\url{https://maneage.org/pdf/slides-intro.pdf}}\\
@@ -90,9 +90,6 @@
   \end{frame}
 
 
-
-
-
   \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}
@@ -239,6 +236,62 @@ for computational reproducibility]
 
 
 
+  \begin{frame}{Our solution: CiSE 23 (3), pp 82-91: \textcolor{blue}{\href{https://doi.org/10.1109/MCSE.2021.3072860}{DOI:10.1109/MCSE.2021.3072860}}, \textcolor{blue}{\href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}}}
+    \begin{columns}
+      \column{0.4\linewidth}
+      \includegraphics[width=\linewidth]{img/maneage-paper.png}
+      \column{0.6\linewidth}
+      \includegraphics[width=\linewidth]{img/maneage-webpage.png}
+      \begin{center}
+        \huge{https://maneage.org}
+      \end{center}
+    \end{columns}
+  \end{frame}
+
+
+
+  \begin{frame}{Recognition 1: RDA adoption grant (2019) to IAC for Maneage}
+      \begin{center}
+        \includegraphics[width=3cm]{img/rda.png}\hspace{1cm}
+        \includegraphics[width=1.8cm]{img/iac.png}
+        \includegraphics[width=\linewidth]{img/h2020.jpg}
+      \end{center}
+
+      \vspace{1cm} For Maneage, the \alert{IAC} is selected as
+      a \alert{Top European organization} funded to adopt RDA
+      Recommendations and Outputs.
+
+      \vspace{1cm}
+      \scriptsize
+      \begin{itemize}
+      \item Research Data Alliance was launched by the \alert{European
+        Commission}, NSF, National Institute of Standards and
+        Technology, and the Australian Government’s Department of
+        Innovation.
+      \item RDA Outputs are the technical and social infrastructure
+        solutions developed by RDA Working Groups or Interest
+        Groups that enable data sharing, exchange, and
+        interoperability.
+      \end{itemize}
+
+      \vspace{0.2cm}
+  \end{frame}
+
+
+
+
+
+  \begin{frame}{Recognition 2: ``News and Views'' in Nature Astronomy (\textcolor{blue}{\href{https://doi.org/10.1038/s41550-021-01402-3}{DOI:10.1038/s41550-021-01402-3}})}
+    \begin{center}
+      \includegraphics[width=0.8\linewidth]{img/nature-astronomy.png}
+    \end{center}
+
+    \vspace{-2mm}
+    \footnotesize Free-to-read link: \textcolor{blue}{\url{https://rdcu.be/cmYVx}}
+  \end{frame}
+
+
+
 
 
   \begin{frame}[t]{Definitions \& Clarification \hspace{1.6cm} {\normalsize(from the National Academies report in 2019, \href{http://doi.org/10.17226/25303}{DOI:10.17226/25303})}}
@@ -355,14 +408,15 @@ for computational reproducibility]
   \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
   \newcommand{\sver}{}
   \begin{frame}{General outline of a project (after data collection)} \include{tex/project-graph} \end{frame}
-  \begin{frame}{Different package managers have different versions of software (repology.org, 2019/11/20)}
+  \begin{frame}[t]{Different package managers have different versions of software (repology.org, 2021/12/02)}
     \begin{columns}
       \column{7cm} \center
       Astropy\\
-      \includegraphics[width=2.2cm]{img/distros-astropy.pdf}
+      \includegraphics[width=2.8cm]{img/distros-astropy.pdf}
       \column{7cm} \center
       GNU Astronomy Utilities (Gnuastro)\\
-      \includegraphics[width=2.7cm]{img/distros-gnuastro.pdf}
+      \includegraphics[trim={0 8cm 0 0}, clip, width=2.9cm]{img/distros-gnuastro.pdf}
+      \includegraphics[trim={0 0 0 16cm}, clip, width=2.9cm]{img/distros-gnuastro.pdf}
     \end{columns}
   \end{frame}
   \newcommand{\srep}{}
@@ -387,13 +441,13 @@ for computational reproducibility]
       al. 2020, CiSE, DOI:\textcolor{blue}{\href{https://doi.org/10.1109/MCSE.2019.2949413}{10.1109/MCSE.2019.2949413}}).
     }
   \end{frame}
-  \begin{frame}{Impact of ``Dependency hell'' on native building in various hardware (CPU architectures)}
+  \begin{frame}{Impact of ``Dependency hell'' on native building in various hardware (CPU architectures), retrieved from Debian on 2021/12/02}
     \begin{columns}
       \column{7cm}
-      \includegraphics[width=0.9\linewidth]{img/cpu-arch-astropy.png}
+      \includegraphics[width=\linewidth]{img/cpu-arch-astropy.png}
       Astropy depends on Matplotlib
       \column{6cm}
-      \includegraphics[width=0.9\linewidth]{img/cpu-arch-gnuastro.png}
+      \includegraphics[width=1.05\linewidth]{img/cpu-arch-gnuastro.png}
       GNU Astronomy Utilities doesn't.
     \end{columns}
   \end{frame}
@@ -1237,6 +1291,7 @@ for computational reproducibility]
 
