From 4464a4dc3cdba7ce8ed3b961c0e0cf1809332c45 Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Wed, 20 Nov 2019 14:10:27 +0000 Subject: Updated and slightly modernized slides prior to the RDA Webinar Several figures were added to highlight the major points and add better examples. --- img/firstpage-190911230-highlighted.png | Bin 0 -> 688614 bytes img/firstpage-190911230.png | Bin 0 -> 687448 bytes img/firstpage-191101430-highlighted.png | Bin 0 -> 695062 bytes img/firstpage-191101430.png | Bin 0 -> 693821 bytes img/inputs-highlighted.png | Bin 159316 -> 248325 bytes img/inputs.png | Bin 159037 -> 245617 bytes img/m51-amateur.jpg | Bin 0 -> 370734 bytes img/rda-europe.png | Bin 0 -> 34531 bytes img/reproducibility-crisis.jpg | Bin 0 -> 624574 bytes reproducible-paper.tex | 226 ++++++++++++++++++++++---------- 10 files changed, 154 insertions(+), 72 deletions(-) create mode 100644 img/firstpage-190911230-highlighted.png create mode 100644 img/firstpage-190911230.png create mode 100644 img/firstpage-191101430-highlighted.png create mode 100644 img/firstpage-191101430.png create mode 100644 img/m51-amateur.jpg create mode 100644 img/rda-europe.png create mode 100644 img/reproducibility-crisis.jpg diff --git a/img/firstpage-190911230-highlighted.png b/img/firstpage-190911230-highlighted.png new file mode 100644 index 0000000..1237aab Binary files /dev/null and b/img/firstpage-190911230-highlighted.png differ diff --git a/img/firstpage-190911230.png b/img/firstpage-190911230.png new file mode 100644 index 0000000..ed16f38 Binary files /dev/null and b/img/firstpage-190911230.png differ diff --git a/img/firstpage-191101430-highlighted.png b/img/firstpage-191101430-highlighted.png new file mode 100644 index 0000000..e700e8e Binary files /dev/null and b/img/firstpage-191101430-highlighted.png differ diff --git a/img/firstpage-191101430.png b/img/firstpage-191101430.png new file mode 100644 index 0000000..abadde2 Binary files /dev/null and b/img/firstpage-191101430.png differ diff --git a/img/inputs-highlighted.png b/img/inputs-highlighted.png index f2a24f4..f1f6b9b 100644 Binary files a/img/inputs-highlighted.png and b/img/inputs-highlighted.png differ diff --git a/img/inputs.png b/img/inputs.png index 9ecbbf5..8651c10 100644 Binary files a/img/inputs.png and b/img/inputs.png differ diff --git a/img/m51-amateur.jpg b/img/m51-amateur.jpg new file mode 100644 index 0000000..46bb2fe Binary files /dev/null and b/img/m51-amateur.jpg differ diff --git a/img/rda-europe.png b/img/rda-europe.png new file mode 100644 index 0000000..d6e0f9c Binary files /dev/null and b/img/rda-europe.png differ diff --git a/img/reproducibility-crisis.jpg b/img/reproducibility-crisis.jpg new file mode 100644 index 0000000..362576a Binary files /dev/null and b/img/reproducibility-crisis.jpg differ 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} -- cgit v1.2.1