For the Academic Theorist Hulk in All of Us

June 11, 2010 8:30 PM

Mendeley is a cross-platform research management tool which features article databasing, PDF annotation, online backup, private, shared and public collections, metadata lookup on Google Scholar, direct exporting of multiple citation styles to Word, OpenOffice and BibTex, the ability to add documents directly from a web browser, and social networking with other members in your field of study. Like Zotero (previously), but out of the browser and with note-taking abilities. For Windows, Mac and Linux.
posted by l33tpolicywonk (27 comments total)

Is this the same Mendeley that people have been asking about in AskMe for some months?
posted by pineapple at 9:24 PM on June 11, 2010

Credit where credit is do: I heard about Mendeley in this AskMe by oinopaponton. Still, wanted to bring it to the blue for people like me who have always assumed their folder hierarchy was the best way to sort all their articles.
posted by l33tpolicywonk at 9:28 PM on June 11, 2010

Yes! It's a beautiful program. This student would wither without.
posted by Schlimmbesserung at 9:38 PM on June 11, 2010

So what's the catch? How does it pay off for them?
posted by five fresh fish at 10:12 PM on June 11, 2010

five fresh fish: "So what's the catch? How does it pay off for them?"

500 MB of online space for free. They're promising to sell more storage space in the future. It's worth noting, though, that online storage isn't required: you can set it to sync your whole library, just some collections or nothing and can choose whether it syncs just your metadata or the metadata and the files. It looks like they're trying to get volunteer professors on campuses to spread the program's use. I'd also guess that the data (some of which you can see here) that they get from keeping a ton of public research archives is worth something to people in the academic publishing business. You can read the TOS here if you're curious, but there doesn't seem to be anything worthy of note, other than they collect aggregate data on all the papers in the database.
posted by l33tpolicywonk at 10:21 PM on June 11, 2010

I've been a user of Papers for quite a while, but it seems to have stagnated somewhat over the last year or so. How does Mendeley compare? At first glance, it seems to be like Papers on crack. The good kind.
posted by StrangerInAStrainedLand at 10:30 PM on June 11, 2010

I've been waiting for them to release a 1.0 to post it to the blue, but honestly it is already very useful software at this point.
posted by parudox at 10:33 PM on June 11, 2010

direct exporting of multiple citation styles to Word, OpenOffice and BibTex,

Does this work? Well? As in, I can select a new formatting style and it will go through and update all the references and the bibliography through the whole paper? In OpenOffice? And I can then send that document to a colleague who can then work on it, add references, and send it back to me?

If so, I'm heading off to burn my copy of Endnote on a pyre.
posted by Jimbob at 10:37 PM on June 11, 2010

Looks to be closer to Sente than "Papers on crack". That said, it's cross-platform, and syncing and the notetaking / annotation interface appears to be superior to that of Sente.

Jimbob: "If so, I'm heading off to burn my copy of Endnote on a pyre."

Wait, you're a Mac user, right? And you didn't do that after using EndNote for 5 minutes? ;-)
posted by Pinback at 10:43 PM on June 11, 2010

I have a bibtex database with almost 2000 items in it. I can't see a way to import this. I remember Zotero had a bibtex import feature; anyone know if Mendeley does?
posted by Philosopher Dirtbike at 11:02 PM on June 11, 2010

Wait, you're a Mac user, right?

Actually, I'm not - why, is Endnote for the Mac even worse? I detest EndNote, and have for close to a decade now. But it's only thing I've found that has ever actually come close to doing what I need, so I've been stuck with it (much as I've been stuck with MS Word).
posted by Jimbob at 11:08 PM on June 11, 2010 [1 favorite]

I tried Mendeley and the killer flaw was you couldn't make sub-collections. Zotero lets you have collections and sub-collections and I use these like folders and sub-folders, even though they're semantically not quite the same thing. Apparently I'm doing it wrong and should use tags or labels but bleh whatever. It's currently a "planned" feature; once they make it I'll probably switch from Zotero, because Mendeley is more elegant in a lot of ways, and Firefox tends to leak memory and it's sometimes a pain to be stuck using it when all I need is my references. I already use Mendeley as an intermediary to get my Zotero library into bibtex because Mendeley is better at making persistent citation tags.
posted by PercussivePaul at 11:16 PM on June 11, 2010

ProfHacker had a good review of these type of programs. I linked to this on AskMe the other day.
posted by k8t at 11:34 PM on June 11, 2010 [1 favorite]

Mendeley is one of the buggiest programs I've ever used. It crashes to the point of being unusable (at least on Ubuntu) and is an incredibly aggravating experience. By crashes often, I mean the problem crashes and loses all new data every single time a PDF is viewed.
posted by null terminated at 11:48 PM on June 11, 2010 [3 favorites]

Jimbob: "I can select a new formatting style and it will go through and update all the references and the bibliography through the whole paper? In OpenOffice?"

