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Protocol Sheet template base

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      example.tex
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example.tex View File

@@ -1,29 +1,37 @@
\documentclass[a4paper]{tufte-handout} \documentclass[a4paper]{tufte-handout}


\title{An Example of the Usage of the Tufte-Handout Style\thanks{Inspired by Edward~R. Tufte!}}
\title{Protocol number X - Title Y}


\author[The Tufte-LaTeX Developers]{The Tufte-\LaTeX\ Developers}
%\author[]{Daniel Klapak ,Sarah Broadfoot ,Gregory Penner,Anup Singh ,Eshwar Inapuri [https://doi.org/10.1371/journal.pone.0205460] }


\date{03 February 2022} % without \date command, current date is supplied
\date{04 April 2022} % without \date command, current date is supplied


%\geometry{showframe} % display margins for debugging page layout
\usepackage[utf8]{inputenc} \usepackage[utf8]{inputenc}
\usepackage[english]{babel} \usepackage[english]{babel}
\usepackage[sfdefault, light]{FiraSans} \usepackage[sfdefault, light]{FiraSans}
\usepackage[T1]{fontenc} \usepackage[T1]{fontenc}
\usepackage{parskip}
\usepackage{textcomp} \usepackage{textcomp}
\usepackage{array}
\usepackage{enumitem,amssymb}
\newlist{todolist}{itemize}{2}
\setlist[todolist]{label=$\square$}


\usepackage{graphicx} % allow embedded images \usepackage{graphicx} % allow embedded images
\setkeys{Gin}{width=\linewidth,totalheight=\textheight,keepaspectratio} \setkeys{Gin}{width=\linewidth,totalheight=\textheight,keepaspectratio}
\graphicspath{{graphics/}} % set of paths to search for images
\graphicspath{ {./images/} } % set of paths to search for images
\usepackage{amsmath} % extended mathematics \usepackage{amsmath} % extended mathematics
\usepackage{booktabs} % book-quality tables \usepackage{booktabs} % book-quality tables
\usepackage{units} % non-stacked fractions and better unit spacing \usepackage{units} % non-stacked fractions and better unit spacing
\usepackage{multicol} % multiple column layout facilities \usepackage{multicol} % multiple column layout facilities
\usepackage{lipsum} % filler text \usepackage{lipsum} % filler text
\usepackage{fancyvrb} % extended verbatim environments \usepackage{fancyvrb} % extended verbatim environments
\usepackage{multicol}
\setlength{\columnsep}{0.75cm}
\fvset{fontsize=\normalsize}% default font size for fancy-verbatim environments \fvset{fontsize=\normalsize}% default font size for fancy-verbatim environments



% Standardize command font styles and environments % Standardize command font styles and environments
\newcommand{\doccmd}[1]{\texttt{\textbackslash#1}}% command name -- adds backslash automatically \newcommand{\doccmd}[1]{\texttt{\textbackslash#1}}% command name -- adds backslash automatically
\newcommand{\docopt}[1]{\ensuremath{\langle}\textrm{\textit{#1}}\ensuremath{\rangle}}% optional command argument \newcommand{\docopt}[1]{\ensuremath{\langle}\textrm{\textit{#1}}\ensuremath{\rangle}}% optional command argument
@@ -35,262 +43,126 @@
\newenvironment{docspec}{\begin{quote}\noindent}{\end{quote}}% command specification environment \newenvironment{docspec}{\begin{quote}\noindent}{\end{quote}}% command specification environment


\begin{document} \begin{document}
\footnotesize


\maketitle% this prints the handout title, author, and date \maketitle% this prints the handout title, author, and date



\vspace{-2em}

\begin{abstract} \begin{abstract}
\noindent \noindent
This document describes the Tufte handout \LaTeX\ document style.
It also provides examples and comments on the style's use.
Only a brief overview is presented here;
for a complete reference, see the sample book.
\footnotesize
Summary of the Current experiment can be provided here in this paragraph
\end{abstract} \end{abstract}


%\printclassoptions

The Tufte-\LaTeX\ document classes define a style similar to the
style Edward Tufte uses in his books and handouts. Tufte's style is known
for its extensive use of sidenotes, tight integration of graphics with
text, and well-set typography. This document aims to be at once a
demonstration of the features of the Tufte-\LaTeX\ document classes
and a style guide to their use.

\section{Page Layout}\label{sec:page-layout}
\subsection{Headings}\label{sec:headings}
This style provides \textsc{a}- and \textsc{b}-heads (that is,
\Verb|\section| and \Verb|\subsection|), demonstrated above.

