Wednesday, December 15, 2010

Which Reference Management Software do you use? (Reader Poll)

When I started grad school I started using Reference Manager (RefMan), similar to EndNote, to manage my references and bibliographies. It's a real pain, and I often feel like I'm powering my computer with the endless pumping and clicking of the mouse that it takes to import a reference into my library.

Recently I've started using Zotero because of how easy it is to import references, store PDFs, and sync between computers. It also integrates with MS Word and allows you to insert citations and format a bibliography using any of EndNote's styles. And it's free.

Before I make the switch and leave RefMan for good, I would love to see what everyone else here uses to manage references. I know many of you use social bookmarking sites like CiteULike,, FriendFeed and others to save and share literature, but I'm really interested to see what software you use while writing to manage references and format bibliographies, and how satisfied you are with what you use.

Thanks for responding! Check back in a few days and I'll summarize what you all said.


  1. Even one better, Zotero provides a nice plugin for OpenOffice/NeoOffice. No fuss, no muss.

    btw -- I also use Connotea, although for very different reasons. When I need to incorporate any of those references into Zotero -- it's a two-click process (one to export; then another to import!).

  2. Do you ever use Sweave or one of the extensions for writing reports? I like the idea of it, but haven't jumped in and tried it.

  3. I've never really taken the time to learn Sweave. I use R for nearly everything except logistic regression (Stata's domain), but it's rare that journals outside computer science, bioinformatics, or statistics will accept LaTeX files for publication. When you collaborate with physicians and epidemiologists MS Word using tracked changes is the standard. As much of a productivity boost as Sweave provides, it just doesn't work for most genetic epidemiologists.

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