My impression is that Mendeley will take over. They are a bunch of super fast guys. They have almost a monthly new version.
Zotero should definitely try to associate with them. Zotero is still ahead on single-click-in-your-library, but their product is or will soon be superior. I regret to say that because I am definitely for the opensource option.

@DNAcombo: that's an entirely superficial assessment.

If you're an historian, or a legal scholar, I'd venture to say that Zotero is far ahead of Mendeley. And the open source nature of Zotero, while not fully exploited by the Zotero team (which I think holds them back) is no trivial thing. You need to ask yourself, what happens to your data and your documents if Mendeley''s business model fails?

OTOH, Mendeley may have some current advantages if you're in the sciences and big on the collabroation features that Zotero has long promised, but not (yet) delivered.

Here's the thing, though: both Zotero and Mendeley have the same basic vision. They just have slightly different plans to get there.

For that reason, I actually think there's a lot of room for useful collaboration, and have told both developers the same:

1. fully open data sharing and exchange; RDFa and bibo support is a really easy way to go a long way with this, but I've yet to see it in either project)


2. CSL integration; both support it, but there's room for improvement


3. implementing a standard API in word-processors so that we can have real interop here

Rather than getting into a pissing contest about which project is better, then, I'd like users to press the developers of each project to actually deliver on the openness that is the foundation of both of their visions. There's no reason both projects can't flourish.

Yes, it is (though they've suggested there's room for open sourcing at least part of their stuff).

I suppose I'm taking a particular interpretation of what they're up to, suggesting that it can't succeed unless it's based on open data and open standards, that's it's certainly not in their users' interest if it's not, and so framing expectations ;-)

More practically, I want to see them work together where they can (on the issues I note).

Perhaps it would be more helpful to clarify which parts you want open-sourced? The software code or the data? And the reason for doing so. I'm failing to see the logic. I think Mendeley's intention is to open up the data via APIs (with consideration to privacy of course).

I don't see why they need to open up the code to the software though, same would go for Zotero. Do you demand the same of Google Scholar? Apple? Microsoft? It would only make sense if they run out of funding, otherwise investors would hardly be willing to continue financing the project. This isn't like MySQL or Ubuntu that started from a single altruistic individual or group of developers. There are a few vocal supporters of open-source, but the majority of users will not care as long as data and privacy are not abused and open-source does not solve that problem.

I don't see why they need to open up the code to the software though, same would go for Zotero.

As this is your first post, I question the motivation a bit. However, I'll bite.

Open source guarantees the program will be available, at least as-is, in the future. Mendeley is currently available at no cost after you register. But they could change this, and decide to charge for their program. Or they could go out of business. You would no longer be able to download their program.

Open source allows other to submit bugfixes and to add features. This is already happening with Zotero. Mendeley has said part of their business plan is to charge money for "premium features." Because the program is proprietary, there may be no way for non-paying users to gain access to those features.

Open source allows usage on more platforms. Mendeley is better than most proprietary apps in this regard: they offer their program on x86-(32,64) Linux, for example. But I run Zotero on ppc-Linux and FreeBSD and other platforms. I'd be able to run it on future platforms too.

Do you demand the same of Google Scholar?

I don't give Google Scholar data or rely on it as my only source of data.

Apple? Microsoft?

Ditto, but also note these companies are MUCH larger than Mendeley, so the threat of them collapsing is much lower.

It would only make sense if they run out of funding, otherwise investors would hardly be willing to continue financing the project.

Given the current financial outlook & the huge risks in any for-profit software startup, you shouldn't dismiss this possibility.

This isn't like MySQL or Ubuntu that started from a single altruistic individual or group of developers.

Neither of these were altruistic ventures. MySQL AB and Canonical are for-profit companies.

There are a few vocal supporters of open-source

And I'm obviously one, but you'll find others here too.

but the majority of users will not care as long as data and privacy are not abused and open-source does not solve that problem.

open source does make the data as open as it could possibly be, though.

CB: Note that the risk argument was not the only one I raised. It is still valid for products that use "open APIs" or allow "open file formats" to be exported from them, though.

What happens if you forget to or can't export before the ship has sunk? Google is "too big to fail," but POP & IMAP would do you no good if you hadn't already downloaded all your mail through one of them if their servers went down.

