As academics we spend a lot of time reading, and a lot of time procrastinating.  At one point, my favorite procrastination activity was obsessively researching the “best” way to organize research papers for reading (instead of, you know, reading them).  I’ve had many systems; some paper based, and now mostly electronic.  I’ve finally settled on a system that works for me.

My system has two parts.  One half is for organizing papers with Mendeley so that finding them is easy and creating bibliographies is a snap.  The other half of the system is Dropbox, which helps me get the most of out the time I spend reading.

The most powerful part of my system is that I can easily find papers and view my annotations from any device.  I can mark up PDFs with a tablet and then easily see my notes later on my desktop or even on my phone.  And I managed to get it all done for free!  Here’s how I did it:

Organizing papers

I settled on Mendeley to organize my papers.  I had tried Zotero and Papers in the past, but I like that Mendeley is free (or freemium) and isn’t tied to a web browser (like Zotero was when I put my paper organization system together).

Mendeley has several key advantages

  1. Organizes papers into a special folder, and gives them meaningful names (this is the most important by far, for my system)
  2. Allows for organization of papers into research topics and sub-topics
  3. Can sort by date added
  4. Easy Bibiography creation and citation management

Mendeley has one big disadvantage

  1. Annotations made within the Mendeley app can’t be viewed outside of the app without exporting the PDFs from Mendeley first.

My system allows me to take advantage of the free organizational features of Mendeley, while also allowing me to annotate my PDFs with any app that can interface with Dropbox.  An added bonus: I bypass 2GB limit that Mendeley has for their free accounts.

Here’s what I did: I set my paper organization folder to be in Dropbox.  To do this, open preferences, select “File Organizer” and check the “Organize my files” checkbox and set the directory to something in your Dropbox folder.  Now, whenever you add a paper to Mendeley, it will automatically be copied to your Dropbox.  Now you can access that paper from any app that interfaces with Dropbox, and any computer with an internet connection (through the dropbox web interface, or through the Dropbox app itself).  You can even see your papers on your phone and tablet!

Mendeley can also use a consistent naming scheme within your folder.  I chose to use Author-Year-Title for my file names, but you can use any combination of those three attributes, plus journal name.  I happen to remember first authors and years better than journal names and titles, so this works well for me.  Mendeley can also put each paper into a folder based on these same attributes, but I personally found having all of the papers in one directory to be most useful.  Then I can sort the folder by date modified to get the most recent papers filtered to the top.

Though you can hack Mendeley to store your database file in Dropbox, I think this is a recipe for disaster.  If you have Mendeley open on two computers, for example, one could overwrite the database changes made by the other and then you’ll lose any record of the papers you added in between.  If you use more than one computer for dropbox, this is just asking for trouble.  So I suggest using Mendeley to sync your library database, but not your PDFs.  Instead, use Dropbox for PDF syncing.  To turn off PDF syncing in Mendeley select All Documents in the left frame, right click, “Edit Settings” and un-check “Synchronize attached files”.

Reading Papers

There are many apps to annotate PDFs that include a Dropbox interface.  I use iAnnotate on my Android device and drawboard PDF on my Microsoft Surface.   I don’t really annotate anything on my iPhone, but on the off occasion I read a paper on my iPhone, I just use Dropbox’s built in reader.

Keeping your papers in Dropbox also frees you up to use whatever annotation software works best for a particular project.  Perhaps for reading papers all you need is a highlighter and a few notes.  For proofing other people’s writing and for paper reviews, I really like to write in the margins, so something with good pen support is ideal.

My paper reading workflow goes like this:

  1. Download a paper to my computer.  Go to Mendeley and select the folder the paper belongs in.  My folders are organized into general research areas (e.g. Brain, Machine Learning).
  2. Add the paper to the folder using Mendeley.
  3. Check that the author names, journal name and year were extracted correctly (Mendeley is very good at this when it comes to Journal papers, but conference papers, less so).
  4. Read the paper, usually on an a tablet with pen support.  However, I do sometimes still print out papers to read.  When I do this I try to copy my general thoughts back into an annotation on the PDF, but this is definitely one place where my system breaks down.

You can open papers for reading on your computer in two ways:

  1. To read in Mendeley,  double click the paper’s entry
  2. To read using another app, right click and select “Open File Externally”.

Citing Papers

Now for citing your perfectly organized papers.  I use Latex to write papers, so I use bibtex to cite papers.  Mendeley automatically makes a bibtex library for you, and the keys are always Firstname<year> like Fyshe2013 (or Fyshe2013a,Fyshe2013b, Fyshe2013c … if I had a productive 2013).  This is probably why I remember first authors and years so well, because that’s how you cite them in Latex.  If you don’t want to remember how to spell someone’s last name (Kriegeskorte, I’m looking at you), just select the paper you want to cite in Mendeley and hit ctrl-k.  Now the citation command is copied to your clipboard (magical!).

Mendeley can keep an up-to-date bibtex file ready and waiting for you on your computer.  Under Preferences, Bibtex check the “Enable Bibtex syncing” box and set the path.  I like one bibtex file for everything, because I often cite papers from multiple research areas.  Now I just copy that bibtex file to the directory where I’m writing my paper and every citation I’d ever want to make is right there waiting for me.  I use this perl command to strip out the URLs before I copy a bibtex file over because it makes the actual references shorter which can help with page limits when writing papers.

perl -ple 's/url.*//' <path to>/library.bib > <path to paper writing dir>/library_nourl.bib

Mendeley can also give you a nice bibliography on the fly;  just select the papers you’re interested in and hit ctrl-c.  I find this helpful when I want to email a bunch of references to someone.

I hope this tutorial was helpful, and that it allows you to stop procrastinating and get back to work!


  1. You could use Google Drive instead of Dropbox for your paper backend, and they give up to 15GB of space free.
  2. If you use more than one computer to add papers to Mendeley, Mendeley will not sync the file locations across computers (even if they are identical).  That means the paper will show up in Mendeley’s database (i.e. as a row in Mendeley’s interface), but Mendeley will act like there is no file for the paper (though of course it’s in your synced Dropbox folder).  This is probably the biggest flaw in my system, because it means you can’t easily open some files from inside of Mendeley.  Instead you have to navigate to your Mendeley folder and find them there.  That folder can be sorted by file name which,  if you use my setup, is the first author’s last name, so finding a paper is really quite easy.  With OS X’s spotlight you can also search for files named e.g. “Rafidi” and that will help you find the file you’re looking for quickly too.