Yesterday, I was helping another colleague get set up with markdown for his dissertation and realized that I did not have a convenient way of giving him the CSL file that I use to automagically format my footnotes according to the Chicago Manual of Style. So here is a link to this file posted to Gist.

CSL is an open standard that defines how bibliographic elements are put together (e.g. parentheses versus footnotes). You can use this with many tools, but I use it with Pandoc. To get it to work, you need to define two files when you run Pandoc:

1. You need the --bibliography flag to point to a BibTeX file with your bibliographic information so that Pandoc knows which author wrote which book. (This is the format that BibDesk and JabRef save in automatically.)
2. You need the --csl flag to point to the CSL file so that Pandoc knows how you want things to look.

An example command might look like this:

pandoc --bibliography=~/Dropbox/mybib.bib --csl=~/Dropbox/chicago.csl -o test.html test.md

You can have multiple CSL files for different formats, say one for author–date and one for footnotes. Then, on a project-by-project basis you can easily switch between them without having to change your source document. The source will just contain a Pandoc citation that looks like this [@gerson03 67] and it will get formatted differently based on which CSL you use.