Commit: 8ab3ea2c714565a16a5c74324176c068559622ca - myprojects-hg-reborn (hg)

Commit MetaInfo

• Revision: 8ab3ea2c714565a16a5c74324176c068559622ca (tree)
• Zeit: 2018-02-02 19:48:50
• Autor: Lorenzo Isella <lorenzo.isella@gmai...>
• Commiter: Lorenzo Isella

Log Message

A very good template for dark presentations with Beamer. Remember to compile with Lualatex.

Ändern Zusammenfassung

• add: latex-documents/beamer_new_dark.tex

Diff

diff -r 60627963308d -r 8ab3ea2c7145 latex-documents/beamer_new_dark.tex
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/latex-documents/beamer_new_dark.tex	Fri Feb 02 11:48:50 2018 +0100
@@ -0,0 +1,552 @@
+\documentclass[12pt,t]{beamer}
+\usepackage{graphicx}
+\setbeameroption{hide notes}
+\setbeamertemplate{note page}[plain]
+
+% get rid of junk
+\usetheme{default}
+\beamertemplatenavigationsymbolsempty
+\hypersetup{pdfpagemode=UseNone} % don't show bookmarks on initial view
+
+% font
+\usepackage{fontspec}
+\setsansfont{TeX Gyre Heros}
+\setbeamerfont{note page}{family*=pplx,size=\footnotesize} % Palatino for notes
+% "TeX Gyre Heros can be used as a replacement for Helvetica"
+% In Unix, unzip the following into ~/.fonts
+% In Mac, unzip it, double-click the .otf files, and install using "FontBook"
+%   http://www.gust.org.pl/projects/e-foundry/tex-gyre/heros/qhv2.004otf.zip
+
+% named colors
+\definecolor{offwhite}{RGB}{249,242,215}
+\definecolor{foreground}{RGB}{255,255,255}
+\definecolor{background}{RGB}{24,24,24}
+\definecolor{title}{RGB}{107,174,214}
+\definecolor{gray}{RGB}{155,155,155}
+\definecolor{subtitle}{RGB}{102,255,204}
+\definecolor{hilight}{RGB}{102,255,204}
+\definecolor{vhilight}{RGB}{255,111,207}
+\definecolor{lolight}{RGB}{155,155,155}
+%\definecolor{green}{RGB}{125,250,125}
+
+% use those colors
+\setbeamercolor{titlelike}{fg=title}
+\setbeamercolor{subtitle}{fg=subtitle}
+\setbeamercolor{institute}{fg=gray}
+\setbeamercolor{normal text}{fg=foreground,bg=background}
+\setbeamercolor{item}{fg=foreground} % color of bullets
+\setbeamercolor{subitem}{fg=gray}
+\setbeamercolor{itemize/enumerate subbody}{fg=gray}
+\setbeamertemplate{itemize subitem}{{\textendash}}
+\setbeamerfont{itemize/enumerate subbody}{size=\footnotesize}
+\setbeamerfont{itemize/enumerate subitem}{size=\footnotesize}
+
+% page number
+\setbeamertemplate{footline}{%
+    \raisebox{5pt}{\makebox[\paperwidth]{\hfill\makebox[20pt]{\color{gray}
+          \scriptsize\insertframenumber}}}\hspace*{5pt}}
+
+% add a bit of space at the top of the notes page
+\addtobeamertemplate{note page}{\setlength{\parskip}{12pt}}
+
+% a few macros
+\newcommand{\bi}{\begin{itemize}}
+\newcommand{\ei}{\end{itemize}}
+\newcommand{\ig}{\includegraphics}
+\newcommand{\subt}[1]{{\footnotesize \color{subtitle} {#1}}}
+
+% title info
+\title{Open access publishing}
+\subtitle{A researcher's perspective}
+\author{\href{http://kbroman.org}{Karl Broman}}
+\institute{\href{https://www.biostat.wisc.edu}{Biostatistics \& Medical Informatics} \\[2pt] \href{http://www.wisc.edu}{University of Wisconsin{\textendash}Madison}}
+\date{\href{http://kbroman.org}{\tt \scriptsize kbroman.org}
+\\[-4pt]
+\href{https://github.com/kbroman}{\tt \scriptsize github.com/kbroman}
+\\[-4pt]
+\href{https://twitter.com/kwbroman}{\tt \scriptsize @kwbroman}
+}
+
+
+\begin{document}
+
+% title slide
+{
+\setbeamertemplate{footline}{} % no page number here
+\frame{
+  \titlepage
+  \note{These are slides for a talk I will give on 30 Oct 2014, at a
+    symposium on scholarly publishing.
+
+    I'm a statistician. My research focuses on genetics, and
+    most of my papers are in genetics journals.
+
+    So in commenting on open access, I'm focusing on scientific
+    publications, and perhaps more narrowly, on the biological
+    sciences.
+} } }
+
+
+
+\begin{frame}{Access in action}
+\subt{Interesting reference}
+
+% \bigskip
+% \centerline{
+% \ig[height=0.75\textheight]{Images/img01.jpg}
+% }
+
+\note{I'll begin with an illustration of what I mean by
+  access.
+
+  Some time back, I was reading a manuscript and saw an
