Academic Markdown - writing scientific articles and a whole thesis in markdown

After some very unpleasant experiences of collaboratively writing papers, proposals or my thesis either in Microsoft Word, Google Docs or Overeaf.com (previously WriteLatex), I tried to give authoring in markdown another shot. All of my documentation I already do in markdown (in Vim) on a daily basis. And whenever required I can just produce beautiful PDF documents or HTML versions of READMEs or notes. So why not use this very legible format for bigger documents?

A good primer can be found here: http://blog.kdheepak.com/writing-papers-with-markdown.html

Pandoc is pretty much required for this to work at the moment, because delivers the best ecosystem of markup extensions, filters, documentation and input/output formats. It is written in Haskell and thus a hefty installation of the Haskell compiler is required before installing Pandoc itself in most cases (my old laptop did not have enough memory to compile the package with default configurations) and Haskells nice package manager Cabal itself was kind of hard to install on older systems because of missing dependencies.

My make command for markdown files in Vim is now:

autocmd BufRead,BufNewFile *.md setlocal filetype=markdown spelllang=en_us spell makeprg=pandoc\ --filter\ pandoc-citeproc\ -o\ %<.pdf\ %

and I plan to include the following filters:

--filter pandoc-fignos \
--filter pandoc-eqnos \
--filter pandoc-tablenos \

but should really define this on a document basis in the meta-header with panflute.

Also, I will try to implement my own acronym/abbreviation filter that replaces the first occurrence of things like 'ncRNAs' with 'non-coding RNAs' if defined like ~ncRNA: non-coding RNA.

I will add to this blog post as my experience progresses.

Pandoc-Scholar is another project for setting up Pandoc for collaborative writing.

some very old posts to this topic