Of Research Managers (The Software Formerly Known as Citation Managers)

Danah Boyd’s recent decision to stop using Mendeley because of that software’s acquisition by Elsevier has created [quite a stir][], by all accounts. I will leave the discussion about parent companies and publishing companies to others. What I found interesting was that Boyd was not particularly drawn to Zotero, and no one in the comments section was particularly drawn to recommend Zotero. Instead, there is a number of alternatives presented: Citavi, Colwiz, Qiqqa, to name but three I hadn’t heard of before.

Once upon a time, there were three by five cards, and they did a lot of work. They both managed quotations and they managed references. Sometimes they even managed notes and composition. But they were, despite their dependability and their lack of need of batteries, quite difficult to work with. Their lack of easy discovery meant an inordinate amount of shuffling was always involved every time you picked up your deck; they randomly went astray (in much the same way that socks do in the laundry); and they required duplication of effort because one was always copying things from them into something else. They were, in other words, ripe for the kind of things that computers do well: search, sort, and copy. Copy seems like the most trivial of that list, but the fact is that copying by hand almost always introduces the possibility of some random, all too human, error being introduced into a manuscript, something small that you were unlikely to catch but large enough to be embarrassing. Such possibilities still exist, of course, but just not having to re-write a quotation, or only having to type it once seems like an honest to goodness blessing.

Searching and sorting is, of course, the stuff of databases, but that’s a word that scares most people and with so many writers turning to computers as the basis for writing and revising, it wasn’t long before enterprising individuals fine-tuned a database into a citation program that was fairly easy to use by non-programmers — mind, I remember a number of us bashing together HyperCard stacks at some point in the late eighties, early nineties in order to build our own citation management “systems.” Those early programs were useful in a very limited fashion. I remember using an early version of EndNote alongside some early word-processing software for academics — it had a name like *Lexus* I want to say — but I also remember that I was using “borrowed” copies of both programs because as a student I could ill afford either or both.

Fast-forward twenty years and EndNote is still around and I draw a salary. However, since my state seems dead-set on squeezing academics out, I can still ill afford the software. The good news is that there are a number of alternatives: [BookEnds][], [Sente][], [Papers][], [ReferenceManager][], to name but a few of the commercial options, let alone [Zotero][] in this list or BibDesk.

What’s fascinating is how much computers have changed the nature of what’s possible. For many of these apps, managing references is the least of what they do. In fact, almost all of them now bill themselves as *research managers*. Zotero’s home page offers a succinct formulation of the functionality researchers, scholars, and scientists have come to expect: “Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share your research sources.”

I have and, occasionally, use Zotero. The qualification of “occasionally” marks my quibble that I don’t find Zotero necessarily “easy-to-use” — largely because its UI is so clunky, making some of its functionality almost impossible to discover — but the application does do what we now expect of such programs: we want to be able to record a reference (often by having the software take the notes for us just by pointing it at a URL or DOI), perhaps even download the PDF and keep track of it, allow us to make notes and keep track of them, and then work with colleagues near and far on a project.

Because I don’t find Zotero necessarily intuitive, I have in fact purchased and used BookEnds (which I was originally drawn to because I was using the outstanding word-processing software [Mellel][]) and I have downloaded and played with [Mendeley][]. The problem with any of these solutions is that they have, for the most part, not been taken up by a larger community, and, really, in the research business, the network effect matters a great deal. If you’re in the business of sharing knowledge, you need to be using what others are using. (It is for this reason, and only this reason, that a copy of Microsoft Word still resides on my computer, but I’m telling you, colleagues in the humanities, the sooner we embrace LaTeX, the better — I’ll have more to say about this soon.) Which is why I use Zotero at all.

And also why I found the list of, apparently European, alternative research managers so interesting. Let’s take a look at each of these in more detail:

* [Citavi][], it turns out, is Windows-only. So, no.
* [Colwiz][] seems to offer a one-stop shop for, well, practically everything. It says it can do all the standard things we now expect of reference managers, and it also offers task management. Much of the collaboration — sharing of documents and notes, assignment of tasks — seems to occur through the Colwiz cloud, which always struck me as Mendeley’s weakness as well. (More about this in a moment.) **UPDATE**: Colwiz is an Adobe Air application that requires you to sign in to run — when I cancelled sign in so that I could explore the app, the app itself quit. *Bad, Colwiz, bad!*
* [Qiqqa][] bills itself as “PDF management software”, which seems rather old-fashioned at this point, but in addition to its ability to organize PDFs, it also has some AI that “reveals connections about, and between papers and concepts in a totally unique way” — I’m guessing some form of latent semantic mapping — as well as the ability to annotate PDFs, sync things to the cloud, and create bibliographies (but only in Word it seems). And, eh, Qiqqa is only available for Windows and Android. No Mac, no Linux. (And no iOS, since they bring up Android.)

Syncing across computers and now other kinds of devices (i.e., tablets), as well as across users within a group seems increasingly important to a wide range of researchers. Being in the midst of a collaborative research project myself, I find myself realizing how useful this ability to sync and share can be.

Again, it’s the network. (Tim O’Reilly has been [noting][] this for many years now.) One of the things that hampered my investment in Mendeley was the reverse side of the network coin: whose network is it? Mendeley was marvelous for being free and quite usable, but the network, in the end, belonged to them. Zotero opens this up a bit, but they do have to find a way to pay for infrastructure, which is not really one’s social network, but the PDFs one accumulates, which Zotero wants to keep in its own infrastructure.

