Technology and Teaching: FUN with Mendeley

FUN with Mendeley:

The Swiss-Army Knife of Reference Managers That You Really Ought to Try

Bob Calin-Jageman


Are you on Mendeley yet?  Mendeley is the new end-all-be-all of software for academics.  It's a reference manager, a pdf organizer, a file synchronizer, an academic free-associator, a microblogging platform, and an academic social network.  Sounds terrible, right?  Normally, software that tries to do it all ends up being a disaster (I'm looking at you Outlook).  But Mendeley is gooood.  It makes the never-ending process of managing your reference collection simple and easy.  Along the way, it adds in features you never dreamed of in a reference manager, but that you'll soon find indispensable.  Best of all, it's free (mostly) and works on all platforms (even Linux, for the FUN members out there kicking it open-source style).

Mendeley is the best reference manager around.  That's the number one reason to check it out.  You can ignore all the other bells and whistles and get up and running with Mendeley as a great reference manager in no time.  Just download, install, and start slurping up articles into Mendeley.  Mendeley can import records from PubMed and many other search indexes.  Unlike Endnote and Reference Manager, however, Mendeley has an emphasis on Pdf records: it can scan a folder of pdfs, recognize their meta-data, and add them to your reference collection.  You can even setup a 'watched folder' on your desktop--save a pdf to it, and Bam! it's in your reference collection.  Did Mendely get the meta-data wrong?  Just put in the PMID and it will re-pull the data directly from the Web.  Mendeley can also get full records from DOIs and ISBNs: no need for manual entry.

Once you get some articles into Mendeley, it has nice facilities for taking notes, organizing into collections, tagging with keywords, etc.  The search feature is fast and it indexes the full-text of the pdfs in your collection!  It's crazy how quickly and easily you can put your finger on just the right information once you've stocked up Mendeley with your library of pdfs. (Pro tip: Mendeley struggles with older pdfs; have an undergrad work on matching these with their PMIDs and correcting the meta-data for you.  They get work-study, you get a pristine database, angels get wings).

Like other reference managers, Mendeley also helps you write and organize manuscripts.  Plugins automatically install for Word and Open Office Writer--no complex setup.  As you write, you can pull up a dialog to search your library and pop in a citation.  When you're finished, just click 'update bibliography' and the reference section is auto-generated in the style of your choice.  Mendeley's styles are archived in an online library, and it is very extensive (and customizable). 

If you are used to End Note or Reference Manager, the transition to Mendeley is quite easy--you'll actually be blown away at how much easier it is to use.  The emphasis on Pdfs is a bit different, though.  Mendeley is not as good as End Note and Reference Manager at slurping down huge sets of abstracts (e.g. it can't search PubMed directly).  Mendeley's design philosophy, however, is focused on managing actual documents over abstracts (though it does fine with these).  If End Note is your archive of papers you meant to read, Mendeley is your archive of papers you've actually read (or will soon).  It's a critical difference.  Personally, this took me a little while to get used to, but I've found it is a very worthwhile change.  Rather than having an aspirational database bloated with articles I've barely screened, Mendeley is my living database of things I know well (at least well enough to have pulled the pdf).  Therefore, searching the database and writing papers with it is a lot more useful--it's like searching your own brain (but less prone to tip-of-the-tongue phenomena).

Mendeley is a strong enough reference manager that my university's library recently ditched their old reference management software.  Mendeley has now been installed across campus, students are registered for the basic-level free account, and all library training now features it.  Student seem to love it, too.

Sync your library.  Mendeley also adds some cool bells and whistles to the basic notion of a reference manager.  First up. it can synchronize your database to "the cloud' and across devices.  The meta-data and notes are synchronized for free.  Pdfs are synchronized up to 1GB for free, more than that and you have to start paying (though plans are reasonable and available for both individuals and institutions).   So imagine: you pull a pdf at your office, save it to your 'watched folders' directory, and it pops up a few minutes later on your Mendeley app on your iPad.  You can read it and take notes while watching Fringe that night, and your notes will be back on your desktop in the morning.  Mendeley will get you reading more of what you meant to read!  One caveat--the apps available for Android currently suck. 

Social media bells and whistles.  Normally I react to social media about as well as my beloved Aplysia react to salt (you've never seen that?  it ain't pretty).  I've never wanted or needed to Tweet anything, and I hope no admissions initiative will ever change that.  I've been surprised to find, then, that I love the social media side of Mendeley.  Let's start with it's recommendation engine--because it's synchronizing many libraries to the cloud Mendeley can tell you some articles not in your library but in the libraries of other academics like you.  Some of the recommendations are pretty good! 

Mendeley also gives you a profile and you can 'friend' other academics.  It's kind of like Geekbook--a social network for people who know what a PMID is (no friend requests from your aunt!  yes!). 

Mendeley also has Groups that you can start or join.  Public groups can be as large as you want.  The main activity of a group is to share and comment on articles.  It's a cool way to crowd-source keeping up with interesting topics in your field.  For public groups, however, only the reference is shared (not the pdf).  Private groups are the same, but limited to 10 people and the pdf is also shared.  Pro tip: if you have a couple of friends at a big university, start a private reading group with them.  It will be fun and they can easily slide you pdfs! 

I've found private groups to be perfect for small seminars: I can post pdfs, students can post pdfs, we can all comment on papers and on each other's comments.  The size restriction means it can only be done with very small classes, but in these cases Mendeley can basically replace Blackboard.   My lab now runs with a private Mendeley group as well--once a student joins the lab I add them to the group and they have access to all the Pdfs for the lab: background reading, recent pubs, etc.  Finally, you can use a group as a 'microblog'--just set one up on your own, and add articles/comments as you'd like.  RSS feeds are available for each group.

Try it out.  Well, this pretty much outs me as a huge Mendeley fanboy.  But that's fine.  It's made my writing process easier, it's helped me read more, and it's given me a much easier way to ensure my research students have access to all the papers they need.  All that for $0.00 really is worth getting excited about.  So take some time this summer and give it a whirl  If you do, please do email me with your likes/dislikes.  I'll live tweet them all summer long.