The Tufte-\LaTeX\ classes will emit an error if you try to use
\linebreak\Verb|\subsubsection| and smaller headings.

% let's start a new thought -- a new section
\newthought{In his later books},\cite{Tufte2006} Tufte
starts each section with a bit of vertical space, a non-indented paragraph,
and sets the first few words of the sentence in \textsc{small caps}. To
accomplish this using this style, use the \Verb|\newthought| command:
\begin{docspec}
\doccmd{newthought\{In his later books\}, Tufte starts\ldots}
\end{docspec}

\subsection{Sidenotes}\label{sec:sidenotes}
One of the most prominent and distinctive features of this style is the
extensive use of sidenotes. There is a wide margin to provide ample room
for sidenotes and small figures. Any \Verb|\footnote|s will automatically
be converted to sidenotes.\footnote{This is a sidenote that was entered
using the \texttt{\textbackslash footnote} command.} If you'd like to place ancillary
information in the margin without the sidenote mark (the superscript
number), you can use the \Verb|\marginnote| command.\marginnote{This is a
margin note. Notice that there isn't a number preceding the note, and
there is no number in the main text where this note was written.}

The specification of the \Verb|\sidenote| command is:
\begin{docspec}
\doccmd{sidenote[\docopt{number}][\docopt{offset}]\{\docarg{Sidenote text.}\}}
\end{docspec}

Both the \docopt{number} and \docopt{offset} arguments are optional. If you
provide a \docopt{number} argument, then that number will be used as the
sidenote number. It will change of the number of the current sidenote only and
will not affect the numbering sequence of subsequent sidenotes.

Sometimes a sidenote may run over the top of other text or graphics in the
margin space. If this happens, you can adjust the vertical position of the
sidenote by providing a dimension in the \docopt{offset} argument. Some
examples of valid dimensions are:
\begin{docspec}
\ttfamily 1.0in \qquad 2.54cm \qquad 254mm \qquad 6\Verb|\baselineskip|
\end{docspec}
If the dimension is positive it will push the sidenote down the page; if the
dimension is negative, it will move the sidenote up the page.

While both the \docopt{number} and \docopt{offset} arguments are optional, they
must be provided in order. To adjust the vertical position of the sidenote
while leaving the sidenote number alone, use the following syntax:
\begin{docspec}
\doccmd{sidenote[][\docopt{offset}]\{\docarg{Sidenote text.}\}}
\end{docspec}
The empty brackets tell the \Verb|\sidenote| command to use the default
sidenote number.

If you \emph{only} want to change the sidenote number, however, you may
completely omit the \docopt{offset} argument:
\begin{docspec}
\doccmd{sidenote[\docopt{number}]\{\docarg{Sidenote text.}\}}
\end{docspec}

The \Verb|\marginnote| command has a similar \docarg{offset} argument:
\begin{docspec}
\doccmd{marginnote[\docopt{offset}]\{\docarg{Margin note text.}\}}
\end{docspec}

\subsection{References}
References are placed alongside their citations as sidenotes,
as well. This can be accomplished using the normal \Verb|\cite|
command.\sidenote{The first paragraph of this document includes a citation.}

The complete list of references may also be printed automatically by using
the \Verb|\bibliography| command. (See the end of this document for an
example.) If you do not want to print a bibliography at the end of your
document, use the \Verb|\nobibliography| command in its place.

To enter multiple citations at one location,\cite{Tufte2006,Tufte1990} you can
provide a list of keys separated by commas and the same optional vertical
offset argument: \Verb|\cite{Tufte2006,Tufte1990}|.
\begin{docspec}
\doccmd{cite[\docopt{offset}]\{\docarg{bibkey1,bibkey2,\ldots}\}}
\end{docspec}

\section{Figures and Tables}\label{sec:figures-and-tables}
Images and graphics play an integral role in Tufte's work.
In addition to the standard \docenv{figure} and \docenv{tabular} environments,
this style provides special figure and table environments for full-width
floats.

