% !TeX encoding = UTF-8
% !TeX spellcheck = en_US
% !TeX root = WSP.tex


% What is a scientific paper: formal view
% Title, Authors, affiliations, abstract, sections, figures, tables, references
% Each journal has its format
% My god: its so comlpex
% Solution: Separation of content and presentation
% LaTeX: what is it ?
% LaTeX: How ? 
\section{A scientific paper}
\subsection{Papers share the same structure}

\begin{frame}{The process of publishing a scientific paper}
\begin{Boite}
{Choose the right journal}
\begin{itemize}
\item \href{http://factuel.univ-lorraine.fr/sites/factuel.univ-lorraine.fr/files/field/files/2018/04/cp_ul_engagement_science_ouverte_en_1.pdf}{Get inspired by your university policy}
\item Choose a journal that is read by your targeted audience
\item If you can, choose Open Access journals
\item \href{https://scipost.org/journals/}{Read the editorial guidelines}
\end{itemize}
\end{Boite}
\pause
\begin{Boite}
{Write and publish}
\begin{itemize}
\item Write your paper \hfill this class
\item Send it to journal
\item Wait for reviewing
\item Make corrections if necessary
\item Publication occurs if reviewers agree
\end{itemize}
\end{Boite}
\end{frame}


\begin{frame}{The first page of a scientific paper}
\begin{columns}
\begin{Column}
\begin{Boite}{~}
\begin{itemize}
\item<1-> Informative short title
\item<2-> Ordered author list
\item<3-> Affiliations
\item<4-> Keywords
\item<5-> Article history
\item<6-> Abstract
\item<7-> Contact information
\item<8-> Article reference
\end{itemize}
\end{Boite}
\only<1-|handout:0>{
\begin{BoiteCentre}{~}
\only<1|handout:0>{A good title will pop up in web searches}
\only<2|handout:0>{\href{https://en.wikipedia.org/wiki/Academic_authorship}{Get the author order wrong and make enemies}}
\only<3|handout:0>{Institutions are touchy on affiliations}
\only<4|handout:0>{Keywords index your paper on a worldwide basis: get them right}
\only<5|handout:0>{Dates ! Who was the first ? Dow long was it reviewed ? Date of publication ?}
\only<6|handout:0>{The abstract is an ultra short summary of the paper emphasizing new findings}
\only<7|handout:0>{How you can be contacted for further information}
\only<8|handout:0>{journal, volume \& page number ; Digital Object Identifier\dots}
\end{BoiteCentre}
}
\end{Column}
\begin{Column}
\begin{Boite}{}
\href{http://resolver.ebscohost.com.bases-doc.univ-lorraine.fr/openurl?sid=EBSCO:edselp\&genre=article\&issn=18787649\&ISBN=\&volume=6\&issue=6\&date=20151201\&spage=573\&pages=573-579\&title=European\%20Geriatric\%20Medicine\&atitle=Research\%20paper\%3A\%20Writing\%20a\%20scientific\%20article\%3A\%20A\%20step-by-step\%20guide\%20for\%20beginners\&aulast=Ecarnot\%2C\%20F.&id=DOI:10.1016/j.eurger.2015.08.005&id=PMID:}{\includegraphics[width=\linewidth]{HWSP_Elsevier}}
\end{Boite}
\end{Column}
\end{columns}
\end{frame}