 
 
+
   \begin{frame}{Publication of the project}
 
     A reproducible project using Maneage will have the following
@@ -1251,19 +1306,25 @@ for computational reproducibility]
     \alert{negligible} compared to a single figure in a paper
     (usually $\sim100$ kilo-bytes).
 
+    \pause
+
     \vspace{7mm} The project's pipeline (customized Maneage) can be
     \alert{published} in
     \begin{itemize}
     \item \alert{arXiv}: uploaded with the \LaTeX{} 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{Software Heritage} which is a long-term archival repository for source code, providing permanent links to cite any part of the code.
-      For example see the \textcolor{blue}{\href{https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://gitlab.com/makhlaghi/maneage-paper.git}{Maneage paper's source there}}.
+      \textcolor{blue}{\small\href{https://arxiv.org/abs/1505.01664}{arXiv:1505.01664}} or \textcolor{blue}{\href{https://arxiv.org/abs/2006.03018}{arXiv:2006.03018}}).
     \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.3408481}{zenodo.3408481}}) and given a unique DOI.
+      \textcolor{blue}{\small\href{https://doi.org/10.5281/zenodo.3872247}{zenodo.3872247}}) and given a unique DOI.
+      \begin{itemize}
+      \item ... and put links to data in paper! See ending of caption of Figure 1 in the \textcolor{blue}{\href{https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9403875}{Maneage paper}}.
+      \end{itemize}
+    \item \alert{Software Heritage}: to archive the full version-controlled history of the project.\\(for example
+      {\small \textcolor{blue}{\href{https://archive.softwareheritage.org/swh:1:dir:33fea87068c1612daf011f161b97787b9a0df39f;origin=http://git.maneage.org/paper-concept.git/;visit=swh:1:snp:89af43c4b076a17d9298299f224247038af355ea;anchor=swh:1:rev:313db0b04bd3499f83d9e79fd7e92578cd367c2b}{swh:1:dir:33fea87068c1612daf011f161b97787b9a0df39fk}}})
+      \begin{itemize}
+      \item ... and put links to exact parts of the code! See caption of Listing 1 in the \textcolor{blue}{\href{https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9403875}{Maneage paper}}.
+      \end{itemize}
     \end{itemize}
   \end{frame}
 
@@ -1344,32 +1405,44 @@ for computational reproducibility]
 
 
 
-  \begin{frame}{RDA adoption grant (2019) to IAC for Maneage}
-      \begin{center}
-        \includegraphics[width=3cm]{img/rda.png}\hspace{1cm}
-        \includegraphics[width=1.8cm]{img/iac.png}
-        \includegraphics[width=\linewidth]{img/h2020.jpg}
-      \end{center}
 
-      \vspace{1cm} For Maneage, the \alert{IAC} is selected as
-      a \alert{Top European organization} funded to adopt RDA
-      Recommendations and Outputs.
+  \begin{frame}{Summary:}
 
-      \vspace{1cm}
-      \scriptsize
-      \begin{itemize}
-      \item Research Data Alliance was launched by the \alert{European
-        Commission}, NSF, National Institute of Standards and
-        Technology, and the Australian Government’s Department of
-        Innovation.
-      \item RDA Outputs are the technical and social infrastructure
-        solutions developed by RDA Working Groups or Interest
-        Groups that enable data sharing, exchange, and
-        interoperability.
-      \end{itemize}
+    Maneage is introduced as a customizable template that will do the
+    following steps/instructions (all in simple plain text files).
+    \begin{itemize}
+      \item \alert{Automatically downloads} the necessary
+        \emph{software} and \emph{data}.
+      \item \alert{Builds} the software in a \alert{closed
+        environment}.
+      \item Runs the software on data to \alert{generate} the final
+        \alert{research results}.
+      \item Only parts affected by a modifcation are re-done.
+      \item Using LaTeX macros, paper's figures, tables and numbers
+        will be \alert{Automatically updated}.
+      \item The whole project is under \alert{version control} (Git)
+        \alert{encouraging tests/experimentation}.
+      \item The \alert{Git commit hash} of the project source, is
+        \alert{printed} in the paper and \alert{on output} data
+        products.
+      \item \colorbox{green!30!white}{These slides are available at
+        \textcolor{blue}{\url{https://maneage.org/pdf/slides-intro.pdf}}.}
+    \end{itemize}
 
