Endnote vs …. well, everything else



Just before I handed in my thesis two things happened, which, up to then I had thought were PhD student urban myths:

A whole journal came out full of articles that ‘scooped’ my thesis topic (gah!!)
Endnote bugged out and turned all my 400 odd references into gibberish (instant coronary!!!)

My supervisor solved crisis number one with a single phone call. “It’s a good thing Inger,” he said cheerfully “Just point out in the introduction that the journal was published after you finished and this is evidence that the topic is hot“. Mischief managed (this strategy works really well by the way, even if you don’t have to employ it from desperation).

The Endnote problem was a doozy though.

No students on the PhD floor at the University of Melbourne had experienced anything like it. Those who eyeballed my tattered thesis looked horrified. I could read their thoughts: Thank god this isn’t me! Believe me when I say this does not make you feel any calmer.

Frantic calls to the library resulted in pointers to some very helpful material, but that didn’t help. In the end, my mad skills of Google led me to an obscure Endnote support forum. On it was a post which detailed the problem I was having, but the posted answer didn’t work for me. I put a cry for help on the same forum and crossed my fingers. Over night a kind soul answered and fixed my problem.

Thank you internet!

But no thank you Endnote, you failed me in my hour of need. Up to that point I loved you, but ever since, no matter how often someone tells me you have lifted your game, you have been officially Dead To Me. I’d heard rumours there were better reference managers out there, so I got my thesis handed in and looked around for an alternative solution. These days I would just ask Twitter what my options were, but back then such research was more random. A photocopied flyer, which my friend Dr Scott Mayson picked up in a seminar room, led me to Mendeley.

I liked Mendeley instantly. It works in a similar way to iTunes in that you can make a ‘playlist’ for each topic and it’s social, so you can share your reference data with others. Your data is in the cloud, so no more data sticks and version control issues. The interface is lovely and clean which was an unexpected bonus (I think it’s a pity that the aesthetics of software design for functional programs doesn’t often get that kind of treatment). I spent a day or so transferring my data and LOVED the way it renamed all my PDFs in a consistent format at the press of a button.

Being a social sharing kind of person I put together a research education bibliograhy and linked it to the blog. I made an open Twitter literature list, added a few references and published it on the web. I woke up the next morning to find that many kindly souls had posted new references to it – instant literature searching! I was captivated and told all my friends about my new toy, trying to lure them away from the Endnote mothership.

But, like so many intense love affairs, the lustre eventually wore off and my eye began to wander. Once you have loved and lost a reference manager, it is so much easier to move on. I was transferring my writing practice into Scrivener at that point, and people on Twitter told me that cite while you write referencing worked better with Zotero.

Zotero is made by the clever folks at Mozilla. The key feature of Zotero is the way it integrates with your Firefox web browser, plus Cloud, open source, sharing, automatic metadata scraping …oh – and free. What’s not to love?

Well I tried Zotero for a couple of months and, to be honest with you, I just couldn’t warm to it. After the aesthetic and functional design of Mendeley it felt hard to use and I never did quite work out how to synch it properly. It may well have had something to do with my migration to Mac from PC and the digital chaos that ensued, but I quickly tired of fighting with the interface. I know many people love it, but – not for me.

It seemed that Zotero was destined to be my rebound reference manager love affair. It was time to settle down and get married. All this moving around was hurting my paper kids. My digital life needed some order and routine so I turned again to Twitter with my wish list for a new reference manager. The wish list read:

1.Easy to use interface
2.Compatibility with Scrivener
3.Good search functions and ability to keep notes
4.The ability to auto-populate fields with meta-data from PDFs
5.The Cloud. Baby.

. @vanderaj pointed out my wish list was unrealistic and suggested I try Papers2 for the Mac. While Zotero and Mendeley were free, Papers2 was $80, but there was a free trial for a month. It had everything I wanted but the Cloud, but that wasn’t a deal breaker because in the meantime I had rejigged the way my hardware worked.

Mr Thesiswhisperer is a professional software engineer. He watched me struggle with three computers (home, office and laptop) and decided the way I was working was inefficient (you have to love the way geeks think). He replaced all the computers with one slim, light 11 inch Mac Book air.

Instead of maintaining and synching data on multiple computers and remote servers, I now cart all my data with me, which would be dangerous if Mr Thesis Whisperer had not also installed Time Machine. When I turn on my laptop inside my house, Time Machine finds me and slurps up all my latest work. So fantastic – we live in the future right?

Anyway, Papers2 turned out to have a great search function, combined with note taking and highlighting capacities. It is wonderful at scraping meta data from PDFS and populating fields like author and publisher. Often these are not properly done in the first place (honestly – I really do wonder what we pay those journal publishers for). If Papers2 doesn’t get the fields quite right you can ask it to search the web and find a match.

Thanks to @jasondowns and @scottmayson I have discovered other cool features such as the ability to set up a proxy and search databases like Google scholar from within the interface, which enables me to import from the web, seamlessly, with one click.

In other words, I’m happy with Papers2 for most of what I do (but I still use Mendeley to compile libraries on to share on the web). I this story shows how the choice of reference manager is deeply personal and contingent on a whole lot of factors. Sometimes I yearn for other features, but the more I get to know Papers2, the more I appreciate its trusty and efficient design. Deep lasting love is always like that, at least so I’ve found.

That’s my story – what’s yours? Did you stick with your first reference manager or kiss a lot of frogs until the right software came along? Perhaps you have some other, totally radical solution for keeping your references in order? Would love to hear your stories in the comments.