One of the goals of ProfHacker is to experiment with new things and share our results, in the hopes that our experiences—whether positive or negative for us—may be useful to others. To that end, we might step out of our comfort zones and work with software (or processes or pedagogy) that we might not otherwise try. If you think about it, such a move can only ever be positive in the long run—either we learn something new and exciting and improve our workflow or we gain perspective on what it is about the status quo that we like so much.
Such is the case here; when I said I was going to write a post on Mendeley, the cross-platform desktop and web-based research management tool, everyone said “You? Who wears your Zotero jacket everywhere you go?” Hey, what I can I say? I wanted to see what all the hype was about.
Before I continue, let me just say that this post is in no way a Mendeley vs. Zotero smackdown. While I firmly believe such a post is in my future, this isn’t it. Consider this a brief introduction to some of the key features of Mendeley and an invitation for new or existing users to discuss the tool in the comments section.
“With Mendeley, research papers get scrobbled”
This heading is the title of a Wired UK post on Mendeley. The verb “to scrobble” was coined by the music service Last.fm, and it means “to automatically add the tracks you play to your Last.fm profile with a piece of software called a Scrobbler.” When the music you play is scrobbled, it is added to your profile which in turn allows the Last.fm service to generate personal “top music” charts, to provide recommendations based on the music you listen to the most, and to connect you to like-minded listeners among the Last.fm community.
Now, why on earth is that important?
Because if you look at the Mendeley “About Us” page, you’ll notice that most of the minds behind Mendeley were responsible for Last.fm, and the Last.fm/scrobbling/community concept is exactly what they’ve brought to Mendeley. [They say so on YouTube, so it must be true.]
As a Last.fm user [who had to stop because I was using it almost too much] and an academic, conceptually this was really appealling. Then I realized that people in my field were not really part of the Mendeley community; the special value-added of this particular tool unfortunately does not reflect my reality. But, if it did, I can easily see how this is a valuable tool because it already handles the basics just about as well as the tool I do use.
Key Features
The key features of Mendeley are roughly organized into three categories:
- Organize: indexes and organizes your PDF (and other) documents into a bibliography, all the while gathering details and building an index that then allows you to search, custom categorize, and cite from these materials. In addition to drag-and drop functionality, the Mendeley Web Importer and COinS support allow you to quickly access and import documents from other resources (see list at the site). Again, here your mileage may vary as to usefulness, depending on your field. Once you have your documents in Mendeley, you can read, search, annotate, and highlight within the integrated PDF viewer; this is why Mendeley was mentioned by users and reported in Ryan Cordell’s post How Do You Organize and Annotate PDFs? (Reader Response Roundup).
- Share: at its core, Mendeley is a social network; you can create groups, invite friends (fellow researchers), and stay up to date on what people are reading (or, at least, what they’ve added to Mendeley). Again, this assumes that people in your field are actually using it. Currently, Mendeley users tend to be in the sciences.
- Discover: going hand in hand with the social/sharing aspects is the discover network—or the potential for one. You can “navigate the web of knowledge” and view the most read authors, journals, and publications within your field or other fields, as tags and other keywords are extracted by the items in users’ libraries.
Fundamentally, Mendeley is a bibliographic database, like EndNote, Zotero, and others. It does what you expect of such software: store, organize, sync your research, allow you to annotate it, make it available for export and other uses. It includes plugins for Microsoft Word and OpenOffice so you can cite while you write and generate bibliographies when you’re through.
The “extra” or value-added features of Mendeley compared to other tools includes the collaboration aspects and the research trends both within your library and your field as a whole.
Intrigued? Read more.
Technical Notes
There are two pieces to the Mendeley system: the desktop software and the cloud-based storage. You can download and install Mendeley Desktop for free—it is available for Windows, Mac, and Linux—and use it simply as a single-machine/local document manager. However, to gain access to the collaborative tools (and to backup your data) you must also have an account with Mendeley Web. The basic account is free but there are upgrade options depending on storage space and number of shared collections.
What About You?
What I’ve learned in my brief time with Mendeley is that it isn’t for me, primarily because the community aspects aren’t there in my field [I do realize that I could begin to change that by being part of it] and the software I use works just fine for me. However, I can easily see why so many people find Mendeley useful.
I will note that the “Import from Zotero” feature worked seamlessly; I seeded my Mendeley account with all of my Zotero data so I would have something to work with as I worked through the tool. Given the syncing abilities, it would be possible (and not terribly difficult or time consuming) to, say, work with Zotero as your primary tool yet sync with Mendeley so as to increase the content in your field and just add to the community in general. If you’re looking to try Mendeley and you already have a Zotero account, I recommend importing your library in this way and playing around with the data you’ve already collected.
What about you? Do you use Mendeley? If so, what are the features you find most appealling? Let us know in the comments, and please identify your discipline, as I think that matters in this case.
