Research Hack: Paper and Reference Management

Research Hacks are a series of blog posts about some of the tools, applications, and computer programs that I use in my workflow. Some of these I began using when I was a graduate student, and others I have picked up more recently. This is the second post in the series (see the first post Feedreaders and Aggregators.)

Electronically managing the absurdly large volume of articles, reports, book chapters and other writings that academics procure is a huge way to save time and increase production. My initial way to manage these files (often PDFs) was to include them in a folder that corresponded to a particular project or paper. Because I could never find the article again (Spotlight was a long way from working well at this point), I often had multiple copies of the same paper residing on my computer. This also meant that I had multiple annotations across these papers.

When one summer I realized that I had 11 copies of a paper on covariational reasoning (the topic of my dissertation) on my computer I laughed at the absurdity of this system and vowed to fix it. This is when I found Papers.

Papers (now in its second version—Papers2) is a management system for a person’s “research library” (as they refer to it). It is sort of like iTunes for PDF files. You have a “library” of files (only one place on your computer) and these are displayed in the Papers application (just like iTunes). You can then have “playlists” in which you put these files, but without creating multiple copies! For example, you could have “playlists” containing the references for each paper you are currently writing.

Screenshot of the Papers2 application

The search feature is great. If you are an organization nut like myself, you can also input all sorts of meta-data (publication type, tag words, photos, links to supplementary material, etc.). Papers can also output references for BibTeX or Endnote and has integration with Scrivener and Word. There are limited annotation tools within Papers (although more in v2.1) at this point, but rumor has it that is a big part of the future. There are also several workarounds using Dropbox, Skim, etc. Lastly there are iPhone and iPad apps for Papers that I think are beautiful. Reading articles on the iPad is one of the coolest things ever.

Papers on the iPad

Unfortunately Papers is not free (but there is a substantial discount for students). Also, as far as I know, it is only available for Mac users. There are several other management and reference systems available as well. Two of those are Zotero and Mendeley.

Each system has features that are really cool and some that aren’t as well developed. Why did I choose Papers? At the time it was pretty much there only one choice at the time that existed in a state that actually worked. (I seem to recall Mendeley was just released as a beta version.) Would I make the same choice now? I am not sure, but I think so. My second choice would be Zotero. (I am a little concerned about what will happen to Mendeley now that it has been purchased by Elsevier.)

No matter what choice you make, let me make several suggestions.

  1. Begin using it immediately.
  2. Begin entering meta-data for every paper you have right away. Don’t be chincy here. Yes, I know it is time-consuming, but that just gets worse as you accumulate more and more articles. Some of this can be automated depending on the recency of the paper, etc.
  3. Learn how to use it to input references into a paper.
  4. Figure out a workflow for paper annotation (taking notes, highlighting, etc.)

Summer is a wonderful time to learn a new software program or computing language. Happy computing!