\begin{frame}{The paper body}{Sections, subsections, figures \& tables}
\begin{columns}
\begin{Column}
\begin{Boite}
{~}
\begin{itemize}
\item Introductory section
\item<2-> Sections and subsections
\item<3-> Self-consistent figures
\item<4-> Self-consistent tables
\end{itemize}
\end{Boite}
\only<1-|handout:0>{
\begin{BoiteCentre}{~}
\only<1|handout:0>{The introductory section sets the paper background. It can, or not, have a title.}
\only<2|handout:0>{Sections are compulsory, except in letters. Subsections are not.}
\only<3|handout:0>{Figures are \alert{self-consistent} and have \alert{numbers and captions}. They are placed above or below the text.}
\only<4|handout:0>{Tables are a special type of figure, with separate numbers.}
\end{BoiteCentre}
}
\end{Column}
\begin{Column}
\begin{BoiteCentre}
{}
\only<1-2|handout:0>{\includegraphics[height=0.75\paperheight]{HWSP_Elsevier_2}}
\only<3-|handout:1>{\includegraphics[height=0.75\paperheight]{HWSP_Elsevier_6}}
\end{BoiteCentre}
\end{Column}
\end{columns}
\end{frame}

\begin{frame}{The paper end}{Conclusion, acknowledgments and references}
\begin{columns}
\begin{Column}
\begin{Boite}
{~}
\begin{itemize}
\item Conclusion
\item<2-> Acknowledgments
\item<3-> Other mandatory sections
\item<4-> References
\end{itemize}
\end{Boite}
\only<1-|handout:0>{
\begin{BoiteCentre}{~}
\only<1|handout:0>{The conclusion summarizes the main findings}
\only<2|handout:0>{The acknowledgments section is used only when people or institutions outside the authors should be acknowlded}
\only<3|handout:0>{Depending on journal, other mandatory sections may be required}
\only<4|handout:0>{References are a big subject in themselves}
\end{BoiteCentre}
}
\end{Column}
\begin{Column}
\begin{BoiteCentre}
{}
{\includegraphics[width=\linewidth]{HWSP_Elsevier_7}}
\end{BoiteCentre}
\end{Column}
\end{columns}
\end{frame}

\subsection[References]{References, so important references}

\begin{frame}{The need for refences}{Standing on the shoulders of giants}
\begin{Boite}{A scientific issue}
In a scientific paper, \emph{all sayings} must be
\begin{itemize}
\item either demonstrated,
\item or taken from an identified \alert{referenced} source.
\end{itemize}
\end{Boite}
\pause
\begin{Boite}{A network issue}
The way papers are linked through proper referencing
\begin{itemize}
\item shows the links between scientific domains,
\item shows how people work together,
\item provides a world-wide basis for scientific knowledge\footnote{See \href{https://upload.wikimedia.org/wikipedia/commons/2/2e/WMF_Metrics_and_Activities_Meeting_-_September_2016.webm\#t=00:30:35}{wikicite}, \href{http://crossref.org}{crossref}  \&  \href{https://i4oc.org/}{the initiative for open citations}}.
\end{itemize}
\end{Boite}
\end{frame}

\begin{frame}{Do not forget the references}{Researchers and advisors are touchy about references}
\begin{BoiteCentre}{An acknowledgment issue}
Using other people work without citing it properly is \alert{BAD}.

A good citation allows to find the way to the original work.
\end{BoiteCentre}
\pause
\begin{BoiteCentre}{An evaluation issue for researchers}
The quality of a researcher's work is often evaluated on the number of times her/his papers are cited.

\alert<2>{Career and salary may depend on it.}
\end{BoiteCentre}
\pause
\begin{BoiteCentre}{A reputation issue for institutions}
International ranking is often based on papers citations rather than on papers themselves.

Institutions issue affiliation rules to ensure proper automatic  attribution.
\end{BoiteCentre}
\end{frame}

\begin{frame}{Reference management}{Real time tracking of the papers you read to ease proper referencing upon writing}
\begin{Boite}{\href{https://www.zotero.org/}{Zotero}\hfill UL favorite}
\begin{itemize}
\item Keeps tracks of web searches as you read
\item Keep references in collections
\item Allow participative work on a reference collection
\item Easy export for one click proper citations
\item Allow to match most journals citation habits
\item \href{https://bu.univ-lorraine.fr/formations/formations-doctorants-chercheurs}{Full training courses available here} 
\end{itemize}
\end{Boite}
\pause
\begin{Boite}
{Many other reference managers exist\hfill \emph{e.g.} \href{http://www.jabref.org/}{JabRef}}
\url{https://en.wikipedia.org/wiki/Comparison_of_reference_management_software}
\end{Boite}
\end{frame}

