Once upon a time, scientific journals required you to submit manuscripts for review in specific formats, and many hours were spent by graduate students and postdocs as they sadly reformatted after every rejection.
Out of this frustration, biopreprint was born: a A LaTeX class and associated files for generating preprints for
journal submissions that would generate PDF files that looked more or less like what the journals expected. If you would like to use this system, please take a look at the latex_maint branch.
With the rise of BioRXiv and other preprint repositories, most journals now accept initial submissions in any format, so my lab now uses a much simpler workflow based on pandoc. The output looks professional but not excessively polished (please, don't use two-column formats), and includes various features like double-spacing and line numbers that your reviewers will love.
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Use
manuscript.mdto draft your manuscript in pandoc-flavored markdown. You can use LaTeX math mode and citations. Add references toreferences.bibor set thebibliographymetadata field to point to your.bibfiles. -
When the text is reasonably complete, run
pandoc --template=preprint-template.tex -o manuscript.tex manuscript.mdto generate the LaTeX template. -
Continue any further work in
manuscript.tex -
Generate the PDF for submission by running
pdflatex manuscriptthenbibtex manuscript. Then runpdflatex manuscriptuntil it stops mentioning citations and references. -
Good luck!
A few journals (looking at you, Science) still require manuscripts to be submitted in Word format. Good news! You can use pandoc to convert your LaTex file to docx. For example, this command does a pretty good job of getting you most of the way to a submittable document.
pandoc --bibliography=references.bib --csl=cslfiles/science.csl -o manuscript.docx manuscript.tex
You can find CSL files in various places around the web. There are a few in the cslfiles directory to get you started.