Over the last few weeks, I have posted several snippets of code and explanations regarding the way I work with Skim and BibDesk. Initially, I started writing these posts just so that I could have some documentation for myself lest I forget how all these pieces work in two years, but I have also had some colleagues in the philosophy department ask about my system, so I have tried to make the explanations comprehensible to them as well. The following is a list of those posts with a brief description of what they include.


A brief introduction to Skim and an explanation of its advantages as a PDF reader.
Skim URLs
A system-wide URL scheme so that I can open to a particular page of a PDF from anywhere. Looks like this: sk://mccabe94#57.
Skim Links
Using the above URL scheme, a script that automatically generates markdown formatted citations or links to the current page of the PDF open in Skim.
Marginal Notes
A script to quickly set Skim’s defaults so that all new marginal notes fit a book’s margins in an appropriate font size.
Export Notes
A script that goes through a PDF, gathers all the textual notes, and outputs a nicely formatted markdown document opened in Marked. It even includes table of contents information from the PDF and bibliographic information from BibDesk.


A brief intro to BibDesk and an explanation of how to generate preformated footnotes without using LaTeX.
An explanation with examples of citations using Pandoc and LaTeX.
A simple script for opening BibDesk and running a search from anywhere—like Spotlight for your bibliography.