\section{Separation of content and presentation}
\subsection{A concept to ease and enhance writing}
\begin{frame}{Focus on content, not on presentation}{All journals have different guidelines for presentation, though all articles share the same structure}
\begin{Boite}{Jourrnal articles share the same structure}
\begin{itemize}
\item All journal articles have title, authors, affiliations, abstract, references\dots
\item which are \alert{typeset differently}, depending on the journal.
\end{itemize}
\end{Boite}
\uncover<2->{
\begin{Boite}{Scientific writing is focusing on content}
\begin{itemize}
\item OK for writing a short descriptive title, a meaningful abstract and properly referencing others work
\item<3-|alert@3> But who cares about character font or size and paper layout ?
\item<4-|alert@4> Not the scientist job ! Leave it to a software that knows better.
\end{itemize}
\end{Boite}
}
\end{frame}

\newcommand{\ML}{\alert{ML}}
\begin{frame}[fragile]{Markup languages: a universal solution}{X\ML, HT\ML, Wiki\ML, SVG, PDF\dots and \LaTeX}
\begin{Boite}
{Specify \alert{what} things are, not \emph{how}\hfill \emph{This is a title}}
\begin{lstlisting}
\title{My really neat short and descriptive title}
\end{lstlisting}
\end{Boite}
\pause
\begin{Boite}{Abstract example}
\begin{lstlisting}
\begin{abstract}
A good research paper can be hampered by a poor abstract. The students following this class should thus focus on paper content rather than on its layout, so that they can summarize it properly in an attractive abstract.
\end{abstract}
\end{lstlisting}
\end{Boite}
\end{frame}

\begin{frame}[fragile]{OK, I specify \alert{what} things are}{Who will specify \alert{how} things are ?}
\begin{Boite}
{The rendering job is done by a software, upon your directives}
\begin{itemize}
\item The web browser renders the HT\ML\ language
\pause
\item  \LaTeX renders \alert{this presentation} as directed:
\begin{lstlisting}
\documentclass{beamer}
\mode<presentation> {
  \usetheme{Warsaw}
  \usecolortheme{wolverine}
  \setbeamercovered{dynamic}
}
\usepackage[frenchb,english]{babel}
\usepackage[utf8]{inputenc}
\usepackage{xcolor}
\usepackage{listings}
\title{How to write a scientific paper}
\author{N.~Fressengeas}
...
\end{lstlisting}
\end{itemize}
\end{Boite}
\end{frame}

\begin{frame}{Portability: another advantage of Markup languages}
\begin{Boite}
{In the HT\ML\  world}
Think of responsive websites which can be rendered differently on computers and smartphones using the same source code
\end{Boite}
\pause
\begin{Boite}
{In the \LaTeX  world}
\begin{itemize}
\item The same \LaTeX code can render articles for different journals
\item \LaTeX code is plain text, available on all platforms
\item \LaTeX code is stable through time
\item \LaTeX can, in some conditions, be converted to HT\ML
\end{itemize}
\end{Boite}

\end{frame}

\subsection{\LaTeX, a scientific writing tool}

\begin{frame}{\LaTeX, a typesetting system}{Read more: \href{https://tobi.oetiker.ch/lshort/lshort.pdf}{The not so short introduction to \LaTeX} or \href{http://tex.loria.fr/general/flshort-3.3.pdf}{Une courte (?)
introduction à \LaTeX}}
\begin{Boite}
{Origins}
\begin{itemize}
\item Written originally in 1983 by Leslie Lamport
\item Uses \TeX\ for typesetting
\item Free open source sofware
\item Current \LaTeX\ engine: \texttt{pdflatex}
\end{itemize}
\end{Boite}
\uncover<2->{
\begin{Boite}
{\LaTeX\  step by step}
\begin{itemize}
\item<2-|alert@2> Use your favorite text editor to produce \LaTeX\  code
\item<3-|alert@3> Run the \texttt{pdflatex} engine on the source code to get the PDF
\item<4-|alert@4> View the result with your favorite viewer
\end{itemize}
\end{Boite}
}
\end{frame}