Just tested this because you mentioned it: yes.

"And I can then send that document to a colleague who can then work on it, add references, and send it back to me?"

As far as I can tell and assuming they're running the same software setup, yes. When I saved, closed and reopened a document, I was able to manipulate the citations in the same way: add, delete and change style.

Philosopher Dirtbike: "I have a bibtex database with almost 2000 items in it. I can't see a way to import this. I remember Zotero had a bibtex import feature; anyone know if Mendeley does?"

According to the FAQ, yes. Additionally, you can import to Zotero and keep Mendeley and Zotero synced constantly - if you have Zotero installed, it should ask if you want to do that when you set up Mendeley.
posted by l33tpolicywonk at 11:55 PM on June 11, 2010

I use it on OS X, switched away from BibDesk. The social collaboration features are really what set it apart in my opinion.
posted by onalark at 1:58 AM on June 12, 2010

It's nice, and they're definitely heading in the right direction. I don't doubt that it's the right tool for lots of people. But it still needs a fair amount of polish.

I tried importing my modest bibtex database. Yes, it works. But it has trouble with special characters. It can scan a folder for PDFs, extracting information automatically and matching existing entries if it can. But the extraction is often quite poor, and I end up with duplicate entries or incorrect metadata. It has a great feature to correct data via a Google Scholar search or via looking up the DOI online. But it pulls in data incorrectly via both, making many entries worse (changing papers in conference proceedings into books, tossing the conference title, dropping all but the first author, etc.). If that worked consistently well and if they added a "correct all via Google Scholar / DOI" button, then that would be a killer feature for me.

I happily went to report bugs, but they use Uservoice as their combined bug report / suggestion / feedback platform. It's decent for suggestions (and the de rigeur voting), but it's a poor platform for bug reports. I can either sign in with my Facebook or other social hoo-hah account (I'm wary) or make a brand new account (I'm lazy). Luckily, I'm not the first to notice this, and they're on it.

All that said, I'll probably switch over from good ol' Jabref some time soon. I'll just need a good chunk of a day to import and manually clean up the data.
posted by whatnotever at 3:36 AM on June 12, 2010

Mendeley has promise. I use it right now but am still in the waiting-for-it-to-crap-out phase of new software acceptance.

So far, it's been quite good...VERY good in fact.

Biggest problems I've noted:

1)could not completely import my ~2000 pdf library: it would hang up and around the 1700th pdf--my solution was to just stop there and add the remaining pdf's as i need them.

2)internal search feature is only global and i cannot search by field (for example if i search for an author, i not only get their papers, but papers that have cited their papers)

3)internal pdf viewer has very limited note-taking features; it's easy enough to click on the pdf file in Mendelely and open it in your favorite pdf viewer but having all this internal would be very nice.

All in all, Mendely has been very stable and the cross-platform compatability might make it a contender (along with EndNote X3) for being the documents manager to have. I'm looking forward to seeing how Mendeley develops.

It's certainly worth a close look, even at this beta stage.
posted by DavidandConquer at 5:09 AM on June 12, 2010 [1 favorite]

It's currently a "planned" feature; once they make it I'll probably switch from Zotero, because Mendeley is more elegant in a lot of ways, and Firefox tends to leak memory and it's sometimes a pain to be stuck using it when all I need is my references.

They're making stand alone zotero now, too. No hope of a chrome interface. I just trust the makers of Zotero more: it's a public service project by an academic group, and they don't expect to make money on it.
posted by a robot made out of meat at 5:12 AM on June 12, 2010

I keep getting excited every time I see a program like this (Zotero, Papers...) and then when I actually try using it I find the overhead is greater than just typing in the references myself. But the idea is very appealing!
posted by escabeche at 5:28 AM on June 12, 2010

Hopefully it will improve with time but as it stands I find it completely unusable. And I've tried, thrice! The updates seldom address massive bugs. Like show stopping bugs. Here's a greatest hits compilation:

-Everytime you delete a PDF from your library, it's space is never freed up on the server (that 500mb goes fast). Try maxing your space then delete your entire library to start fresh. Sounds simple but.... mendeley online still thinks you used up your 500mb of space.

-Deleting from database doesn't delete the actual file (so your HDD is litered with files you deleted ages ago).