+  article of interest.}
+\end{frame}
+
+
+\begin{frame}{Test Slide by Lorenzo}
+  \subt{An optional subtitle} \\
+  Now some real content
+
+  \bi
+\item my first item
+  \item and my second one
+  \ei
+Now I try to enumerate stuff
+  
+  \begin{enumerate}
+\item my first item (enumerated!)
+  \item and my second one
+  \end{enumerate}
+It looks like is OK as a template I may use. Remember to compile with Lualatex!
+  
+% \bigskip
+% \centerline{
+% \ig[height=0.75\textheight]{Images/img01.jpg}
+% }
+
+\note{I'll begin with an illustration of what I mean by
+  access.
+
+  Some time back, I was reading a manuscript and saw an
+  article of interest.}
+\end{frame}
+
+
+
+
+\begin{frame}{Access in action}
+\subt{Google Scholar}
+  
+\bigskip
+% \begin{center}
+% \ig[width=0.70\textwidth]{Images/img02.jpg}
+
+% \onslide<2> {
+%   \vspace*{-0.55\textheight}
+%   \hspace*{0.15\textwidth}
+%   \ig[width=0.70\textwidth]{Images/img03.jpg}
+% }
+% \end{center}
+
+\note{If I paste the article title into Google Scholar, I immediately
+  find the paper and can go directly to the journal.
+
+  But I was sitting at home on my couch.
+
+  And they charge \$40 for a 7 page paper!
+
+  I could get the article through the UW Libraries web site, but it's
+  a bit of a hassle.}
+\end{frame}
+
+
+
+
+\begin{frame}{What's the deal with the prices?}
+
+\vspace{24pt}
+
+{\scriptsize \color{gray}
+\renewcommand{\arraystretch}{3}
+\begin{tabular}{p{3.2in}@{\hspace*{1cm}}l}
+Broman K, Speed T, Tigges M ({\color{white} 1996}) Estimation of antigen-responsive T
+cell frequencies in PBMC from human subjects. {\color{white} \mbox{J Immunol Meth}} 198:119{\textendash}132
+& {\color{vhilight} \footnotesize \$39.95}  \\
+Broman KW, Weber JL ({\color{white} 1999}) Method for constructing confidently ordered
+linkage maps. {\color{white} Genet Epidemiol} 16:337{\textendash}343  & {\color{vhilight}
+ \footnotesize   \$35.00} \\
+Broman KW, Feingold E ({\color{white} 2004}) SNPs made routine. {\color{white} Nat Methods} 1:104{\textendash}105
+& {\color{vhilight} \footnotesize  \$18.00} \\
+Broman KW ({\color{white} 2005}) Mapping expression in randomized rodent
+genomes. {\color{white} Nat Genet} 37:209{\textendash}210 & {\color{vhilight} \footnotesize  \$18.00}
+\end{tabular}
+}
+
+\note{I went back to some of my early papers, and found these
+  outrageous prices.
+
+  \$18 for a 2-page paper?
+
+  I understand that the publishing industry has a long history of
+  screwy pricing, but you'd have to be either \textbf{desperate} or
+  \textbf{stupid} to pay this.
+
+  And for that 1999 Genetic Epidemiology article, published by Wiley,
+  you have to register in order to find out that it's \$35 for just 24
+  hours of access.
+}
+\end{frame}
+
+
+
+\begin{frame}{Access in action}
+\subt{There's also PubMed}
+
+\bigskip
+% \begin{center}
+% \ig[width=0.7\textwidth]{Images/img13.png}
+
+
+% \onslide<2>{
+%   \vspace*{-0.45\textheight}
+%   \hspace*{0.55\textwidth}
+%   \ig[width=2in]{Images/free_in_pmc.png}
+% }
+
+% \end{center}
+
+\note{If I'd used PubMed rather than Google Scholar, I could have
+  gotten to the published paper in just a few clicks, because the
+  manuscript is in PubMed Central.
+
+  PubMed Central is only for federally-funded research, has a one year
+  embargo, and (as here) might not include the published version of the
+  paper.
+
+  PubMed Central is a good thing, but one generally can't wait a year,
+  it's unfortunate that the published versions aren't always included,
+  and from an author's point of view it can be a real hassle.
+}
+\end{frame}
+
+
+\begin{frame}{Another example}
+
+\bigskip
+
+\begin{center}
+
+% \hspace{-0.15\textwidth}
+% \ig[height=0.7\textheight]{Images/feingold_pubmed.png}
+
+% \onslide<2->{
+%   \vspace*{-0.65\textheight}
+%   \hspace*{-0.10\textwidth}
+%   \ig[height=0.75\textheight]{Images/feingold_paywall.png}
+% }
+
+% \onslide<3->{
+%   \vspace*{-0.87\textheight}
+%   \hspace*{0.38\textwidth}
+%   \ig[height=0.92\textheight]{Images/feingold_paper.png}
