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Generic Manuscript Template

abstract guidance

I draft the abstract after defining the scope of the paper with the Introduction and outlining the key results in the Results section and maybe the Discussion section. I usually rewrite the abstract after the first draft is finished. The abstract is often single-spaced. I enclosed the abstract in the singlespace environment.

keyword guidance

The paragraph environment in LaTeX does not have a native analog in org. However, org will implement the paragraph command on export to PDF.

\paragraph{ Keywords:} I draft the keywords in the writing document and select the best up to the allowable limit. \paragraph{Abbreviations:} GUI: graphical user interface, IDE: integrated development environment

Introduction

introduction guidance

The Introduction is not a literature review. That is a separate class manuscript.

The first paragraph defines the scope of the problem and why it is important. It might cite several key contributions in the area \cite{Acharya2011SolvingProbabilisticProgrammingProblemsInvolvingMultiChoiceParameters, Luft2007EfficientOptimizationOfCrystallizationConditionsByManipulationOfDropVolumeRatioAndTemperature}. I like to use the author-year format to make it easier for reviewers, regardless of the required format. Numbered formats are harder to lookup. The last sentence should set up the first sentence of the following paragraph by hinting at possible approaches to the question or problem at hand.

The second paragraph starts with the central hypothesis that addresses the question or problem alluded to in paragraph one. A summary of our approach follows this. A sentence or two may be expended on summarizing what we found. The last sentence describes the audience of the article.

Materials and Methods

methods guidance

This section is a series of subsections that may or may not be in chronological order. This section is often placed after the Discussion section.

Results

results guidance

Paragraph One: Map of the Results section. This introductory paragraph is usually missing, but no editor has ever asked me to delete it. This paragraph tells the reader in more detail than the Introduction what they can expect to see and the order in which the results will be presented.

Most important result

most important result guidance

Cover the results in decreasing importance relative to the degree to which they address the paper’s central hypothesis. If they have no relevance, save them from another paper. Chronological order is usually a poor choice. End each paragraph with a conclusion.

Please take a look at tables and figures using their labels. For example, see the hot figure (Fig. \ref{fig:labelA}). The numbering of the figures is handled automatically, so you can reorganize them without renumbering them.

Second most important result

guidance second most important result

See hot numbers in (Table \ref{tab:first}). The numbering of the tables is handled automatically, so you can reorganize them without renumbering them.

Third most important result

guidance third most important result

Inline equations are placed between dollar signs: $y = mx + b$. Display equations are placed between double-dollar signs or inside an equation environment. These environments are not floats. You can define a custom float to enclose them and place them inside the float to enable the use of captions as I did below. The \emph{equ} environment is defined in the preamble.

\begin\begin{equ}[htp] \begin{equation} i \hbar \frac{d}{d t}|Ψ(t)\rangle=\hat{H}|Ψ(t)\rangle \end{equation} \caption{Eq. \label{Eq:first}Schrodinger’s time-dependent wave equation.} \end{equ}

Fourth most important result

guidance fourth most important result

Code listings also have to be enclosed inside floats to have captions. The caption can be placed above or below the code listing.

These environments must be enclosed in the single-space environment to retain single-line spacing in the code block.

The minted package provides syntax highlighting. The \mintinline{bash}{-shell-escape} must be used on compiling.

Fifth most important result

Sixth most important result

guidance sixth most important result

There could be up to four more subsections in a results-heavy paper.

There are usually four graphics and two tables in a minimal publishable unit. This is a weak guideline because of the trend to use multipanel figures. I have seen figures with ten panels. Is this one figure or ten?

Delete all results that are less important or do not address the central hypothesis.

Nonsense text

Discussion

discussion guidance

How our results relate to the results of others. (Avoid using merged Results and Discussion sections. They rarely work well. This is a research paper, not a seminar).

Paragraph One: Map of the Discussion section. This paragraph usually needs to be included to orient the reader.

Paragraphs two and beyond must end with conclusions in their last sentences. The conclusion can be a call to do more research.

Lay out the topics of declining importance.

Delete the paragraph with no bearing on the central hypothesis.

Nonsense text

Acknowledgments

acknowledgments guidance

Acknowledgments of core facilities and grant support. Double-check the grant numbers. It is easy to make typos in these. These acknowledgments are critical to the continued support of grants.

Bibliography

List of Tables

tables guidance

Tables should be one per page.

The manual assembly of tables is a challenge for beginners. Pandas, R, and the Python package latextable \url{https://github.com/JAEarly/latextable} can write out LaTeX tables. Tables are easy to assemble in org-mode in Emacs and exported to LaTeX. Markdown tables can be exported to LaTeX with pandoc. There are online tools to aid in assembling LaTeX tables: \url{https://www.tablesgenerator.com/}.

The first table below was made with vanilla LaTeX. The second table was made with the booktabs package: The horizontal rules are of different weights in the latter table.

There is a \emph{longtable} package for supporting tables spaning more than one page. It is also possible to have tables oriented in the landscape orientation via the \emph{lscape} package.

\begin{table}[htp] \centering \caption{\label{tab:first} My summary statistics in the default LaTeX table. Dummy data.} \begin{tabular}{lllll}\hline Parameter & Group A & Group B & Group C & Group D \ \hline Length ($μ$m) & 100 & 150 & 175 & 250
Weight (ng) & 10 & 50 & 40 & 50\ Density (g/m) & 0.01 & 0.03 & 0.09 & 0.77\ \hline \end{tabular} \end{table}

\begin{table}[htp] \centering \caption{\label{tab:second} My summary statistics made with the booktabs package. Dummy data.} \begin{tabular}{lllll}\toprule % l c and r control the alignment of the text in the table fields Parameter & Group A & Group B & Group C & Group D \ \midrule Length ($μ$m) & 100 & 150 & 175 & 250
Weight (ng) & 10 & 50 & 40 & 50\ Density (g/m) & 0.01 & 0.03 & 0.09 & 0.77\ \bottomrule \end{tabular} \end{table}

guidance list of figures

One figure per page.

\begin{figure}[htp] \begin{center} \includegraphics[width=3.25in]{./figs/wcPlot} \caption{\label{fig:labelA} This beautiful graph relates X to Y. } \end{center} \end{figure}