Preprint classes for biological journals
TeX
Latest commit d2d4cbc Jul 20, 2016 @dmeliza add some example citations

README.org

LaTeX Preprint Class for Biology Journals

#-*- mode: org -*-

A LaTeX class and associated files for generating preprints for journal submissions. Many journals accept submissions directly in LaTeX format and provide their own classes and styles for doing so. A large majority of biology journals are not so obliging, but many manuscripts submission systems will accept PDF files. The journal may ask for a document in some other format when the article is accepted, but if the article needs to be shopped around (a rather high probability in my world), reformatting a LaTeX file is much, much easier.

The class is based around the CTAN package nature, written by Peter Czoschke, using his NPG style bibliography and adding additional style and bst files for other journals. My LaTeX hacking skills are rather primitive and this should be considered as a general resource rather than a fully-fledged package. Assistance in further development is certainly welcome.

Instructions

The preprint class contains many of the packages and options I commonly use in writing a scientific manuscript. Journal-specific formatting is provided by a number of classes inheriting from preprint.

If you’re reading this document in Emacs in org-mode, you can use the instructions to generate a template document by typing C-c C-v C-t or executing the following command (type C-c C-c while in the code block)

(org-babel-tangle)

Preamble

The preprint classes are based on article, so you can pass any arguments in the documentclass command that you would to article. Do not use the preprint class itself, but select one of the classes specific to a journal or publishing group.

\documentclass[english]{neuron}

Document

The preprint class defines a number of environments that can be used to format the front page, abstract, and other sections that often have variant names.

Affiliations

The affiliations environment is a special list that prefixes each item with a superscript number. Add superscript numbers to the author command corresponding to each affliation. To suppress numbering for an item supply an empty optional argument.

\title{Auditory processing in the avian forebrain}
\author{C Daniel Meliza\textsuperscript{1} \& Distinguished Mentor\textsuperscript{1,2}}

\begin{document}
\maketitle
\begin{affiliations}
\item Department of Organismal Biology and Anatomy
\item Department of Psychology
\item[] University of Chicago, Chicago, Illinois 60647, USA
\end{affiliations}

Front matter

Front matter can include running titles, corresponding author, acknowledgements, etc. The frontpage environment is a simple single-spaced list.

\begin{frontpage}
  \item[Running title:] Cortical processing in avian forebrain
  \item[Corresponding Author:] ~\\
C. Daniel Meliza\\
Department of Organismal Biology and Anatomy\\
The University of Chicago\\
1027 E 57th Street\\
Chicago, IL 60647, USA\\
Ph. (773) 702-8090\\
Fax (773) 702-0037\\
\end{frontpage}

Sections

Each of the standard sections of a paper (Abstract, Introduction, Methods, Results, Discussion) have a corresponding environment. This allows the style files to control formatting and title according to the journal’s style.

Note, however, that the ordering of the sections is not defined by the style, but by their actual order in the text, so some rearrangement may be necessary.

\begin{abstract}
  May have a heading, and could be boldface
\end{abstract}

\begin{introduction}
  May have a heading

  \subsection{Introductory subsection}
  Subsection titles may be allowed

\end{introduction}

\begin{methods}
  May be called any number of things
\end{methods}

\begin{results}
  The most straightforward section
\end{results}

\begin{discussion}
  May be titled differently
  \subsection{Discussion subsection}
  Discussion subsections may be allowed
\end{discussion}

\paragraph{Acknowledgements}  This section may need to go in the front
matter, which is up to the user.

References

Citations and reference lists are handled with natbib. Use the \citep command for most citations and preprint will select the correct format (author-date, superscript or parenthetical numbers). Some manual adjustment may be necessary when part of the citation goes in the text; e.g. “the striking work by Meliza et al. (2006)”.

% The \references command creates section heading if needed, and
% clears the page if needed
\references{mybibliography}

Suppress subsection headings in formats that do not allow them.

Figures

Figures are generally submitted separately from the document text, so preprint suppresses any includegraphics commands. Two options for including figure legends are supported. One is to use normal figure float environments at any point in the text, followed by a \listoffigures command where the legends should appear. The other is to use unfloated \includegraphics commands followed by \captionof{figure}. The latter is a bit more flexible.

Additional control can be obtained with the subfig package.

\begin{figure}
\includegraphics{MyFigure}
\caption{ Cumulative Response Distributions\newline
Note that the usual double-slash does not insert a newline in the caption.}
\label{fig:response-dist}
\end{figure}

\listoffigures
\end{document}

Supported Formats

The following formats are current as of May 2011.

Nature Neuroscience (and probably other NPG journals): natneurosci.cls

Superscript citations, untitled Introduction. Figure Legends should come between Acknowledgements and Methods.

Neuron (and probably other Cell Press journals): neuron.cls

Author-date citations, abstract called Summary, methods called Experimental Procedures. Adds an environment called highlights which is a list of main findings that should follow the Summary

Journal of Neuroscience: jneurosci.cls

Author-date citations, methods called Materials and Methods. Journal requires quite a bit of front matter.

Journal of Neurophysiology

License

All modifications to the nature package are Copyright 2011 C Daniel Meliza (dan@meliza.org)

This work may be distributed and/or modified under the conditions of the LaTeX Project Public License, either version 1.3 of this license or (at your option) any later version.

The latest version of this license is in http://www.latex-project.org/lppl.txt and version 1.3 or later is part of all distributions of LaTeX version 2005/12/01 or later.

This work has the LPPL maintenance status `maintained’.

The Current Maintainer of this work is C.D. Meliza

This work consists of the files jneurosci.bst, jneurosci.cls, natneurosci.cls, naturemag.bst, neuron.bst, neuron.cls, and preprint.cls