Leaving aside who owns the network, another dimension of these apps is that they are primarily focused on keeping materials in sync. While it’s true that I want my notes with me always. I don’t necessarily want to keep my PDFs with me. In fact, rarely do I want to keep all the PDFs I have downloaded with me. I am usually interested in a subset, which I would happily designate as “make available off-line” if I were given the opportunity.

What I really want is a library to which I have access. What I really want, in other words, is the original promise of the internet which we all imagined back in the nineties but which we seem to have forgotten in the intervening years.

In the mean time, I would settle for some system, a la iTunes’ “Cloud Match” that would allow me to get access to PDFs to which I have legal access. In that way, a server system need not be overloaded with everyone’s library. Annotations could, like any image management system, be manage and maintained by the user’s setup. This would, I think, significantly reduce the pricing of such services, of which I am shy, again because I have to be extremely conservative when it comes to my budget.

Were the NEH or the Mellon Foundation to make any additional investment in a cyberinfrastructure for the humanities, I think this is it. And it needs to be a national infrastructure. I trust and like the good folks at Zotero, but they are not a national body. It astonishes me that the NSF and Arxiv are two different infrastructures, though, for all I know, the NSF funds, or funded, Arxiv.

Of course, I have been making much the similar argument at the local level: that the university library is the new communications platform. I think other universities have made huge strides here, and I am glad for them. Perhaps I imagine a national infrastructure because that may very well be the only way I get into this game, but I also think that a national, or even international infrastructure (or federated national infrastructures), are the only way forward.

Research management is, I think, too important to be left to individual users to bear the time and cost of setting up and maintaining such things. The contemporary cohort of research management software has gone a long way in relieving researchers of the burden of such work, but in realizing the importance of networks, both for working across a range of devices but also a range of users, I think we have highlighted the real need for a thorough revision of the way we approach supporting a robust research infrastructure, one that is open, accessible, and affordable to anyone interested in making the investment.

My thanks, by the way, to [Tim O’Reilly][] for being the one to bring all of this to my attention. One day, Mr. O’Reilly, I hope to work for you.

[quite a stir]: http://www.zephoria.org/thoughts/archives/2013/04/11/mendeley-elsevier.html
[BookEnds]: http://www.sonnysoftware.com
[Sente]: http://www.thirdstreetsoftware.com/site/SenteForMac.html
[Papers]: http://www.papersapp.com/papers/
[ReferenceManager]: http://www.refman.com
[Zotero]: http://www.zotero.org
[BibDesk]: http://bibdesk.sourceforge.net
[Mellel]: http://www.redlers.com
[Mendeley]: http://www.mendeley.com
[Citavi]: http://www.citavi.com
[Colwiz]: https://www.colwiz.com
[Qiqqa]: http://www.qiqqa.com
[noting]: http://radar.oreilly.com/2010/03/state-of-internet-operating-system.html
[Tim O’Reilly]: https://twitter.com/timoreilly/statuses/322755746456535040

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3 thoughts on “Of Research Managers (The Software Formerly Known as Citation Managers)

  1. I’ve been admonished for not using one of these services- I’ve tried several, but they always seem to add extra work. Clunky interfaces and limited usability mean they lose out to my own file organization system that I have in my OS. The databases forward their web 1.5 models and tout them as the new new, but the pay walls and compartmentalization are ultimately holding us back. I feel overwhelmed by the fragmentation at times. I’m fascinated by how research expectations have changed over the past few years. My students, in particular, aren’t satisfied with just using databases, they want to know how all of these systems interact and how to make sense of them, and I find myself ill-equipped to provide answers. I don’t recommend they use zotero; it just feels like throwing software at problems and not actually solving any.

  2. John–thanks for your essay, which is very helpful. I think that the primordial activity at the root of these systems conditions them still and accounts for differential uptake (scientist disinterest in Zotero, for instance). There is a lot more going on, of course, from UI to ideology.

    As you note, index cards are part of the ancient roots. Zotero, in my view, begins with a historian or a literary critic in an archive (“alone”) with a stack of index cards. (See the centrality of note taking inside present day Zotero. I was told that there was an older digital note taking system out of which it grew, the name of which I no longer know.)

    From what I can tell, the primordial image for Mendeley is something like a research university science professor (not “alone”) passing out a photocopy of an article to the member of “his” (or perhaps her…) “lab” at the end of a lab meeting in anticipation of a upcoming “journal club” meeting.

    Again, I did not even want to mess with Mendeley so I am thinking out loud on the basis of user commentary, but the collaboration tools are clearly different. Part of this relates to borderline piracy (and Zotero users tend to want to build a better world while understanding the laws that they would change, while some other kinds of scholars just want to do what they want to do, regardless of current law), but it is also about collaboration practices. DH, for instance, is very collaborative, but humanists and (to a degree also social scientists) are conditioned by a solo tradition, whereas lab culture is now basic to the sciences and thus collaboratory practices also come easier (although science collaboration looks rather hierarchical to me…). Mendeley love and Zotero ambivalence, as well as the basic differences between them as tools, are somehow, I think, entangled with these macro-disciplinary differences.

  3. Not addressing your larger concerns, but note that as of Zotero 4.0 you can set PDF download for “as needed”. And, of course, as opposed to Mendeley, Zotero has always allowed you to sync PDFs via a WebDAV service which could be on your own or your institutions server.

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