Techie Notes

Writing Open Access Papers like a Pro

Tagged: openscience

I decided to try writing papers pretty much the same way I write programs.

My goal was:

  1. to have the whole process open from the very start
  2. to use Open Source tools including Vim – my editor of choice
  3. to use LaTeX – Open Source editor and markup language
  4. to keep live updates of resulting PDF so I have an immediate feedback after saving my files

Here are steps to achieve this on Ubuntu Linux:

Install LaTeX

sudo apt-get install texlive-full

And you can go for a walk, go for a lunch, watch a movie… It will take a while.

Install tmux and tmuxinator

See my post about them

Download template for a paper

In this case I want to target BMC Bioinformatics, so I took a BMC template

Unzip template and copy it into a suitable place

I did create ~/papers/gnparser directory for this project

Make tmuxinator configuration

Mine looks like this:

# ~/.tmuxinator/parpaper.yml

name: parpaper
root: ~/papers/gnparser

# Optional tmux socket
# socket_name: foo

# Runs before everything. Use it to start daemons etc.
# pre: sudo /etc/rc.d/mysqld start

# Runs in each window and pane before window/pane specific commands. Useful for
# setting up interpreter versions.  pre_window: rbenv shell 2.0.0-p247

# Pass command line options to tmux. Useful for specifying a different
# tmux.conf.  tmux_options: -f ~/.tmux.mac.conf

# Change the command to call tmux.  This can be used by derivatives/wrappers
# like byobu.  tmux_command:

# Specifies (by name or index) which window will be selected on project
# startup. If not set, the first window is used.  startup_window: logs

  - editor:
      layout: 006f,123x31,0,0{80x31,0,0,13,42x31,81,0,16}
        - vim -p ./gnparser.tex ./gnparser.bib
        - clear && latexmk -pvc -pdf -bibtex gnparser.tex
  - bash:

Add .latexmkrc file to the paper directory

Mine tells to run latexmk continuously and use evince as pdf viewer

$pdflatex = 'pdflatex -interaction=nonstopmode';
$pdf_previewer = "evince";

Start the project!

In my case

mux parpaper

And I am all set! On the left I have vim editor window, on the right I have live output from latexmk on continuous building of the PDF. If I see a trouble with PDF building – I run

pdflatex gnparser.tex

To see and correct problems

LaTeX on VIM

And PDF is automatically updating on every write

latexmk makes pdf

Enjoy GitHub ecosystem

Now I put the paper on GitHub and enjoy all the niceties GitHub gives to users. I can plan my work ahead using GitHub Issues, get changes from coathors through pull requests, and with ZenHub installed I can even setup agile-like iterations and see burndown while I am progressing on paper