\begin{frame}{\LaTeX\ all-in-one writing environment}{TexStudio, Kile, TeXShop, TeXMaker, WinEdt,TeXnicCenter\dots}
\begin{Boite}{All-in-one environments simplify the use of \LaTeX}
\begin{itemize}
\item Integrated code writing, \LaTeX-compiling and PDF viewing
\item In-line help on code writing
\item Multiple file management
\item Spell-checking
\item \dots
\end{itemize}
\end{Boite}
\pause
\begin{Boite}{Collaborative online environment}
\begin{itemize}
\item \href{https://v2.overleaf.com/}{Overleaf} for collaborative \LaTeX
\item \href{https://cocalc.com/}{CoCalc} for a collaborative environment including \LaTeX\  and various scientific softwares, allowing interactions between them\footnote{For example: embed \texttt{R}, \texttt{sage} ou \texttt{python} calculations in \LaTeX}
\end{itemize}
\end{Boite}
\end{frame}

\begin{frame}[fragile]{\LaTeX, dedicated to scientists}{A few features}
\begin{BoiteCentre}
{Focus on content, forget about presentation}
A state-of-the-art typesetting system will do the presentation for you
\end{BoiteCentre}
\pause
\begin{BoiteCentre}
{Neat equation rendering}
 \begin{lstlisting}
 \[\sum_{n=1}^{+\infty}\frac{1}{n^2}=\frac{\pi^2}{6}\]
 \end{lstlisting}
 \[\sum_{n=1}^{+\infty}\frac{1}{n^2}=\frac{\pi^2}{6}\]
\end{BoiteCentre}
\pause
\begin{BoiteCentre}{Journal specific class files}
Specifying the journal as your document class will set lay-out up for you
\end{BoiteCentre}
\end{frame}

\subsection{\LaTeX\  How To through practice}
\lstset
{
    language=[LaTeX]TeX,
    breaklines=true,
    basicstyle=\tt\tiny,
    keywordstyle=\color{blue},
    identifierstyle=\color{magenta},
}
\begin{frame}[fragile]{My first article}
\begin{columns}
\begin{Column}
%\begin{Boite}{}
\begin{lstlisting}
\documentclass[12pt]{article}
\title{My very first article in \LaTeX}
\author{Nicolas Fressengeas}
\begin{document}
\maketitle
\begin{abstract}
This is my very first article in \LaTeX. I will thus try to keep this abstract short
\end{abstract}
An introductory material can come before the first section
\section{\LaTeX\  is so great}
I love using \LaTeX. That is the reason why this section is named this way.
\section{Make the students understand it}
There is simply no other way to write, or beam, science. May my students understand this after this class !
\section{Conclusion}
This is nearing to the end of the first part of this class dedicated to tools. Now is the time to practice, before going into more scientific details.
\end{document}
\end{lstlisting}
%\end{Boite}
\end{Column}
\begin{Column}
%\begin{Boite}{}
\includegraphics[width=\linewidth]{FirstArticle/MyFirstArticle}
%\end{Boite}
\end{Column}
\end{columns}
\end{frame}


\begin{frame}{Learn \LaTeX\  How--To through practice}
\begin{BoiteCentre}{}
Typeset a Wikipedia article of your choice using \LaTeX.

Leave out and figures and references, for the moment.

\alert{Try to target a specific journal using its \LaTeX\   class.}
\end{BoiteCentre}
\end{frame}