How can I use org-mode to write LaTeX for scientific journals?

Question

I write most text using org-mode nowadays, and I often use it to generate PDF via LaTeX (xelatex, specifcally). But now I want to use it to write scientific articles, and journals often want me to use a specific style. This includes a .cls-file, which is easy enough using org-latex-classes, but quite often, they require a specific setup following \begin{document} (i.e. a specific abstract section, funky author and affiliation, etc, and I don't see how to do that. That is, I now do this within a #+begin/end_latex section - but this needs to be completely rewritten if I switch style.

I realize I probably need to fiddle with the LaTeX code at some point, but I'd like to minimize this fiddling as far as possible, and I'd like to be able to switch from one journal to another with a minimum of fuss, and keeping my org-mode source as intact as possible.

Answer 1

See item 3 at http://kitchingroup.cheme.cmu.edu/blog/2014/08/08/What-we-are-using-org-mode-for/

There is a list of papers there we have written in org-mode and exported to LaTeX. We have probably 8 more since that post.

In the SI you can find the org-source embedded in the PDF, and here: Spencer D. Miller, Vladimir V. Pushkarev, Andrew J. Gellman and John R. Kitchin, Simulating Temperature Programmed Desorption of Oxygen on Pt(111) Using DFT Derived Coverage Dependent Desorption Barriers, Topics In Catalysis, 57(1), 106-117 (2013). http://link.springer.com/article/10.1007%2Fs11244-013-0166-3 you can even find our manuscript embedded.

You may also want to checkout https://github.com/jkitchin/org-ref for citation management and https://github.com/jkitchin/jmax/blob/master/ox-manuscript.el for how we do our exports.

Answer 2

Depending on the amount of latex polishing you need to do, you may find it simpler to just add some things to your org file, and use a little bit of babel directly. Here is a snippet of how the start of one my files might look. Some of things are in there, because I will also have the R code for the statistical analyses in the org file in order to be able to have a more reproducible work flow:

# -*- mode: org; org-export-babel-evaluate: nil -*-
#+Title: This is my title 
#+Author: An Author, Another Author, and Last Author
#+Options: toc:nil ':t *:nil -:nil ::nil <:nil ^:t author:t d:t H:5 |:t
#+Property: header-args:R :session *myarticlessection* :results output :exports both :cache yes
#+Latex_Class: article
#+Latex_Class_Options: [12pt]
#+Latex_Header: \usepackage{amsmath}
#+Latex_Header: \usepackage[T1]{fontenc}
#+Latex_Header: \usepackage{mathptmx}
#+Latex_Header_Extra: \linespread{1.5} 
#+LATEX_HEADER: \usepackage[citestyle=authoryear-icomp,bibstyle=authoryear, hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true] {biblatex}
#+Latex_header: \addbibresource{myarticles.bib}

#+BEGIN_SRC latex :results output
\begin{abstract}
Here is where I put the abstract.
\end{abstract}
#+END_SRC

#+RESULTS:
#+BEGIN_LaTeX
\begin{abstract}
And this is where it ended up after evaluating the babel block.
\end{abstract}
#+END_LaTeX

Answer 3

I used org-mode to write several papers, including my PhD thesis. It helped me greatly to keep track of open problems, priorities, annotations etc.

I use a small custom converter that reads the .org file and exports parts of it to a .tex file. Note that "normal" org-mode text (including headings, text, priorities, keywords etc.) is not exported, just the stuff between #BEGIN_LaTeX and #END_LaTeX tags. This way, you can make annotations as you see fit, which won't appear in the published text.