End of my EndNote not the end of the world

I recently found myself without my beloved referencing software and had to discover the free alternatives.  You should try Zotero – it will probably win you over!  It even has a few features which you might find make it even make it better than EndNote.  

My Zotero LibraryAs you develop as an academic you embrace technology because it makes life easier.  One of the tools you’d now consider critical to your life is your electronic reference manager.  These tools save you hours because they capture search results direct from PubMed and automate numbering and bibliographies in your papers – priceless!

I had the good fortune of developing my skills as an academic at The University of Sydney.  In large institutions reference management quality software such as EndNote is widely available and after a while you open it nearly as often as your email.

Having taken long-term leave and made a temporary move to the Republic of Ireland to work on a research project I found myself without my beloved software.  Disaster – or is it?  You will be comforted by the fact that there are a multitude of free alternatives.  One such tool, Zotero , has won me and others over.

Here is a summary of a few of the things you’d find are different:

The good

  • You can have multiple folder levels so you can store your publication library in the tree-like structure it probably resembles.
  • It is super-easy to eliminate duplicate records (warning: if you have a huge number (over 1000!) this can be tiresome – I ended up implementing a cool program to automate a left click)
  • Zotero integrates directly into any browser (except Internet Explorer).  You click 1 button and most online publications (including almost any journal) download automatically into your library, storing the PDF if freely available.
  • The program can automatically sync your library with the Zotero server so that you can access everything online or on multiple computers (like EndNote web).
  • You can set up collaborative groups and share access to a reference library (privately or publicly) you can also do in EndNote but the Zotero interface for invitations is easy to use. When you are writing all sources are used to search for the citation you are looking for.

The not so good

  • I miss being able to search PubMed directly from EndNote (you can search for a PMID, DOI or ISDN in Zotero if you know it)
  • I really miss being able to “search for pdf” but am amazed at how many journals are already open access or have open archives (e.g. published >12months are available free)
  • Zotero is only free for up to 300mb of synced storage.  Relatively cheap storage options  (2,6,10,25GB) are available.
  • It slows down a bit once you add a lot of references. After adding my entire EndNote library my collection contains around 1000. I’m also synced with a 5000 reference group. Not as snapp as it was but still usable.


Zotero has come to the rescue and provides a sound & free alternative to EndNote for reference management.  Now that Mendeley has been sold Zotero is likely to become many people’s default. I know I’m only just discovering the power of this new tool but am ever weary of things to watch out for.  Have you used Zotero?  Is there anything I’ve missed that you love or dislike?  Most importantly, do you have any time-saving tricks for reference management?