-      \vspace{0.2cm}
+    \begin{tcolorbox}[width=\linewidth, boxsep=1pt, left=1pt, right=1pt,
+                      top=1pt, bottom=1pt]
+      For a technical description of Maneage's implementation, as well
+      as a checklist to customize it, and tips on good practices,
+      please see this page:
+
+      \textcolor{blue}{\url{https://gitlab.com/maneage/project/-/blob/maneage/README-hacking.md}}
+
+      \vspace{3mm}
+      \hfill \colorbox{green!30!white}{Feel free to contact me: \textcolor{blue}{\large{\url{mohammad@akhlaghi.org}}}}
+    \end{tcolorbox}
   \end{frame}
+\end{document}
+
 
 
 
@@ -1405,91 +1478,49 @@ In summary, they only \alert{store a built} environment (they are outputs, not g
 
 
 
-\begin{frame}{Existing technologies (Package managers)}
-
-  \begin{itemize}
-  \item \textbf{Operating system package managers:}
-    \begin{itemize}
-      \setlength\itemsep{2mm}
-    \item For example \texttt{apt} or \texttt{yum} for Debian-based and RedHat-based GNU/Linux operating systems\\(the most common way to install software).
-    \item Tightly intertwined with the operating system's components\\(arbitrary control of software versions is not easily possible).
-    \item Older software (for example +5 years) is usually removed.
-    \end{itemize}
-  \item \textbf{Conda/Anaconda:}
-    \begin{itemize}
-      \setlength\itemsep{2mm}
-    \item Conda has build instructions for software and their dependencies.
-    \item But it doesn't go down to the C library or the lower-level components of operating system.
-    \item It is written in Python (can't be used later when current Python is depreciated).
-    \item Authors of Uhse+2019\footnote{\url{http://dx.doi.org/10.1002/cppb.20097}} report\footnote{\url{https://github.com/conda-forge/conda-forge.github.io/issues/787}} that their Conda environment breaks roughly every 3 months\\(Conda environments need to be updated to be used later! Breaking reproducibility).
-    \end{itemize}
-  \item \textbf{Nix, or GNU Guix:}
-    \begin{itemize}
-      \setlength\itemsep{2mm}
-    \item Deliver perfectly reproducible builds (bit-wise reproducibility of software), needs root access.
-    \item Doesn't \emph{require} documentation of dependencies.
-    \end{itemize}
-  \item \textbf{Spack:} Similar to Nix/Guix but written in Python.
-  \end{itemize}
-\end{frame}
-
-\begin{frame}{Existing technologies (workflow tools)}
-  \begin{itemize}
-    \setlength\itemsep{4mm}
-  \item \textbf{Binder:} (\url{https://mybinder.org}) Docker+Conda.
-  \item \textbf{Galaxy:} (\url{https://galaxyproject.org}) A web-based user interface, primarily designed for genomics. The GUI make it hard to automate, and has too many dependencies. Very similar to GenePattern (2008 to 2017): with +40,000 users and $\sim4000$ jobs running per week, but cut due to funding.
-  \item \textbf{Sciunit:} (\url{https://sciunit.run}) Parses program binaries to try to infer their dependencies and copy them.
-  \item \textbf{Popper:} (\url{https://falsifiable.us}), HCL (previously used by GitHub Actions) + Conda + Docker.
-  \item \textbf{WholeTale:} (\url{https://wholetale.org}) Jupyter + Conda + Docker.
-  \item \textbf{Image Processing On Line (IPOL) journal:} The best example of publishing algorithms/methods I have seen, only useful for very basic/low-level software.
-  \end{itemize}
-  \alert{Summary}: except for IPOL, most solutions surveyed have far too many dependencies to be usable \alert{beyond the immediate future}.
+%\begin{frame}{Existing technologies (Package managers)}
+%
+%  \begin{itemize}
+%  \item \textbf{Operating system package managers:}
+%    \begin{itemize}
+%      \setlength\itemsep{2mm}
+%    \item For example \texttt{apt} or \texttt{yum} for Debian-based and RedHat-based GNU/Linux operating systems\\(the most common way to install software).
+%    \item Tightly intertwined with the operating system's components\\(arbitrary control of software versions is not easily possible).
+%    \item Older software (for example +5 years) is usually removed.
+%    \end{itemize}
+%  \item \textbf{Conda/Anaconda:}
+%    \begin{itemize}
+%      \setlength\itemsep{2mm}
+%    \item Conda has build instructions for software and their dependencies.
+%    \item But it doesn't go down to the C library or the lower-level components of operating system.
+%    \item It is written in Python (can't be used later when current Python is depreciated).
+%    \item Authors of Uhse+2019\footnote{\url{http://dx.doi.org/10.1002/cppb.20097}} report\footnote{\url{https://github.com/conda-forge/conda-forge.github.io/issues/787}} that their Conda environment breaks roughly every 3 months\\(Conda environments need to be updated to be used later! Breaking reproducibility).
+%    \end{itemize}
+%  \item \textbf{Nix, or GNU Guix:}
+%    \begin{itemize}
+%      \setlength\itemsep{2mm}
+%    \item Deliver perfectly reproducible builds (bit-wise reproducibility of software), needs root access.
+%    \item Doesn't \emph{require} documentation of dependencies.
+%    \end{itemize}
+%  \item \textbf{Spack:} Similar to Nix/Guix but written in Python.
+%  \end{itemize}
+%\end{frame}
+%
+%\begin{frame}{Existing technologies (workflow tools)}
+%  \begin{itemize}
+%    \setlength\itemsep{4mm}
+%  \item \textbf{Binder:} (\url{https://mybinder.org}) Docker+Conda.
+%  \item \textbf{Galaxy:} (\url{https://galaxyproject.org}) A web-based user interface, primarily designed for genomics. The GUI make it hard to automate, and has too many dependencies. Very similar to GenePattern (2008 to 2017): with +40,000 users and $\sim4000$ jobs running per week, but cut due to funding.
+%  \item \textbf{Sciunit:} (\url{https://sciunit.run}) Parses program binaries to try to infer their dependencies and copy them.
+%  \item \textbf{Popper:} (\url{https://falsifiable.us}), HCL (previously used by GitHub Actions) + Conda + Docker.
+%  \item \textbf{WholeTale:} (\url{https://wholetale.org}) Jupyter + Conda + Docker.
+%  \item \textbf{Image Processing On Line (IPOL) journal:} The best example of publishing algorithms/methods I have seen, only useful for very basic/low-level software.
+%  \end{itemize}
+%  \alert{Summary}: except for IPOL, most solutions surveyed have far too many dependencies to be usable \alert{beyond the immediate future}.
 \end{frame}
 
