Folks have been clamoring for a Papers vs. BibDesk post and here it is, finally. Since I don’t actually use Papers, this post is more of a listing of my reasons for sticking with BibDesk for the time being. This topic has been discussed elsewhere and is sure to be visited many times in the future on AstroBetter, so consider this post just one part of a much bigger discussion.
There are different things to look for in an article management tool. I want my app to be as one-stop shopping as possible: I want to be able to search, import, organize, assign BibTeX cite keys, and annotate all in one place. BibDesk does most of those things while, as far as I can tell, Papers really only excels at searching and importing. Papers gurus, I’m counting on you to speak up in the comments if I’ve missed something. Below, I’ve listed the main functionalities, in rough order of importance to me, and which application I think handles them best.
- Keywords/Tags: Bibdesk
- Keywords play a starring role in BibDesk, occupying the left column in the main page while in Papers they are hidden in Notes. With BibDesk I can highlight multiple articles and quickly specify if I only want articles with ALL of those keywords, or papers with ANY of the selected keywords. This ability to easily tag articles with multiple keywords and then search based on them is a huge advantage of BibDesk over Papers but I think Papers will catch up soon.
- PDF Annotations: Bibdesk + Skim
- Annotations added in the PDF reader app Skim show up as Notes in BibDesk so you don’t even have to open the PDF to see the text you’ve highlighted or underlined. (Skim vs. Acrobat vs. Preview is a can of worms that I choose to leave for another day.) Improved annotation functionality and integration with Skim is likely for future versions of Papers.
- Search and Import: Papers
- Papers auto-magically imports articles and metadata and downloads the PDF while importing an article into BibDesk is (usually) a multistep process. The way I do it is browse to the article’s ADS entry, scroll down, clink on “Bibtex entry for this abstract”, highlight the bibtex, switch to BibDesk, use alt-command-L to add a new publication from the clipboard. BibDesk does have a Papers-like single-click import for articles on arxiv.org, but not for ADS. Looks like this ADS to BibDesk app is on the right track, but it only works with Safari, not Firefox. Getting this functionality built into BibDesk would rock.
- Cite Keys: BibDesk
- BibTex + AstroNat is what you should be using to include references in LaTeX articles prepared with AASTeX. Again, a full discussion of BibTeX is left for another day, but suffice it to say, being able to assign memorable cite keys to articles is important. To be honest, I’m not quite sure how Papers assigns cite keys to new articles. BibDesk autogenerates cite keys based on a user-defined format. I’m partial to first author + two digit year (Custom format string:%a1%y). And then I just add a sequential number to the cite key for the autonaming and autofiling of the associated PDFs.
- Slick UI: Papers
- You gotta admit, Papers sure is pretty while BibDesk leaves something to be desired. The most recent update to BibDesk (1.3.22) helped a little, but it’s still not as clean as Papers even though they both use the same 3-column layout.
- Cost: Bibdesk
- Bibdesk is free and open source. Papers costs $42 for non-students, $26 for students.
- Reading Papers: Papers
- Papers is great for using as a browser to read PDFs. Papers even has an iPhone app ($10) which enables you to sync a Smart Collection so that the PDFs are at your fingertips when you have some dead time for reading. BibDesk is great for browsing notes or annotations, but not for reading the original papers.
(Updated Nov 2, 2009: Thanks to Marshall for pointing out this functionality that I had overlooked.)
Also consider Mendeley, which is both a desktop and online article organizer.
Alright, there’s by BibDesk biased view, let’s hear from the Paper’s lovers in the comments.