WIP: Resources for the workshop in Lucca

.gitignore

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+*.aux
+*.bbl
+*.blg
+*.log
+*.synctex.gz

resources/latex/F1000_template/f1000_styles.sty

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+\ProvidesPackage{f1000_styles}
+% Packages
+\usepackage{authblk}
+\usepackage[english]{babel}
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage[bitstream-charter]{mathdesign}
+\usepackage{colortbl}
+\usepackage[usenames,dvipsnames,table]{xcolor}
+\usepackage{amsmath}
+\usepackage{graphicx}
+\usepackage{fancyhdr}
+\usepackage{setspace}
+\usepackage[labelsep=period,justification=justified]{caption}
+\usepackage{lastpage}
+\usepackage{xifthen}
+\usepackage{todonotes}
+\usepackage[hmargin=1.8cm,vmargin=2.2cm]{geometry}
+
+% Define the versionDate and flogo commands
+\newcommand{\versionDate}{\footnotesize \textit{F1000Research} 2016 - DRAFT ARTICLE (PRE-SUBMISSION)}
+\newcommand{\flogo}{\includegraphics[height=12pt]{F1000header.png}}
+
+% Section heading styles
+\usepackage[compact]{titlesec} 
+
+\titleformat*{\section}{\Large\usefont{OT1}{phv}{b}{n}\color{darkgray}}
+\titleformat*{\subsection}{\large\usefont{OT1}{phv}{b}{n}\color{MidnightBlue}}
+\titleformat*{\subsubsection}{\large\usefont{OT1}{phv}{b}{n}\color{MidnightBlue}}
+
+% Section heading spacing (reduced space below headings)
+\titlespacing\section{0pt}{3.5ex plus 1.2ex minus .2ex}{0ex}
+\titlespacing\subsection{0pt}{3.25ex plus 1.2ex minus .2ex}{0ex}
+\titlespacing\subsubsection{0pt}{3.25ex plus 1.2ex minus .2ex}{0ex}
+
+% Caption style
+\captionsetup{labelfont={color=red,bf},textfont={color=black,bf}}
+
+% Table style
+\definecolor{DarkKhaki}{rgb}{0.74,0.72,0.42}
+\colorlet{tableheadcolor}{DarkKhaki} % Table header colour = 25% gray
+\newcommand{\header}{\rowcolor{tableheadcolor}} %
+\colorlet{tablerowcolor}{DarkKhaki!50} % Table row separator colour = 10% gray
+\newcommand{\row}{\rowcolor{tablerowcolor}} %
+\newenvironment{tabledata}[1][1]{%
+  \renewcommand*{\extrarowheight}{0.1cm}%
+  \tabular%
+}{%
+  \endtabular
+}
+
+% Define a title note command
+\newcommand\titlenote[1]{\renewcommand\@titlenote{#1}}
+\newcommand\@titlenote{}
+
+% Column separation
+\setlength{\columnsep}{0.25in}
+
+% Page margins, headers and footers
+\pagestyle{fancy}
+\setlength\parindent{0in}
+%\setlength\parskip{0.1in}
+\setlength\headheight{16.5pt}
+\renewcommand{\footrulewidth}{1pt}
+\lhead{\textsc{\flogo}}
+\chead{}
+\rhead{\versionDate}
+\lfoot{}
+\cfoot{}
+\rfoot{\footnotesize Page \thepage\ of \pageref{LastPage}}
+%
+\renewenvironment{abstract}{%
+\usefont{OT1}{phv}{m}{n}
+\hfill\begin{minipage}{0.65\textwidth}
+\rule{\textwidth}{1pt}\\ \textcolor{Orange}{\textbf{\abstractname}}}
+{\par\noindent\rule{\textwidth}{1pt}\end{minipage}}
+%
+\makeatletter
+\renewcommand\@maketitle{%
+\begin{minipage}{0.95\textwidth}
+\vskip 2em
+\let\footnote\thanks 
+{\fontsize{20}{22}\usefont{OT1}{phv}{b}{n} \@title \par {\small{\@titlenote}} }
+\vskip 1.5em
+{\@author \par}
+\end{minipage}
+\vskip 1em \par
+}
+\makeatother
+\renewcommand\Authfont{\fontsize{16}{18}\usefont{OT1}{phv}{b}{n}}
+\renewcommand\Affilfont{\fontsize{10}{12}\usefont{OT1}{phv}{b}{n}}