+% }
+
+% \onslide<4->{
+%   \vspace*{-0.35\textheight}
+%   \hspace*{0.29\textwidth}
+%   \ig[height=0.35\textheight]{Images/feingold_appendix_url.png}
+% }
+
+% \onslide<5>{
+%   \vspace*{-0.90\textheight}
+%   \hspace*{0.48\textwidth}
+%   \ig[height=0.85\textheight]{Images/feingold_paywall2.png}
+% }
+
+\note{As another example, I was interested a paper from the Journal of
+  Dental Research.
+
+  It's less than a year old, so it's not available in PubMed
+  Central.
+
+  I ordered a copy by inter-library loan, but it didn't include the
+  supplemental methods, and those are behind a paywall at the journal!
+}
+\end{center}
+
+\end{frame}
+
+\begin{frame}{Twitter is useful}
+\subt{(for venting\only<2>{ and more})}
+
+\bigskip
+
+% \begin{center}
+
+% \ig[height=0.5\textheight]{Images/feingold_tweet.jpg}
+
+% \onslide<2->{
+%   \vspace*{-0.70\textheight}
+%   \hspace*{0.40\textwidth}
+%   \ig[height=0.95\textheight]{Images/feingold_appendix.png}
+% }
+% \end{center}
+
+\note{I was reduced to venting on twitter.
+
+  But then I got the appendix I wanted by email (twice!), within an
+  hour of my tweet. (Thanks, MM and KW!)
+}
+
+\end{frame}
+
+\begin{frame}[c]{Twitter is useful}
+
+\centerline{\Huge {\#}icanhazpdf}
+
+\note{If you search twitter for {\#}icanhazpdf, you'll find lots of
+  people asking for copies of articles. Quite effective.}
+\end{frame}
+
+\begin{frame}{It's all about money}
+\subt{(Costs in scientific publishing)}
+
+\vspace{24pt}
+
+\bi
+\item {\color<3| handout 0>{hilight} Research}
+\item {\color<3| handout 0>{hilight} Writing}
+\item {\color<3| handout 0>{hilight} Peer review, editorial oversight}
+\item {\color<4| handout 0>{hilight} Journal administration}
+\item {\color<4| handout 0>{hilight} Copy editing, typesetting}
+\item {\color<4| handout 0>{hilight} Distribution}
+\item<2-> {\color<2| handout 0>{vhilight} \color<4| handout 0>{hilight} Profit}
+\ei
+
+\note{Open access is all about money.
+
+Most of the costs behind a research paper are paid by grants or
+institutional funds. For most journals, peer review and editorial
+oversight are unpaid.
+
+There are real costs associated with journals, but in the end they are
+all paid from the same sources (grants and institutional funds).
+
+Do we really want to give away the product of our research and then
+buy it back repeatedly, at great profit to the publishers?
+
+And shouldn't the literature be available generally and not just to
+those with access to well-funded research libraries?
+}
+\end{frame}
+
+\begin{frame}{It's not about}
+
+\vspace{36pt}
+
+\bi
+\itemsep6pt
+\item {Peer review}
+\item {Predatory publishing}
+\item {\color<2->{vhilight} Impact factors}
+\item {\color<2->{vhilight} Evaluating researchers} \\
+{\footnotesize \color{gray} (for grants \& promotions)}
+\ei
+
+\vspace{36pt}
+
+\onslide<2->{ \color{hilight} Well, it sort of is\dots }
+
+\note{The Open Access discussion often gets tied up with discussion
+  about peer review, predatory publishing, and journal impact
+  factors.
+
+  But to me, it is a completely separate issue, whether we want
+  stringent peer review before publication or instead leave the
+  evaluation entirely to post-publication review.
+
+  On the other hand, the current culture is to evaluate researchers
+  based on the perceived quality of the journals in which they've
+  published. This makes it difficult to change to open access.
+
+  If everyone's still going to send their best work to Science,
+  Nature, \& Cell, then that work will continue to be locked up behind
+  pay walls.
+}
+\end{frame}
+
+\begin{frame}{Paying for it}
+
+\vspace{36pt}
+
+\bi
+\itemsep12pt
+\item Traditional approach
+\bi
+\item subscriptions
+\item page charges
+\ei
+\item Open access
+\bi
+\item bigger page charges
+\item submission charges?
+\ei
+\onslide<2->{
+\item Endowments
+\item Direct grants to journals
+}
+\ei
+
+\note{The usual way in which publishing costs are paid are through a
+  combination of subscriptions (both institutional and individual) and