Full page--width figures and tables may be placed in \docenv{figure*} or
\docenv{table*} environments. To place figures or tables in the margin,
use the \docenv{marginfigure} or \docenv{margintable} environments as follows
(see figure~\ref{fig:marginfig}):

\begin{marginfigure}%
\includegraphics[width=\linewidth]{helix}
\caption{This is a margin figure. The helix is defined by
$x = \cos(2\pi z)$, $y = \sin(2\pi z)$, and $z = [0, 2.7]$. The figure was
drawn using Asymptote (\url{http://asymptote.sf.net/}).}
\label{fig:marginfig}
\end{marginfigure}
\begin{Verbatim}
\begin{marginfigure}
\includegraphics{helix}
\caption{This is a margin figure.}
\end{marginfigure}
\end{Verbatim}

The \docenv{marginfigure} and \docenv{margintable} environments accept an optional parameter \docopt{offset} that adjusts the vertical position of the figure or table. See the ``\nameref{sec:sidenotes}'' section above for examples. The specifications are:
\begin{docspec}
\doccmd{begin\{marginfigure\}[\docopt{offset}]}\\
\qquad\ldots\\
\doccmd{end\{marginfigure\}}\\
\mbox{}\\
\doccmd{begin\{margintable\}[\docopt{offset}]}\\
\qquad\ldots\\
\doccmd{end\{margintable\}}\\
\end{docspec}

Figure~\ref{fig:fullfig} is an example of the \Verb|figure*|
environment and figure~\ref{fig:textfig} is an example of the normal
\Verb|figure| environment.

\begin{figure*}[h]
\includegraphics[width=\linewidth]{sine.pdf}%
\caption{This graph shows $y = \sin x$ from about $x = [-10, 10]$.
\emph{Notice that this figure takes up the full page width.}}%
\label{fig:fullfig}%
\end{figure*}

\begin{figure}
\includegraphics{hilbertcurves.pdf}
% \checkparity This is an \pageparity\ page.%
\caption{Hilbert curves of various degrees $n$.
\emph{Notice that this figure only takes up the main textblock width.}}
\label{fig:textfig}
%\zsavepos{pos:textfig}
\setfloatalignment{b}
\end{figure}

Table~\ref{tab:normaltab} shows table created with the \docpkg{booktabs}
package. Notice the lack of vertical rules---they serve only to clutter
the table's data.

\begin{table}[ht]
\centering
\fontfamily{ppl}\selectfont
\begin{tabular}{ll}
\toprule
Margin & Length \\
\midrule
Paper width & \unit[8\nicefrac{1}{2}]{inches} \\
Paper height & \unit[11]{inches} \\
Textblock width & \unit[6\nicefrac{1}{2}]{inches} \\
Textblock/sidenote gutter & \unit[\nicefrac{3}{8}]{inches} \\
Sidenote width & \unit[2]{inches} \\
\bottomrule
\end{tabular}
\caption{Here are the dimensions of the various margins used in the Tufte-handout class.}
\label{tab:normaltab}
%\zsavepos{pos:normaltab}
\vspace{-2em}

\section{Chemicals used :}
\vspace{-1em}
\begin{table}[h!]
\footnotesize
\centering
\begin{tabular}{||c | c | c | c||}
\hline
Chemical name & Provider & Mol wt.(g/mol) & Additional safety requirements \\ [0.5ex]
\hline\hline
1 & 6 & 87837 & 787 \\
2 & 7 & 78 & 5415 \\
3 & 545 & 778 & 7507 \\
4 & 545 & 18744 & 7560 \\
5 & 88 & 788 & 6344 \\ [1ex]
\hline
\end{tabular}
\end{table} \end{table}


\section{Full-width text blocks}

In addition to the new float types, there is a \docenv{fullwidth}
environment that stretches across the main text block and the sidenotes
area.

\begin{Verbatim}
\begin{fullwidth}
Lorem ipsum dolor sit amet...
\end{fullwidth}
\end{Verbatim}
\vspace{-1em}


\begin{fullwidth}
\small\itshape\lipsum[1]
\end{fullwidth}
\section{Experiment}\label{sec:page-layout}
\vspace{-1em}
\begin{multicols}{2}
\subsection{Buffers and solutions}\label{sec:headings}
\begin{todolist}
\item Carboxyl-coated or silica-coated magnetic beads in TE buffer (X µl per sample)\\
\item TE buffer (X µl per sample)\\
\item Isopropanol (X µl per sample) \\
\item 80\% ethanol (X µl per sample) \\
\item Lysis buffer (. X µl per sample) find composition\\


\section{Typography}\label{sec:typography}
\end{todolist}


\subsection{Typefaces}\label{sec:typefaces}
If the Palatino, \textsf{Helvetica}, and \texttt{Bera Mono} typefaces are installed, this style
will use them automatically. Otherwise, we'll fall back on the Computer Modern
typefaces.


\subsection{Letterspacing}\label{sec:letterspacing}
This document class includes two new commands and some improvements on
existing commands for letterspacing.