resources/latex/F1000_template/sample.bib

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+@BOOK{Smith:2012qr,
+	title = {{B}ook {T}itle},
+	publisher = {Publisher},
+	author = {Smith, J.~M. and Jones, A.~B.},
+	year = {2012},
+	edition = {7th},
+}
+
+@ARTICLE{Smith:2013jd,
+	author = {Jones, A.~B. and Smith, J.~M.},
+	title = {{A}rticle {T}itle},
+	journal = {Journal title},
+	year = {2013},
+	volume = {13},
+	pages = {123-456},
+	number = {52},
+	month = {March},
+	publisher = {Publisher}
+}

resources/latex/F1000_template/template.tex

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+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Welcome to Overleaf --- just edit your article on the left,
+% and we'll compile it for you on the right. If you give 
+% someone the link to this page, they can edit at the same
+% time. See the help menu above for more info. Enjoy!
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% For more detailed article preparation guidelines, please see:
+% http://f1000research.com/author-guidelines
+
+\documentclass[10pt,a4paper,twocolumn]{article}
+\usepackage{f1000_styles}
+
+%% Default: numerical citations
+\usepackage[numbers]{natbib}
+
+%% Uncomment this lines for superscript citations instead
+% \usepackage[super]{natbib}
+
+%% Uncomment these lines for author-year citations instead
+% \usepackage[round]{natbib}
+% \let\cite\citep
+
+\begin{document}
+
+\title{\textit{F1000Research} Article Template}
+\titlenote{The title should be detailed enough for someone to know whether the article would be of interest to them, but also concise. Please ensure the broadness and claims within the title are appropriate to the content of the article itself.}
+\author[1]{Author Name1}
+\author[2]{Author Name2}
+\affil[1]{Address of author1}
+\affil[2]{Address of author2}
+
+\maketitle
+\thispagestyle{fancy}
+
+Please list all authors that played a significant role in the research involved in the article. Please provide full affiliation information (including full institutional address, ZIP code and e-mail address) for all authors, and identify who is/are the corresponding author(s).
+
+\begin{abstract}
+
+Abstracts should be up to 300 words and provide a succinct summary of the article. Although the abstract should explain why the article might be interesting, care should be taken not to inappropriately over-emphasize the importance of the work described in the article. Citations should not be used in the abstract, and the use of abbreviations should be minimized. If you are writing a Research or Systematic Review article, please structure your abstract into Background, Methods, Results, and Conclusions.
+
+
+\end{abstract}
+
+\section*{Keywords}
+
+Please list up to eight keywords to help readers interested in your article find it more easily.
+
+\clearpage
+
+\section*{Introduction}
+
+The format of the main body of the article is flexible: it should be concise and in the format most appropriate to displaying the content of the article.
+
+Some examples of commonly used \LaTeX{}  commands and features are listed below, to help you get started.
+
+
+\subsection*{Sections}
+
+Use section and subsection commands to organize your document. \LaTeX{} handles all the formatting and numbering automatically. Use ref and label commands for cross-references.
+
+
+\subsection*{Tables}
+
+Use the table and tabledata commands for basic tables --- see Table~\ref{tab:widgets}, for example.
+\begin{table}[h!]
+\hrule \vspace{0.1cm}
+\caption{\label{tab:widgets}An example of a simple table with caption.}
+\centering
+\begin{tabledata}{llr} 
+\header First name & Last Name & Grade \\ 
+\row John & Doe & $7.5$ \\ 
+\row Richard & Miles & $2$ \\ 
+\end{tabledata}
+\end{table}
+
+\subsection*{Figures}
+You can upload a figure (JPEG, PNG or PDF) using the files menu. To include it in your document, use the includegraphics command (see the example below in the source code).
+
+Please give figures appropriate filenames eg: figure1.pdf, figure2.png.
+
+Figure legends should briefly describe the key messages of the figure such that the figure can stand alone from the main text. However, all figures should also be discussed in the article text. Each legend should have a concise title of no more than 15 words. The legend itself should be succinct, while still explaining all symbols and abbreviations. Avoid lengthy descriptions of methods.
+
+For any figures reproduced from another publication (as long as appropriate permission has been obtained from the copyright holder —see under the heading 'Submission'), please include a line in the legend to state that: 'This figure has been reproduced with kind permission from [include original publication citation]'.