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19 Responses to Using Mendeley for Research Management
niceday - July 19, 2010 at 1:04 pm
I think the reason for lack of community with Mendeley is simple: Mendeley is a for-profit outlet and is not open-source (whereas Zotero is open-source and non-profit). We are just not going to turn over one of our most valuable resources. (Look at all the problems with, say, Facebook’s arbitrary changes to its privacy policies or the awfulness that is Blackboard and you’ll see why we’re wary).Also, Mendeley does NOT sync with Zotero — it just imports your database and thereafter you’re locked in. After having been burnt with proprietary systems that took directions I was not happy with, I’m just not going to join any community that is hosted by a money-making outfit. Anyway, Mendeley does not do anything Zotero does not do better!
jmeloni - July 19, 2010 at 1:58 pm
@niceday I’m not exactly sure the “we” you’re talking about, but 500 million “we”s are perfectly fine turning over privacy to Facebook, institutions keep paying Blackboard despite the problems, etc. I’m not at all saying that’s right — I share your sentiments about open source vs proprietary systems, and Zotero for that matter. But, for a relatively new & niche service, there _are_ hundreds of thousands of Mendeley users — mostly in the sciences, which is not my field. There is a community there within some disciplines. As for my comment about syncing w/ Zotero, it was my experience that it does do a continuous sync. I was adding things via Zotero and having them populate my Mendeley account after the original import. So there’s that. Again, though, I’m not disagreeing with your sentiments.
drgunn - July 19, 2010 at 3:45 pm
As I told niceday in the forum months ago, there’s no lock-in of any sort. The Mendeley FAQ has always stated that all of a users data will always be available to them. It’s just an sqlite database, anyways, so proprietary data formats just aren’t an issue.What niceday is grumpy about (and if you read the forum threads you’ll see this for yourself) is that Mendeley isn’t open source. While I agree that open source is better for many purposes, the situation is different here, because Mendeley has made their research catalog openly available and has provided an API to that data. Academic reference management is an old market with some very entrenched players. It was a conscious decision to take on VC money and try to grow the company as fast as possible and because of that, Mendeley’s research catalog will soon be the largest database of academic literature in the world, and it will be entirely open. I think the good that this will do the world of academia is much larger than had Mendeley been competing with Zotero for contributions from open source developers. Now that Mendeley has reached critical mass and released an API, someone could, and perhaps should, write their own open source client that would do everything Mendeley Desktop currently does. That’s about as far from lock-in as one could possibly get, I think. If anyone would like to talk about this further, they’re welcome to email me at william.gunn@mendeley.com
jmeloni - July 19, 2010 at 4:37 pm
@drgunn Ah. I wasn’t aware that this exchange has a backstory. If I was, I wouldn’t have addressed it directly.In my post I am simply trying to introduce the product—a good product, though not one that I find useful myself for the completely personal reasons I noted—to readers in this space. I’m certainly not finding fault with Mendeley being a for-profit company or the maker of proprietary software. In fact, I’m not finding fault with Mendeley for anything. That’s not what this post was supposed to be about.I am interested to hear you say that Mendeley has reached critical mass, when I’m seeing precious little relevant to my discipline(s)—which is, again, why the value-added features of Mendeley are indeed not value-added to me. As for the “largest database of academic literature in the world,” sure, by sheer numbers of stuff all in one place, and that’s great. But there’s a difference between “largest” and “comprehensive”, and that all depends on the users themselves, etc. In fact, it’s not really in your control—you can only build a usable piece of software and a platform for sharing (which you have, with completely reasonable freemium tiers, etc), and hope for the best.What I hope ProfHacker readers will do is give Mendeley a try if they haven’t before, and talk about their experiences here. And, if they have used it and its value-added social features, talk about how it has transformed their research/experience.
heatherwhitney - July 19, 2010 at 4:48 pm
I’ve gone from EndNote to Zotero to Mendeley, and am now pretty much set on Mendeley. For some reason Zotero just didn’t click with my workflow. Part of it was that I’m using Chrome exclusively now for my browser, and Zotero currently works only with Firefox. Additionally, there’s just something about the user interface that wasn’t working with me. I can’t put my finger on it.I’m very much enjoying having both a desktop and browser setting of Mendeley to work with for my references; for some reason a desktop app makes me feel more grounded. The social connections aren’t yet of much use to me but I think will come in handy in the future if I start collaborating with others (and assuming I can convince them to use it too).
jmeloni - July 19, 2010 at 4:51 pm
@heatherwhitney I’m glad you commented; I hoped you would. Since you’re in the sciences and I am not, do you think there is anything about the way you do your research/your workflow that might be discipline-specific and thus makes Mendeley work better for you? Obviously this is something I’m still trying to figure out.