When setting strings of \allcaps{ALL CAPS} or \smallcaps{small caps}, the
letter\-spacing---that is, the spacing between the letters---should be
increased slightly.\cite{Bringhurst2005} The \Verb|\allcaps| command has proper letterspacing for
strings of \allcaps{FULL CAPITAL LETTERS}, and the \Verb|\smallcaps| command
has letterspacing for \smallcaps{small capital letters}. These commands
will also automatically convert the case of the text to upper- or
lowercase, respectively.
\vspace{-1em}


The \Verb|\textsc| command has also been redefined to include
letterspacing. The case of the \Verb|\textsc| argument is left as is,
however. This allows one to use both uppercase and lowercase letters:
\textsc{The Initial Letters Of The Words In This Sentence Are Capitalized.}


\subsection{Equipment and Setup}\label{sec:sidenotes}


\begin{todolist}
\item Fume hood\\
\item Magnetic stand \\
\item Minifuge \\
\item Heat block \\
\item Pipettes\\
\end{todolist}
\vspace{-1em}


\section{Installation}\label{sec:installation}
To install the Tufte-\LaTeX\ classes, simply drop the
following files into the same directory as your \texttt{.tex}
file:
\begin{quote}
\ttfamily
tufte-book.cls\\
tufte-common.def\\
tufte-handout.cls\\
tufte.bst
\end{quote}


% TODO add instructions for installing it globally
\end{multicols}


\vspace{-1em}


\begin{table}
\centering
\footnotesize
\begin{tabular}{||c | c | c | c||}
\hline
\centering
Reagents &Concentrations & Stock solution & For X ml \\ [1ex]
\hline\hline
GITC & 2 & 3 & 4\\
Tris HCl & 7 & 78 & 5415 \\
Sarkosyl & 545 & 778 & 7507 \\
EDTA & 545 & 18744 & 7560 \\
Antifoam (optional) & 88 & 788 & 6344 \\ [0.5ex]
\hline
\end{tabular}
\end{table}


\section{More Documentation}\label{sec:more-doc}
For more documentation on the Tufte-\LaTeX{} document classes (including commands not
mentioned in this handout), please see the sample book.

\section{Support}\label{sec:support}

The website for the Tufte-\LaTeX\ packages is located at
\url{https://github.com/Tufte-LaTeX/tufte-latex}. On our website, you'll find
links to our \smallcaps{svn} repository, mailing lists, bug tracker, and documentation.

\bibliography{example}
\bibliographystyle{plainnat}

\subsection{Sample collection and TNA purification}

\vspace{-1em}

\begin{table}[h!]
\footnotesize
\begin{tabular}{| m{12cm} | m{1cm} | m{3 cm}|}
\hline
Step & Time & Observations/Notes \\ [0.1ex]
\hline\hline
\begin{todolist}
\item Collect up to 106
cultured mammalian cells in a single well of a deep-well plate
\end{todolist} & & \\
\begin{todolist}
\item Pellet the cells via centrifugation at 500g and discard supernatant
\end{todolist} & 10 min & \\
\hline
\end{tabular}
\end{table}



\section{Observations}
\vspace{-1em}
Add observations here
\vspace{-1em}
\section{Results}\label{sec:results}
\vspace{-1em}
Add results here
\vspace{-1em}
\section{Iterations}
\vspace{-1em}
Add iterations here




\end{document} \end{document}

+ 2
- 2
tufte-common.def View File

@@ -443,10 +443,10 @@
%% %%
% Set page layout geometry % Set page layout geometry


\RequirePackage[letterpaper,left=0.5in,top=1in,headsep=2\baselineskip,textwidth=26pc,marginparsep=2pc,marginparwidth=12pc,textheight=44\baselineskip,headheight=\baselineskip]{geometry}
\RequirePackage[letterpaper,left=0.25in,top=0.25in,headsep=2\baselineskip,textwidth=26pc,marginparsep=2pc,marginparwidth=6pc,textheight=40\baselineskip,headheight=\baselineskip]{geometry}


\ifthenelse{\boolean{@tufte@afourpaper}} \ifthenelse{\boolean{@tufte@afourpaper}}
{\geometry{a4paper,left=19.8mm,top=20.4mm,headsep=2\baselineskip,textwidth=118mm,marginparsep=8.2mm,marginparwidth=49.4mm,textheight=49\baselineskip,headheight=\baselineskip}}
{\geometry{a4paper,left=9.8mm,top=10.4mm,headsep=2\baselineskip,textwidth=118mm,marginparsep=4.2mm,marginparwidth=25.4mm,textheight=40\baselineskip,headheight=\baselineskip}}
{} {}


\ifthenelse{\boolean{@tufte@bfivepaper}} \ifthenelse{\boolean{@tufte@bfivepaper}}


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