The Living Thing / Notebooks :

Academic writing workflow

Minimising the friction of of advertising my thoughts in order to maximise the chance a clever thought makes it out there.

Beautiful typesetting with LaTeX

“Documenting my academic writing workflow and how to improve it”, or, “How I learned to stop worrying and love text files”.

See also text editors, LaTeX, citation management, scientific computation workflow, plain text blogging, markdown.

Science writing blogs

This blog, and virtually all my notes, are in plain text files on my computer, published online as plain html files. It's an informal open notebook.

I had to jump through some hoops to make this work, because I need mathematical markup support and basic citation management. Vanilla, non-academic plain text blogging is simpler. But even this academic stuff is not complicated.

Why bother?

Open notebook science is a thing. It improves reproducibility of research. Personally speaking, it keeps me more rigorous, knowing that the public can see what I am doing, and which half-cocked opinions I am holding. It encourages people to contact me about my ideas.

Further, having a bunch of plain text files is the most simple, convenient and reliable way of taking notes. I'd do it this way even if it weren't going to be online.

If you want more in-depth justifications for open notebooks, see Caleb McDaniel or Ben Marwick's slide deck.

Other examples of online notebooks

Technical details

I publish notes online using Pelican. I see plain text files; you see fancy online HTML. The HTML is automatically served by github pages, which is fast and free. The citations are handled through Zotero. This is a work in progress. This workflow is OK, but I'm experimenting.

Nafiul Islam gives some clever shortcuts on getting live preview using livereload.

For now I mostly edit the text using VS Code, and just GO. The process looks like this:

Screencap of my text editor

On software choice

There are lots of tools to do this. There are in fact a few hundred static site generators for plain text blogging.

Writing papers


Writing papers, especially collaboratively, is a whole other story; you need better media management and citations etc. You might want to try a scientific notebook such as jupyter, knitr etc, which will generate the requisite diagrams etc. rticles, in particular, takes the scientific computation tools and turns them to generating photo-ready journal submissions.

Shut up, just give me minimally painful LaTeX collaboration without any bonus reproducible science features

But if plain LaTeX writing is what you want, And you need to work with collaborators of different technical expertise levels, across various quirky LaTeX setups, here are some options.

Emailing word files between collaborators

You have gone beyond my ability to help you.

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