-If you use google scholar from within mendeley to fix the details on a document, you better not scroll away while it's working, or the document you scrolled to will take on any found details. I overwrote about 10 files with the wrong info before I noticed.

And that's when I tried to start from scratch by deleting my library, which leads to:

-Deleting the library is impossible unless you do it in chunks of about 50-100pdfs (deleting all at once causes a total stall). That took about 30-40 minutes of manually trying to delete my library. I could have been writing a paper instead.

and we're back where I am now. Original library deleted, all online space used by files that technically don't exist. Making synching across computers (the reason I switched to mendely) impossible.

I'd much rather see Mendeley make a usable polished PDF manager and then, and only then, start tacking on all kinds of social networky complexities. Maximum props to these guys, and I will definitely check again in a year's time to see where it's at, but at the moment, I lost too much time wrestling with the program to get it to work, I'm done until a major update.
posted by Smegoid at 7:25 AM on June 12, 2010

OT, en peu:

The phagic aspect of Mendeley seems more in line with Galactus than Hulk. Yet in a (f|b)it of RSS serendipity/juxtaposition I wondered if the title of this FPP alludes to CT’s link to feminist hulk.
posted by mistersquid at 8:35 AM on June 12, 2010

I wondered if the title of this FPP alludes to CT’s link to feminist hulk.

It was.
posted by l33tpolicywonk at 9:53 AM on June 12, 2010

They've chosen a great name, at least.
posted by mendel at 12:02 PM on June 12, 2010

I'm a bit obsessed with Mendeley. My biggest problem was the crashing, but if you get in the habit of syncing every time you make a change, it prevents data loss. I just developed a guide to Mendeley for my research team, which includes some pretty non-computer-savvy people, which I'd be happy to share if you memail me. It's based on Mendeley for Windows, but it's adaptable for Macs.
posted by emilyd22222 at 2:33 PM on June 12, 2010

Wow, so nice to see a posting about this on the blue with such great praise and useful feedback. I usually hangout over on AskMe and almost didn't notice this. I work for Mendeley now, so I can shed some light on some of the issues raised.

FFF: As l33tpolicywonk mentioned, Mendeley is essentially working on the freemium model (more storage space, etc) but they're also exploring ways of working with institutions directly. All the features that are currently free will remain free, and you'll always have access to all your data. Lock-in through proprietary data formats is actively being avoided. There's also an API which will be entirely open soon.

Dirtbike: As others have said, there's bibtex import, but I'd also like to mention that you can specify a collection for Mendeley to make a bibtex file from, and it'll automatically keep the collection and file in sync.

null term: Have you tried a recent release? There have been quite a few bugfixes and speedups, particularly on Linux and Mac.
smegoid: Looks like you hit the bug jackpot there! That's certainly not how it's supposed to work. If you've been working with support on this, all I can say is to hang on tight because 1.0 should be coming out very soon (like days-weeks).
whatnotever: sorry 'bout the uservoice. I don't like it much either, but I can assure you that they use a proper bug tracking system in house, and if you email support they'll start a ticket. There will be a proper forum and wiki as soon as I and my team of advisors can get it ready. In general, if you have metadata extraction issues, emailing the offending item and a copy of your DB to [e-mail] helps us figure out what went wrong the fastest. I'm also more than willing to help anyone. Send me mefimail or regular mail and I'll do what I can to help.

The University Advisor program, BTW, isn't just for professors, or just for people at universities. I guess we could have picked a better name, but the general idea is to have people at their local institutions who can help us out in a sort of grass roots kinda way.

DavidandConquer: The search is actually pretty powerful, but not well explained. Here's some of the things you can do with the search box:
* Phrase search using quotes: "some phrase"
* Searching within fields using fieldname:keyword (eg. title:"web
search"). Supported values for 'fieldname' are: title, note, tag, keyword, author, year.
* Searching for documents/fields not containing particular keywords
using the '-' operator
* The OR operator can be used to search for one of several words.
* To search only a specific collection, just select that collection or smart view in the left pane before doing the search.
* Sticky notes aren't currently searched.
There's more hidden away in the FAQ.
posted by Mr. Gunn at 1:37 PM on June 14, 2010 [1 favorite]

Thanks for dropping in on the discussion Mr. Gunn! It's funny how often we find Metafilterians doing big things in the world. I like the way Mendeley integrates into my workflow, and I am looking forward to new releases. (I also applied to "represent" in Saudi Arabia, we'll see how that goes :)
posted by onalark at 7:08 AM on June 15, 2010