drgunn - July 19, 2010 at 5:29 pm
It’s a good point, Julie, about the difference in uptake among sciences and humanities. All we can do is put out the welcome mat and hope that the added value is enticing enough. To some extent, the relative lack of humanities coverage is an accident of history. The Zotero team is humanities-heavy while the Mendeley team is science-heavy and that’s reflected in the different degrees of coverage. I see that trend changing in the future, though, as the two services have significant non-overlap in features and one can easily use both.Thanks for your useful and well-researched piece.
jmeloni - July 19, 2010 at 5:49 pm
@drgunn The “accident of history” sounds about right, and I also see some sort of future convergence. That’s why I was heartened to see the Zotero import functionality, and—whether this was supposed to happen or not—the Zotero resync w/ Mendeley. I think the interplay between the two will be key to moving users, well, not “over” but perhaps “occasionally into”, the Mendeley social space while working with an interface that perhaps in their discipline or workflow happens to work better. For instance, when I was running tests on particular online journals, Zotero would capture the metadata correctly while Mendeley would not, but then once it was in Zotero, played nice in Mendeley. Perhaps when Zotero moves to standalone or non-FF plugin, there will be additional interface and workflow changes on that side, but as long as the sqlite dbs on both ends are to some degree standardized, stuff can be shared. And there’s no harm in multiple copies of stuff, esp. when they are, fundamentally, being managed — just in two different contexts.[I really didn't want this to be a M vs Z or M-in-terms-of-Z post or discussion but I suppose it's inevitable.]I want both to succeed, because both are different and this isn’t a space that needs a winner per se. It’s a space that just needs to move forward somehow, and Mendeley is definitely doing that.
cyborganize - July 19, 2010 at 6:01 pm
I cannot stop raving about Mendeley (which I discovered thanks to the previous ProfHacker post Julie mentions), so here’s a comment by request!I feel guilty abandoning Zotero, which is a project I heartily support. But now that I’m making virtual coursepacks for all my classes, I needed a more robust and user-friendly interface for organizing them. I know Zotero is capable of doing this, but the browser-based interface felt too lightweight and the file/annotation features too buried for this to really be its strength. Plus I wanted to switch to Chrome. Sorry Zotero!I was trying out Sente, an advanced Mac only bibliography manager known for its awesome PDF annotation capabilities. However, I ran into a deal-breaker in this regard: Sente saves the markup on/in the original PDF files. As a professor who needs to take my own notes AND distribute clean PDFs to students, this is not going to work for me.Mendeley has less options for markup, but they are adequate and more importantly only appear within Mendeley, leaving the files as-is. Because you can both import PDFs to the desktop client and add references from the web, it feels like it does everything that Sente does AND everything that Zotero does. (Although FYI I am running into a problem with Chrome’s pop-up blocker and Mendeley’s web importer that I didn’t have in Firefox.) Plus, Mendeley is the prettiest of all!As for the academic social networking features, I could take them or leave them, but I’m interested to see how they develop as (hopefully) more people in my field (media studies) adopt Mendeley. Be my contact!
brianborchers - July 20, 2010 at 8:03 am
Thanks for the introduction. I’m interested enough that I’ll probably try installing Mendeley and converting my Zotero stuff over to Mendeley. For me, the big (and utterly non-negotiable) issue is the ability to export from Mendeley to BibTeX.
dwilliams5 - July 20, 2010 at 10:50 am
Thanks for flagging this. Since switching to Chrome, I’ve come to much the same point with Zotero as @heatherwhitney and @cyborganize reported. I kept hoping Zotero would evolve to integrate with Chrome, but don’t much motion on that that. Mendeley may be a solution. Thanks again.
jmeloni - July 20, 2010 at 11:04 am
@dwilliams5 9& others) I believe that everyone should try as many things as possible and hit on the solution that works best for them. Though there is movement on the Zotero-with-other-browsers-including-Chrome front, and I’ll talk more about that in a few weeks, definitely give Mendeley a shot.
niceday - July 20, 2010 at 11:19 am
The backstory is exactly what I said — I don’t think academics should trust their most valuable resources to for-profit companies over whom they have no control. Zotero is open-source, university-based and non-profit:-)Once you import into Mendeley, you cannot go back to Zotero. Mendeley can import from Zotero (which everyone can since Zotero is open-source) but not export to Zotero so the decision is irreversible.What Dr.Gunn is referring to as VC is “Venture Capital” — i.e. people who put in money because they want to get out money. I am already pretty sick of the publishing model in which journals take *our* work and then make it inaccessible behind paywalls. Where is the guarantee that at some point in the future Mendeley won’t do something that limits access unless you pay? Especially if it becomes big enough?Facebook is an instructive example — it shows the power of big! They can, it seems, change terms at will and there isn’t much anyone can do about it.So, yes, my beef is Mendeley isn’t just about open source. It’s FOR PROFIT. That will eventually means making money from the users, one way or another. So buyer beware.
