Mendeley: A Reference Manager and More

It is said that the forceps ... for delivering babies ... was invented by a doctor working in the American Midwest* who used it only to deliver the babies of people to whom he was related. The forceps caused babies who might have died during childbirth to live and may have increased the survivorship of the mothers as well. In this way, inclusive reproductive success of Dr. Forceps increased significantly. Presumably, as more people moved into the region, and still more were born there, and the land was divided up and farmed, competition between farmsteads would have increased. By using the forceps to benefit his own kin, and by NOT using it for others (he was the doctor delivering the babies) or even telling anyone else about it, Dr. Forceps increased his own fitness at the expense of everyone else's. Hiding this new and amazing technology was probably an effective Darwinian strategy for him.

I feel about Mendeley much like Dr. Forceps must have felt about his invention, except since I did not invent Mendeley, and other people can and eventually will find out about it, I might as well just give up and let you in on the secret. If you are a researcher, or a writer who writes non-fiction and thus need to keep track of source material, Mendeley will change your life. In a good way. Researchers with Mendeley will have greater Research Success (RS) than those without it.

Here's what Mendeley does.

It is a bibliographic database, where you can keep your reference data (like Endnote, etc).

It extracts bibliographic data when possible from PDF files.

It helps you organize and keep track of the PDF files you've got stored on your hard drive.

It lets you keep some of those PDF files on the Mendeley web site so you can access them, via the web, from somewhere else.

You can sync all this stuff across multiple machines.

You can "cite while you write" depending on the software you use.

You can vacuum bibliographic data off the web from various places.

You can collaborate with others in this endeavor.

In other words, for a researcher, Mendeley is pretty much the most fun you can have with your pants on.

Mendeley is cross platform, and OpenSource.

Here's what makes Mendeley good ... the philosophy of the developers. I've talked to them, I've emailed with them, and I've examined their material and played with their software since it was in Beta. My view of their philosophy may not be what they think their philosophy is, but I personally think it's dead on. Specifically: If there is a thing a researcher wants to do with her or his references, and Mendeley does not do it, that's a bug in Mendeley, and needs to be fixed. If there is a vision, or viewpoint, that a Mendeley developer has about how to do stuff with references, and this is different than what some researchers want to do, the Mendeley vision is wrong, and you can't fix that difference with marketing. But you can fix it with programming. In other words, Mendeley is made for researchers not for a bunch of pasty old vice presidents of some marketing department, or some guy who thinks he has a vision about how things work that we all need to share.

Mendeley is software and connected resources designed to solve a related set of problems. And it does. Moreover, given the way Mendeley has developed over the last year or so, I fully anticipate that the software will continue to amaze and impress.

Details can be found in this fact sheet (PDF), and the main web site is here.

_________

*The forceps were probably invented numerous times, this being one of those times, to the extent that the story I give here is not apocryphal.

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I've been using mendeley for a while, and it is awesome, although I have had some problems with it getting confused over different article details (like missing out authors, or getting journal names confused with dates).
Fortunately Mendeley makes editing your references as easy as editing song details on itunes, and doesn't have Endnotes problem of ruining any changes you've made to your references when you're back's turned.

Mendeley is great! Not open-source though. Just free and cross-platform software.

You might want to check out Paperpile too. Still in beta, and runs only on Linux so far. Has in-built search though. Mendeley only imports from your browser.

http://paperpile.com/beta/

By MadGenius (not verified) on 14 Apr 2010 #permalink

It is so very sexy and exciting that I spent too much time playing with it. I have now managed to index all of the PDFs I have on my internal hard drive. When I have more time I will take the papers I have on the external drives and index them too - I love the functionality of the search function.

MadGenius -

Mendeley also imports from from your computer as well.

So if forceps are a successful Darwinian strategy, what the heck was Caesar up to? ;-)

More seriously, Greg's on the right track and I just wanted to add a bit about the activity stats that are available at Mendeley Web.

The information about what papers you're reading now, while remaining private by default, allows Mendeley to predict other papers you may be interested in or even colleagues you may like to get in touch with. This readership information helps highlight what are the emerging trends in your field. Not only that, it's fun to watch your readership numbers climb.

MadGenius is correct that Mendeley isn't completely open source. It does have some proprietary components, but this isn't being used to enforce data lock-in via proprietary data formats or anything. All userdata will be available to the user for them to use in other services and I expect to see some interesting services built on the Mendeley API when it's available, giving institution-specific research activity snapshots and that sort of thing.

Thanks for the correction on the OpenSourceosity of Mendeley. I've actually talked to the developers about this, I just got it wrong in the post. It uses a combination of OpenSource and proprietary. What I can say is that the developers are committed to Open Source AND to pragmatic solutions, which is actually better than a pure commitment to open source.

It is a pure commitment to open source that causes Ubuntu to be unable to install correctly on any Dell laptop. A tiny tweek once the installation happens fixes that, but the pure commitment to OpenSource seems to keep the Ubuntu community from telling people what this tweek is, or the distributors from just making it work (and it would be legal) automatically during installation.