+
+\begin{figure}
+\centering
+\includegraphics[width=0.4\textwidth]{frog.jpg}
+\caption{\label{fig:your-figure}Your figure legend goes here; it should be succinct, while still explaining all symbols and abbreviations. }
+\end{figure}
+
+
+
+\subsection*{Mathematics}
+
+\LaTeX{} is great at typesetting mathematics. Let $X_1, X_2, \ldots, X_n$ be a sequence of independent and identically distributed random variables with $\text{E}[X_i] = \mu$ and $\text{Var}[X_i] = \sigma^2 < \infty$, and let
+$$S_n = \frac{X_1 + X_2 + \cdots + X_n}{n}
+      = \frac{1}{n}\sum_{i}^{n} X_i$$
+denote their mean. Then as $n$ approaches infinity, the random variables $\sqrt{n}(S_n - \mu)$ converge in distribution to a normal $\mathcal{N}(0, \sigma^2)$.
+
+\subsection*{Lists}
+
+You can make lists with automatic numbering \dots
+
+\begin{enumerate}
+\item Like this,
+\item and like this.
+\end{enumerate}
+\dots or bullet points \dots
+\begin{itemize}
+\item Like this,
+\item and like this.
+\end{itemize}
+
+\section*{Methods}
+Methods should include a brief discussion of allowances made (if any) for controlling bias or unwanted sources of variability, and the limitations of the datasets.
+
+
+\section*{Results}
+This section is not essential for Web Tool papers.
+
+\section*{Discussion}
+The discussion should include the implications of the article results in view of prior work in this field.
+
+\section*{Conclusions}
+Please state what you think are the main conclusions that can be realistically drawn from the findings in the paper, taking care not to make claims that cannot be supported.
+
+
+
+\subsection*{Author contributions}
+In order to give appropriate credit to each author of an article, the individual
+contributions of each author to the manuscript should be detailed in this section. We
+recommend using author initials and then stating briefly how they contributed.
+
+\subsection*{Competing interests}
+All financial, personal, or professional competing interests for any of the authors that
+could be construed to unduly influence the content of the article must be disclosed and
+will be displayed alongside the article.
+
+\subsection*{Grant information}
+Please state who funded the work discussed in this article, whether it is your employer,
+a grant funder etc. Please do not list funding that you have that is not relevant to this
+specific piece of research. For each funder, please state the funder’s name, the grant
+number where applicable, and the individual to whom the grant was assigned.
+If your work was not funded by any grants, please include the line: ‘The author(s)
+declared that no grants were involved in supporting this work.’
+
+\subsection*{Acknowledgements}
+This section should acknowledge anyone who contributed to the research or the
+article but who does not qualify as an author based on the criteria provided earlier
+(e.g. someone or an organisation that provided writing assistance). Please state how
+they contributed; authors should obtain permission to acknowledge from all those
+mentioned in the Acknowledgements section.
+
+Please do not list grant funding in this section.
+
+
+{\small\bibliographystyle{unsrtnat}
+\bibliography{sample}}
+
+\bigskip
+References can be listed in any standard referencing style that uses a numbering system
+(i.e. not Harvard referencing style), and should be consistent between references within
+a given article.
+
+Reference management systems such as Zotero provide options for exporting bibliographies as Bib\TeX{} files. Bib\TeX{} is a bibliographic tool that is used with \LaTeX{} to help organize the user's references and create a bibliography. This template contains an example of such a file, \texttt{sample.bib}, which can be replaced with your own. Use the \verb|\cite| command  to create in-text citations, like this \cite{Smith:2012qr} and this \cite{Smith:2013jd}.
+
+
+% See this guide for more information on BibTeX:
+% http://libguides.mit.edu/content.php?pid=55482&sid=406343
+
+% For more author guidance please see:
+% http://f1000research.com/author-guidelines
+
+
+% When all authors are happy with the paper, use the 
+% ‘Submit to F1000Research' button from the menu above
+% to submit directly to the open life science journal F1000Research.
+
+% Please note that this template results in a draft pre-submission PDF document.
+% Articles will be professionally typeset when accepted for publication.
+
+% We hope you find the F1000Research Overleaf template useful,
+% please let us know if you have any feedback using the help menu above.
+
+
+\end{document}

