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Markdown for Scientific Documents

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szarnyasg edited this page Nov 21, 2014 · 10 revisions

This is a short summary for using Markdown for scientific documents. We try to summarize the "state of the art" as of November 2014.

Note that we do not particularly recommend Markdown for complex scientific documents with many citations, and cross-references. For reference, see comparison of Pandoc and MultiMarkdown.

Markdown engines and wikis

Pandoc

Homepage: http://johnmacfarlane.net/pandoc/

Pandoc is the most feature-complete Markdown engine. It supports math expressions, citations and cross-references.

Pandoc supports various Markdown formats, including GitHub-flavored Markdown (GFM).

You may compile a GFM document with math expressions by issuing the following command:

pandoc post.md --from=markdown_github+tex_math_dollars --output=post.pdf

GitHub Pages

Homepage: https://pages.github.com/

GitHub pages support various Markdown parsers. The list on https://pages.github.com/versions/ contains the following:

  • kramdown
  • redcarpet
  • redcloth
  • rdiscount
  • maruku

The kramdown engine is able to support GitHub-flavored Markdown (GFM), see http://jekyllrb.com/docs/configuration/#kramdown for reference.

kramdown:
  input: GFM

In theory, GFM does not support math mode but kramdown leaves the math expressions unaltered.

GitHub pages is capable of running on a custom domain, e.g. docs.inf.mit.bme.hu points to ftsrg.github.io.

DokuWiki

Homepage: https://www.dokuwiki.org/dokuwiki

Dokuwiki is a PHP-based wiki engine. Markdown is supported by two plug-ins, markdowku and markdownextra. The markdowku plug-in supports standard Markdown, but does not strictly adhere the original specification. Meanwhile, markdownextra supports PHP Markdown Extra, but seems unmaintained.

Gitit

Homepage: http://gitit.net/

Gitit is a wiki engine implemented in Haskell. Gitit stores the wiki in a Git repository.

As far as we are aware, it is the only wiki engine which uses pandoc for processing Markdown.

Madoko

Homepage: https://www.madoko.net/

"Madoko is a fast markdown processor for writing professional articles, webpages, and presentations, with a focus on simplicity and plain text readability. It is especially well suited for high quality scholarly- and industrial documents for the web and print."

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