Android, Mendeley, Referey, and taming the reference beast

Like everyone else in Academia I’m in a constant struggle against information overload.  This comes not only from the overwhelming amount of data from analyses I’m working on, but from an ever-growing stream of scientific literature.  I gave up trying to stay on top of journal tables-of-contents a long time ago, instead I rely on Google Scholar alerts to notify me when relevant publications come out.  Unfortunately this switch didn’t reduce the volume of literature that catches my eye, it merely insured that all the literature would be relevant, interesting, and even more important to file away somewhere and remember.

Some people seem to have a great mental filing system for authors, dates, and subjects of key articles, and can pull a critical reference from the depths of their hard drive based on title alone.  I’m not one of those people.  If I can’t find a reference by a keyword search it doesn’t exist in my universe.  Fortunately, in front of a laptop it is generally possibly to find what you want by keyword search.  Both Windows Search and OSX Spotlight automatically index the contents of pdfs, making it easy to find all the papers in a personal library pertaining to say, Wigglesworthia.  To make this even easier about a year ago I started using Mendeley Desktop, a pretty decent program for organizing and annotating pdfs.  I don’t use Mendeley quite the way its meant to be used however.  The free version of the program comes with a generous chunk of online storage space, which allows you to maintain an online copy of your library that’s accessible from anywhere.  My pdf library is pretty large however, and I’m hesitant to upgrade to the paid version of Mendeley – which comes with more storage space – until I’m really sold on the program (which is happening quickly, aided by the hope that Mendeley’s cite-while-you-write add on will forever remove from my life the horrible, evil, travesty which is Endnote…).

Enter the Android tablet that I recently acquired.  My vision is to be able to sit in a class/seminar/meeting, with that critical paper/fact/reference on the tip of my tongue, and actually be able to LOOK IT UP.  Should be simple enough, right?  Well, maybe.  An additional requirement is that I need to be able to look things up when I’m at sea, in the field, or otherwise not connected to the internet.  This makes it a little trickier.  After reading a number of blog posts from people with similar problems I was able to patch together a solution that works (so far) remarkably well.  The limitations of Android and Apple are equal in this respect, so this solution should be relevant for ipad users too.

My initial though was to migrate my pdf library to Dropbox, and use the Android Dropbox app and native search function to find what I wanted.  Two problems: 1) The Dropbox app doesn’t actually sync files to the tablet (crazy!) and 2) There IS NO native search function on either Droid or Apple ios that searches file contents (crazier still!).  Fortunately I came across Dropsync, a competent little app that picks up where Dropbox falls flat.  With the paid version you can keep select Dropbox folders synced to the SD card in your Droid.  Problem one solved.

If I didn’t need the search function to work without internet I could have downloaded one of a couple of Mendeley-compatible apps, upgraded to the paid version of Mendeley, and lived the life of online library access (ipad owners can cut the middle man and make use of an official Mendely app).  Needing an offline search feature I was pretty well stuck until I found out about Referey (thanks Mendeley, for posting links to third-party apps that help your users…).  Referey was designed with my exact problem in mind.  Here’s how it works:

Having migrated your entire reference library to a folder in Dropbox, you create a symlink in that folder to the sqlite database where Mendeley keeps the index for your library.  On Windows 7 I found the database in C:\Users\Jeff\AppData\Local\Mendeley Ltd\Mendeley Desktop\largedatabasewithyourmendeleyusername.sqlite.  From the destination folder in Dropbox I created a symlink as such:

MKlink largedatabasewithyourmendeleyusername.sqlite "C:\Users\Jeff\AppData\Local\Mendeley Ltd\Mendeley Desktop\largedatabasewithyourmendeleyusername.sqlite"

I believe for Apple/Unix the command is “symlink”.  That keeps both my reference library and the Mendeley index up to date on my tablet.  On your tablet, in preferences, you tell Referey where in your Dropbox (synced with Dropsync, not Dropbox) you’ve stashed the database and your library.  Referey does no further indexing, it simply uses what Mendeley already knows to find what you want in the library.  Pdfs returned in a search can be opened and annotated using whatever app you want (I’m currently using iAnnotate PDF).

For a while I really doubted whether a solution existed for what seems like an obvious problem.  I was pretty happy to find one…