Saturday, February 27, 2010

Mendeley: My New Favorite Reference Manager

This semester, I'm writing my first grant. My graduate program includes a course called Hypothesis Design and Scientific Writing, in which students work with faculty and peers to prepare an application for an NIH National Research Service Award (NRSA). My grant is coming along, but I still have lots of work to do. My goal is to submit the final product to the NIH sometime this summer. If I'm lucky, they'll decide to fund my proposal, and I'll receive additional support for my dissertation research. (Emory Neuroscience students have about a 60% success rate at getting their NRSAs funded, so I have high hopes!)

This grant has required a lot of background reading. I spend my free time in the lab scouring PubMed for relevant articles that will support my hypothesis. I've therefore been required to come up with a system for keeping track of all these papers. After trying several options, I've found Mendeley to be the most useful.

Mendeley shares features with other research bibliography tools like Papers, Zotero, and Quosa, but in general I find it to be more suited to my needs. The Mendeley Desktop program works "like iTunes for research papers." It keeps track of citation information and allows users to sort their references by category. Mendeley stands out, however, by linking the desktop client to web-based services that make my life much easier.

The Mendeley web importer is absolutely dreamy. If I'm looking at an article on Pubmed or on a journal website, I can use the "Import to Mendeley" bookmarklet in Firefox or Safari to automatically add the citation to my Mendeley database. Doing this prompts the user to enter tags and notes about the article right in the browser, which will be carried over to the desktop client as well. This is similar to Zotero's browser-centric approach to reference management, but I prefer Mendeley's approach. The Mendeley bookmarklet is unobtrusive -- it opens a small pop-up window or a new tab every time I add a reference. When I tried Zotero, I didn't like the way that it generated weird browser panes at the bottom of whatever page I was reading when I added a new reference. Adding tags to a Mendeley citation takes just a few seconds and doesn't interrupt my browsing experience -- I just close the tab/pop-up when I'm done. When I want to pore through my references in more detail, I use Mendeley Desktop, which as a dedicated application feels 'separate' from my browser, and makes it easier for me to focus on the articles. I find the interplay between Mendeley Desktop and the web importer to be just right -- this comes in contrast to Quosa, for example, which tries to integrate web-based search into the reference manager, but feels clunky and awkward. I already know how to use PubMed in my browser; I don't want my citation manager to make me learn a different way to search (even though Quosa's automated searches are pretty nifty).

Mendeley also automatically backs up all of my citation information to the cloud. I can log into my Mendeley account from any computer, and if that computer has Mendeley Desktop installed, I can sync the desktop client to my web account by entering my email address and password. The Mendeley account preserves all of a user's citations, as well as custom user-generated notes and tags. So, I can easily access all of my references and notes from home, even if I originally found all of the articles at lab. This is both convenient and smart -- in addition to making my life easier when I need to take a project home with me, this automatically creates two backups of my reference database: one at home, one in the cloud. If my lab computer dies (unlikely for now, since my PI just bought me a shiny new iMac, but it's always a risk), I won't lose my precious papers.

One aspect of Mendeley that doesn't thrill me is the social networking component. My Mendeley account includes a user profile, and I've been encouraged to add 'contacts' who also use Mendeley. I can see how this might be useful for sharing papers between lab members or collaborators, but I don't find it necessary. When my PI wants to send me a paper or an EndNote library, she can just email me the files. And I have some concerns about security -- sharing Mendeley databases with the wrong person might reveal too much about a sensitive line of research. I favor a more open-source approach to science, but many scientists are terrified of being scooped, and would prefer to guard their lab secrets more stringently. Even so, it's quite possible to use Mendeley's other services without creating a list of contacts. And Mendeley uses personalized account info to do a few nifty tricks, like displaying the most popular papers for Biological Sciences, based on which citations were imported by the most Biological Sciences users on a given day. Users can also add papers to the "My Publications" category in their profile, and track the popularity of their own articles on Mendeley.

The web-based features are my primary reason for preferring Mendeley over other options, but I also like Mendeley Desktop a lot. I can attach a PDF to a Mendeley citation, making it easy to browse full-length articles as well as my notes. The desktop client can open tabs containing multiple PDFs and allows highlighting and Post-It style notes right on the article (although for now, these annotations are not kept in the cloud, so I can't highlight a paper at lab and retrieve the same highlighting when I sync Mendeley Desktop at home). I can sort my citations by title, author, publication date, date added to Mendeley, or by my custom tags. Mendeley is also smart enough to show me articles related to a tag even if I didn't tag them that way -- an article that I tagged "review" will come up when I select the "motor neurons" tag, if it talks a lot about motor neurons, even if I didn't add that tag myself.

Mendeley is compatible with EndNote (select any number of citations in Mendeley, export them as an EndNote XML file, and Cite While You Write to your heart's content) and with several word processing programs (obviating the need for EndNote), although it doesn't yet work with Microsoft Word on Macs. I've had no issue using EndNote as a middleman, however. Mendeley can also import citation information from EndNote, Zotero, CiteULike, and RefWorks, making it easy to transition from another reference management system (have not yet tried this myself, since I haven't been working on this project long enough to generate a huge reference database in another system). It's also free! If you're intrigued but not completely sold, check out some other reviews, or just download it and see for yourself.