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LaTeX Template for Scientific Manuscript

There are many LaTeX templates for scientific manuscripts out there (see the writeLaTeX template gallery), but this template is based on a recent manuscript that I put together for Nature Neuroscience. The requirements were annoying and the document ended up being quite complex. My previously helpful manuscript template ballooned with complexity and corresponding hacks and kludges. This template is my attempt at distilling out the hackiness and including nice features that I wish I had had while writing, such as mirroring the supplementary figure captions at the end of the main manuscript, making the figures appear correctly at scale, and handling citations correctly across sections.

File organization

One of the goals here was a modular document, so most of the content is contained in \include'd files. You can change what gets rendered using the \includeonly command in the preamble, and I have a bunch of precooked ones there already (but commented out). (An unfortunate quirk I found is that latexdiff looks for \includeonly commands but doesn't recognize if they are commented out, so I also obfuscated them by inserting asterisks.) I have a script (git-ldiff.sh) for compiling diffs between git revisions using latexdiff, but a current version of latexdiff is necessary to allow recursive \includes. Figures are currently assumed to be PNG images named figures/Figures_<key>.png or figures/SuppFigures_<key>.png. There are additional notes in the comments of main.tex that document how most things work