+  direct charges to the author.
+
+  In the new open access model, the page charges are increased in
+  order to eliminate the subscription fees. One might have a fee for
+  all submitted manuscripts and not just those accepted for
+  publication.
+
+  I've not seen much discussion of other alternatives, but I would
+  prefer to see endowments established, particularly for
+  society journals.  Alternatively, journals might be
+  funded directly through grants.
+}
+\end{frame}
+
+
+\begin{frame}{Invoice}
+
+\bigskip
+% \begin{center}
+% \ig[height=0.75\textheight]{Images/invoice3.jpg}
+
+
+% \onslide<2>{
+%   \vspace*{-0.35\textheight}
+%   \ig[width=\textwidth]{Images/invoice3_clip.jpg}
+% }
+% \end{center}
+
+\note{Here's an invoice for a paper I published in 2012.
+
+  The charges would have been ``just'' \$1700, but I paid an
+  additional \$1200 to have it freely available (otherwise it would
+  have been behind a pay wall for one year).
+}
+\end{frame}
+
+
+
+
+
+
+\begin{frame}{Choices for young investigators}
+
+\vspace{36pt}
+
+\bi
+\item Pay for open access
+\item Support young open access journals
+
+\vspace*{12pt}
+
+\hspace{2cm} {\color{vhilight} \sc or}
+
+\vspace*{12pt}
+
+\item Let subscribers pay \& do more experiments
+\item Continue to go after Science, Nature, \& Cell
+\ei
+
+\note{The page charges, and the continued reliance on impact factors,
+  lead to difficult choices, particularly for young investigators.
+
+  Should I pay for open access, or should I let the subscribers pay
+  and use the savings to do more experiments?
+
+  Should I support open access journals, or should I continue to
+  go after Science, Nature, \& Cell?
+
+  The best scientists may confidently maintain their pure publication
+  record.
+
+  But more mediocre scientists, who may be just scraping by,
+  probably don't feel they have that luxury.  A Nature paper can
+  ``make you.''
+}
+\end{frame}
+
+
+\begin{frame}{What can we do?}
+
+\vspace{36pt}
+
+\bi
+\itemsep12pt
+\item Send our best work to open access journals
+\item Support junior faculty to keep their papers open
+\item Pay attention to the quality of the work
+\bi
+\item[] (not the impact factor of the journal)
+\ei
+\item Raise endowments for trusted journals
+\item {\color<2>{vhilight} Reform copyright law}
+\ei
+
+\note{We need to send our best work to open access journals.
+
+We need to find ways to support our junior colleagues, so that they
+may do so as well.
+
+We need to evaluate people based on their work and not by the name of
+the journal in which it appeared. We all may say, ``Science and
+Nature are often crap and there are lots of fantastic papers that
+appear elsewhere.'' But somehow when we see Nature or Cell on
+someone's CV, we still have an immediate, positive reaction.
+
+I would like to see endowed journals, open forever.
+
+The quickest way to free the product of federally funded research
+would be to reform copyright law. If the product of our research were
+forced open by law, the publishing industry would figure out how to
+pay for it in short order.
+
+But given the state of politics in the US, I'm not too optimistic
+about that.
+}
+\end{frame}
+
+{\setbeamertemplate{footline}{}
+
+\begin{frame}
+\end{frame}
+
+\begin{frame}{Discussion questions}
+
+\vspace{12pt}
+
+{\small
+\bi
+\itemsep12pt
+    \item {\color{lolight} \footnotesize There is an emerging consensus to allow (or
+      even require) self-archiving for the final version of the
+      author's peer-reviewed manuscript, and to give the publisher
+      exclusivity for the published edition.} \\
+      Is this a problem for the researchers that use the content?
+    \item How to encourage researchers to publish in open access
+      journals? How to help with publication charges?
+    \item Should we change how we evaluate scholars, for hiring and
+      promotion?
+    \item Should we give campus authors a chance to "opt-out" of any
+      institutional mandate for open access?
+  \ei
+}
+
+\end{frame}
+
+}
+\end{document}
+
+
+