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Markdown for Science

I'm a big evangelist for using markdown to author documents in a scientific context. I've written about this several times on my blog but decided to put together a repo to help you learn and use this same workflow with a complete set of examples. If you spend a little time going through the tutorials, you'll be able to stop using Microsoft Word entirely and write clean, lightweight markdown files that can easily be version controlled by git. Collaboration with your coauthors would also become way more powerful and simpler.

If you want to learn more about how git can improve your science, read my upcoming article in BMC's source code in medicine and biology.

Copying this repo

If you have git installed, simply clone this repo and you'll have a full set of examples to work with locally. Otherwise just hit the zip button at the top of the main repo to download a copy.

git clone git@github.com:karthikram/markdown_science.git

Table of contents

• Basic setup
  • Tools you'll need
  • Learn markdown formatting in 3 minutes
• Incorporating various elements into markdown files
  • How to cite papers
  • How to include figures
  • How to include tables
  • How to include equations
  • How to embed statistical results
• Advanced formatting
  • Managing styles
  • Automating document generation

A PDF version of these documents are also in the documentation folder for offline access. In progress

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Complete examples

• Writing a short abstract
• Writing a full manuscript with tables, figures and citations
• Writing a class syllabus

If you have additional insights or ideas to share, please feel free to contribute (wiki edits are currently open).