 
 
-
-  \begin{frame}{Summary:}
-
-    Maneage is introduced as a customizable template that will do the
-    following steps/instructions (all in simple plain text files).
-    \begin{itemize}
-      \item \alert{Automatically downloads} the necessary
-        \emph{software} and \emph{data}.
-      \item \alert{Builds} the software in a \alert{closed
-        environment}.
-      \item Runs the software on data to \alert{generate} the final
-        \alert{research results}.
-      \item Only parts affected by a modifcation are re-done.
-      \item Using LaTeX macros, paper's figures, tables and numbers
-        will be \alert{Automatically updated}.
-      \item The whole project is under \alert{version control} (Git)
-        \alert{encouraging tests/experimentation}.
-      \item The \alert{Git commit hash} of the project source, is
-        \alert{printed} in the paper and \alert{on output} data
-        products.
-      \item \colorbox{green!30!white}{These slides are available at
-        \textcolor{blue}{\url{https://maneage.org/pdf/slides-intro.pdf}}.}
-    \end{itemize}
-
-    \begin{tcolorbox}[width=\linewidth, boxsep=1pt, left=1pt, right=1pt,
-                      top=1pt, bottom=1pt]
-      For a technical description of Maneage's implementation, as well
-      as a checklist to customize it, and tips on good practices,
-      please see this page:
-
-      \textcolor{blue}{\url{https://gitlab.com/maneage/project/-/blob/maneage/README-hacking.md}}
-
-      \vspace{3mm}
-      \hfill \colorbox{green!30!white}{Feel free to contact me: \textcolor{blue}{\large{\url{mohammad@akhlaghi.org}}}}
-    \end{tcolorbox}
-  \end{frame}
-\end{document}
-
-
-
-
-
 %  \begin{frame}{Funding to help adoption of template}
 %    \begin{itemize}
 %      \setlength\itemsep{5mm}
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