dabilock - July 20, 2010 at 11:57 am
While experts working on their own research may go from article annotation to writing, students need more structure. They need scaffolding so they read carefully and don’t just cut-paste-regurgitate. They need to be able to ask questions about sources they’re using, so they understand why information from journals differs from magazines, why some databases are more useful than others and guidance throughout the research process. That’s the kind of process being used in this collaboration between an instructor and a librarian: http://www.insidehighered.com/advice/instant_mentor/weir27Given the typical college teaching load, you may not be able to provide students with the scaffolding and feedback that it takes. What software like NoodleTools does is provide an “extra instructor,” at the point of need who answers students’ questions and supports their research process 24/7. And instructors (and instructional librarians that work with them) need a collaboration space where they can monitor and give feedback on students ongoing work. That’s what missing from both of these products.
drgunn - July 20, 2010 at 12:43 pm
niceday – As I mentioned last time you brought this up, there are answers to your questions in the Mendeley FAQ.The founders have repeatedly said that everything that’s currently free will remain free. Mendeley recently started offering paid accounts which give extras like more storage space, so they don’t need to charge for what’s currently free. This is what’s called the “freemium” model, and there’s no lock-in nor will there be.I understand your concerns. I share them, and in fact, the reason I got involved in Mendeley in the first place was because they’re working to change that terrible situation. Don’t take my word for it, though. Check out http://opensciencesummit.com/sponsors/. Mendeley is co-sponsoring with the creative commons.dabilock – You’re right. Mendeley isn’t intended to be a tool for teaching writing, although some do use it in their writing programs. Hopefully it will be a nice adjunct to hands-on instruction.
heatherwhitney - July 21, 2010 at 4:08 pm
Julie,I’ve been thinking more about what makes Mendeley work for me, over Zotero. I can’t speak for all physicists, but for me and my workflow a pdf (or research source in general) needs to be more grounded for me to start working with it. I of course search for and initially view pdfs on the web, but when I decide to include one in my collection of literature it gets saved to a file in my research folders. For me and mind, that file needs to exist off the web. I like that Mendeley has a desktop client that keeps the entire pdf viewable. I didn’t like that Zotero had an online-only add-in that existed on top of the pdf. I hope this makes sense!
adam_smith - July 22, 2010 at 2:02 pm
@heather – while I think that if you’re happy with Mendeley you should probably stay with it, your view of how Zotero works doesn’t seem quite correct – or at least it sounds that way.Every pdf you have in Zotero is on your local harddrive. You can actually drag and drop any pdf directly from within Zotero to your Desktop, e-mail program etc. While Zotero sits within Firefox, you don’t need to be online to access the pdf that way. What is true is that it is somewhat harder to access your pdfs that are saved in Zotero _without_ opening Zotero/Firefox, as they’re by default stored into a somewhat cryptic folder structure with random-folder names. For people uncomfortable with that, it is very easy to use your OS to create a smart folder (Mac), virtual folder (Win XP and Vista), library (Win 7) or saved search (linux) with all your Zotero pdfs in it.http://forums.zotero.org/discussion/8072/linked-attachments-two-requests/#Item_15While I sympathize with niceday’s feelings about open source, I think his fears about lock-in with Mendeley are exaggerated – Mendeley does export standard formats and you won’t really be locked-in. And after constantly declaring that currently free feature will remain free, I find it very hard to believe that they’d want to incur the wrath of their user base by turning around. The revenue generating model remains interesting, though: If it’s just going to be more storage, better social media functions etc. I’d have no problem. If, on the other hand, one of the goals is to make money with users generated content like CDDB doeshttp://en.wikipedia.org/wiki/CDDBI’d be a lot less happy. I think Dr. Gunn is addressing this above refering to the free API – and if that’s right and if that will stay free (which I couldn’t find out quickly) I think that’s pretty fair. I think there are a number of reasons why Zotero is stronger in the humanities: a) it was developed by historians so that’s where the word spread initially b) the superior (I’d argue) facilities for dealing with ordinary webpages and non-academic sites are much more relevant for people in the humanities and social sciences c) at least in the UK and the US people in the humanities and most of the social sciences are further to the left than their natural science colleagues and prefering open source software – especially when it’s very similar in its abilities – is probably still partly a lefty impulse.
heatherwhitney - July 22, 2010 at 2:18 pm
@adam_smith I see your point (and appreciate it!) but I do like having an interface for accessing the pdfs, marking them (such as Mendeley’s “to read” marker) and such. Just not wanting to have to do that through a browser. :-)
wilson_energy - October 11, 2010 at 11:10 am
One thing I haven’t been able to find out about Mendeley is if it also manages and stores non-pdf files, eg. ppt, xls, graphics, etc. I am interested in using the group storage solution with its organizing features but about 40% of my files are not pdfs.