I am a strong advocate of Open Source, but I tend to agree with Linus Torvald himself, who appears to understand the downside of striving for a real purity movement

Simon, I can't find anywhere in that user's agreement that says that Mendeley will start charging for their software at some point. Could you please provide a quote or something? I'm probably just missing it, if you say it's there, I'm sure it is.

Also, Zotero is a Firefox extention. In the past I've chosen my reference managing software very carefully. I have 10,000 print papers and another 20,000 references I regularly search through. I have changed my system from dBase to Access to Endnote to Chaos to Mendely over 30 years.

In other words, the lifespan of my mission-critical reference management exceds that of the average popular browser, and certainly of the average browser plugin.

Plus, I HATE browser plugins. So that's why I did not even try Zotero. Though it looks interesting.

I am not sure I understand this but won't be trying Zotero either, mainly because the only reason I even have Firefox is for a handful of college web access systems that have clumsily implemented some sort of proprietary database/bulletin-board software that must have been deliberately designed not to work with Opera, since there are numerous webpages with identical front-end functionality that work just fine in it. Firefox annoys me because it lets me change far fewer of its options, including hotkey assignments, and because it seems like every change to newer versions of Opera that annoys me (possibly even including 10.5x's flat-out refusal to finish loading certain sites essentially at random) seems to be an imitation of some Firefox feature to make it "friendlier" for users switching.

"Some proprietary components"? "Not completely open source"? Are you kidding me? Mendelay is 99% proprietary. Other than a few Qt libraries that were already open source (and thus had to be kept open), Marndely's only open code is the citation formatting engine they copied from Zotero, again, also already open code.

I like the author's logic on not wanting to change research software frequently, but I don't know that I would bet Mandelay will last longer than Firefox, on part due to Firefox's large and vibrant open source community, and partly because it's not yet clear that Mandelay has a workable business model. How long can their funding hold out?

Karen: Firefox is a web browser. We were discussing a plugin. Firefox needs to exist for the plugin to work, and the plugin has to be maintained to work with whatever Firefox does that requires changes in plugins. That is not even close to what one would base a long term data management solution on, unless it worked entirely with a common file format that other software would be available to use, like bibtex. (Which it might, I have not looked at that.)

Hi Greg and Karen,

it's Victor, one of the founders of Mendeley. Simon's point is partially correct in that not everything that Mendeley offers in the future will be a free of charge (likewise, Zotero also charges for additional storage space). At some point in the near future, we'll start offering additional features/services that users can purchase for a monthly fee, e.g. expanded storage space or advanced collaboration features. However, any features of Mendeley that are free will always remain free.

Karen: Indeed, our Word/OpenOffice Plugins contain code licensed by Zotero under the ECL. Our plugins are likewise open source under the ECL. Besides, we are developing an open-source WYSIWYG Citation Style Editor which will most likely be hosted at http://www.citationstyles.org. It's still very much work in progress, but you can access the code here: http://bitbucket.org/csledit/csl-wysiwyg-editor/ or play around with the status quo here: http://csleditor.quist.de/csleditor/show/1/example-citation-style (the UI will be overhauled completely before it's finished).

All the best,
Victor

Victor, thanks for the clarification.

Personally, I think charging for expanded space is an excellent business model (assuming you are not more expensive than existing cloud services). Collaborative tools .. that depends. Facebook is free (but uses ads). Whatever you do, somebody will figure out a way of doing it for free, most likely on facebook. You might as well go for an ad-based collaboration environment!

(in my humble uninformed opinion)

Will always remain free, eh? Just like Ning?

I didn't mean the initial comment to sound quite so snippy. Apologies for that. I was attempting to make the point that Victor has clarified - that what is currently free will remain free, but that Mendeley will be moving to a so-called 'freemium' model. I agree that this is a very good idea for a business model, providing an income to keep a good product going, without raising the barrier to entry.

I also get the resistance to using browser plugins for such a crucial piece of software. Others may be interested to know that Zotero has just announced (like, yesterday) that they are developing a stand-alone version of their product (http://www.zotero.org/blog/standalone-zotero/).

Simon, thanks for that. It's great news for Zotero and a good step forward for their product. With the number of new startups companies entering the research management space, I have great hopes for real innovation.

Let's remember that citation style managers are essentially a hack to support all the unnecessarily different formats required by different publishers. They're essentially a idiom of print that has been shoveled into the digital world but when documents are rendered from a underlying database as opposed to printed using ink on paper, they can do the formatting at the time of rendering, not the time of writing. Offloading this effort would the allow academics to focus on the actual writing, not the fussy little details of what format things should be in.

The other exciting thing about all the activity in this space is that it sharpens the focus on open access. All these tools work better for their users when there's more OA content available.

I would like to add, as advice for young academics who are worried about the formats of your bibliographies and are willing to go through great lengths to make sure that the ref list for your paper can be generated by pressing a single button: Get a job!

Sure, it's a pain, but fixing up the Bib is not the point. The point is finding what you need when you need it. Focus more on organizing your material with respect to content and use, and less on formatting the bib on the paper you finally produce. If your software does it automatically, nice. If not, just do it yourself. Stop whinging about it.