resources/latex/nature_template/template.bib

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+@Article{Einstein,
+  author =       "Albert Einstein",
+  title =        "{Zur Elektrodynamik bewegter K{\"o}rper}. ({German})
+                 [{On} the electrodynamics of moving bodies]",
+  journal =      "Annalen der Physik",
+  volume =       "322",
+  number =       "10",
+  pages =        "891--921",
+  year =         "1905",
+  DOI =          "http://dx.doi.org/10.1002/andp.19053221004"
+} 

resources/latex/nature_template/template.tex

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+%% Template for a preprint Letter or Article for submission
+%% to the journal Nature.
+%% Written by Peter Czoschke, 26 February 2004
+%%
+
+\documentclass{nature}
+
+%% make sure you have the nature.cls and naturemag.bst files where
+%% LaTeX can find them
+
+\bibliographystyle{naturemag}
+
+\title{Put title here (less than 90 characters).}
+
+%% Notice placement of commas and superscripts and use of &
+%% in the author list
+
+\author{Aauthor$^{1,2}$, Bauthor$^2$ \& LastAuthor$^2$}
+
+
+\begin{document}
+
+\maketitle
+
+\begin{affiliations}
+ \item Put institutions in this environment and
+ \item separate with \verb|\item| commands.
+\end{affiliations}
+
+\begin{abstract}
+For Nature, the abstract is really an introductory paragraph set
+in bold type.  This paragraph must be ``fully referenced'' and
+less than 180 words for Letters.  This is the thing that is
+supposed to be aimed at people from other disciplines and is
+arguably the most important part to getting your paper past the
+editors.  End this paragraph with a sentence like ``Here we
+show...'' or something similar.
+\end{abstract}
+
+Then the body of the main text appears after the intro paragraph.
+Figure environments can be left in place in the document.
+\verb|\includegraphics| commands are ignored since Nature wants
+the figures sent as separate files and the captions are
+automatically moved to the end of the document (they are printed
+out with the \verb|\end{document}| command. However, tables must
+be manually moved to the end of the document, after the addendum.
+
+Citation of Einstein's paper \cite{Einstein}.
+
+\begin{figure}
+%%%\includegraphics{something} % this command will be ignored
+\caption{Each figure legend should begin with a brief title for
+the whole figure and continue with a short description of each
+panel and the symbols used. For contributions with methods
+sections, legends should not contain any details of methods, or
+exceed 100 words (fewer than 500 words in total for the whole
+paper). In contributions without methods sections, legends should
+be fewer than 300 words (800 words or fewer in total for the whole
+paper).}
+\end{figure}
+
+\section*{Another Section}
+
+Sections can only be used in Articles.  Contributions should be
+organized in the sequence: title, text, methods, references,
+Supplementary Information line (if any), acknowledgements,
+interest declaration, corresponding author line, tables, figure
+legends.
+
+Spelling must be British English (Oxford English Dictionary)
+
+In addition, a cover letter needs to be written with the
+following:
+\begin{enumerate}
+ \item A 100 word or less summary indicating on scientific grounds
+why the paper should be considered for a wide-ranging journal like
+\textsl{Nature} instead of a more narrowly focussed journal.
+ \item A 100 word or less summary aimed at a non-scientific audience,
+written at the level of a national newspaper.  It may be used for
+\textsl{Nature}'s press release or other general publicity.
+ \item The cover letter should state clearly what is included as the
+submission, including number of figures, supporting manuscripts
+and any Supplementary Information (specifying number of items and
+format).
+ \item The cover letter should also state the number of
+words of text in the paper; the number of figures and parts of
+figures (for example, 4 figures, comprising 16 separate panels in
+total); a rough estimate of the desired final size of figures in
+terms of number of pages; and a full current postal address,
+telephone and fax numbers, and current e-mail address.
+\end{enumerate}
+
+See \textsl{Nature}'s website
+(\texttt{http://www.nature.com/nature/submit/gta/index.html}) for
+complete submission guidelines.
+
+\begin{methods}
+Put methods in here.  If you are going to subsection it, use
+\verb|\subsection| commands.  Methods section should be less than
+800 words and if it is less than 200 words, it can be incorporated
+into the main text.
+
+\subsection{Method subsection.}
+
+Here is a description of a specific method used.  Note that the
+subsection heading ends with a full stop (period) and that the
+command is \verb|\subsection{}| not \verb|\subsection*{}|.
+
+\end{methods}
+
+%% Put the bibliography here, most people will use BiBTeX in
+%% which case the environment below should be replaced with
+%% the \bibliography{} command.
+
+% \begin{thebibliography}{1}
+% \bibitem{dummy} Articles are restricted to 50 references, Letters
+% to 30.
+% \bibitem{dummyb} No compound references -- only one source per
+% reference.
+% \end{thebibliography}
+
+\bibliographystyle{naturemag}
+\bibliography{template}
+
+
+%% Here is the endmatter stuff: Supplementary Info, etc.
+%% Use \item's to separate, default label is "Acknowledgements"
+
+\begin{addendum}
+ \item Put acknowledgements here.
+ \item[Competing Interests] The authors declare that they have no
+competing financial interests.
+ \item[Correspondence] Correspondence and requests for materials
+should be addressed to A.B.C.~(email: myaddress@nowhere.edu).
+\end{addendum}
+
+%%
+%% TABLES
+%%
+%% If there are any tables, put them here.
+%%
+
+\begin{table}
+\centering
+\caption{This is a table with scientific results.}
+\medskip
+\begin{tabular}{ccccc}
+\hline
+1 & 2 & 3 & 4 & 5\\
+\hline
+aaa & bbb & ccc & ddd & eee\\
+aaaa & bbbb & cccc & dddd & eeee\\
+aaaaa & bbbbb & ccccc & ddddd & eeeee\\
+aaaaaa & bbbbbb & cccccc & dddddd & eeeeee\\
+1.000 & 2.000 & 3.000 & 4.000 & 5.000\\
+\hline
+\end{tabular}
+\end{table}
+
+\end{document}

talks/template.html

@@ -36,6 +36,7 @@ <h1> Some Title </h1>
 ## Slide title
 
 ![](../pics/.svg)<!-- .element: width="250" -->
+![](../pics/building_blocks.svg)<!-- .element: width="500" class="fragment fade-in"-->
 
 <imgcredit>Image author</imgcredit>