Again, Mendeley is better than most. They also use sqlite for their backend, so their core data is more accessible than, say EndNote's. But all you will have if something unexpected happens to Mendeley is your data: you will have to start from zero to be able to use that data. You'll at least have to sit down & figure out the schemas for the database & figure out how to get it into some other program that you'll be able to use. Again, this isn't the worst thing in the world. But it is certainly more costly than what happens if GMU stopped developing Zotero.

There's value in open data. Mendeley isn't a bad product. It is much more friendly to end-users/community than most other proprietary software. (If anything, this makes me a bit more paranoid--I can name dozens of proprietary apps that have been available on Linux that have failed. But I give them credit where it is due.)

I'm just saying there is also plenty of additional value in open source as well.

@noksagt - I saw a link to this post via Twitter and since I am a user of EndNote, Papers, and recently Mendeley I thought I'd chime in. Not trolling. I'm just a believer that not everything needs to be open (in this case code) and that science-related organizations have the right to be for-profit and this can be a good thing.

Though I do advocate for open data and other than EndNote, most companies in this sphere seem to agree. Open data will drive innovation and technology, more so than open technology...in theory.

Thanks for the response.

@DocGene: fair enough, but let's turn the question around: why do you, as you say, believe that "not everything needs to be open (in this case code) and that science-related organizations have the right to be for-profit and this can be a good thing"? You say you believe this, but why? With the collective knowledge and experience that the scholarly community has, why shouldn't we create and sustain these tools ourselves, with complete control over their evolution and long-term viability?

The "free" in "free software" is about much more than cost.

@ adamsmith: I totally agree. Similarly to what Bruce mentioned above, Zotero is far more interesting, at least in the humanities and the arts, also because there are far more item types available in Zotero. Second, Mendeley does not extract meta-data from library catalogues and other websites. As a reference manager or research tool, the Mendeley desktop is much more limited. To give a few other examples:

Advanced power search in M: No; Saved/smart searches in M: No; Cross-referencing or relating items/notes in M: No; Create sub-collections in M: No; Add/create citation styles in M: No; Generate reports in M: No; Snapshots in M: No; Etc.

Yet, as I wrote in my initial post, its online interface seems very promising. I'm sure the Zotero team will eventually incorporate similar features, and perhaps move beyond them. They have always surprised us :) I have a long history with reference managers and Zotero is the first (and still the only tool) that gives me intuitively the feeling that it is developed by scholars, for scholars.

Hi all,

Victor from Mendeley here - I thought I'd chime in! Thanks for all your comments, we do appreciate them.

As Bruce has pointed out, there are similarities in Zotero's and our features, and both of us are already using Citation Style Language (CSL) to format references. Zotero is a great tool, especially for grabbing citations off the web. As far as we're concerned, we'd be happy to collaborate, e.g. (as Bruce suggested) to support a common standard with citation styles or to make our respective word processing plugins interoperable.

For our next major release (due in about six weeks), we're also planning to develop a two-way integration between Zotero and Mendeley - if you have both installed, you should be able to sync your references either way. It would be nice to get the thoughts of Zotero’s team on this! Hopefully, the CiteULike integration should also be up and running by then, so you should even be able to sync your references between all three services.

Finally, allow me to respond to a few comments concerning Mendeley:

"(I don't think, for example, you can change the citation style in an existing document. Can you even auto-generate a bibliography? )"

You can indeed change the citation style in an existing document - since we use CSL, we support the same styles as Zotero does. Multiple Mendeley users can also collaborate on the same document and auto-generate bibliographies when using Mendeley’s “Shared Document Groups”.

"Advanced power search in M: No"

Our interface doesn't show it (yet), but the Mendeley Desktop search field does support Google-style advanced queries like "title:searchterm", "author:searchterm", or placing the searchterm in quotation marks to search for a specific phrase. Obviously, we need to make this clearer.

"Saved/smart searches in M: No"

Indeed, you can't save searches yet. As for "smart" searches, Mendeley Desktop automatically generates author, journal, keyword and tag filters which can be used for searching.

"Generate reports in M: No"

If you use Mendeley Web to sync your documents across computers or manage your reference online, Mendeley Web does generate reports/statistics – maybe not the particular ones you're looking for, and not yet as exhaustive as they could be.

Hope that was informative!

Best wishes from London,
Victor

Well, the biggest advantage of Z over M is the way it can be embeded into my webbrowser - no additional programmes etc. And most important for me is also the way it handles proxies (using Ezproxy to access university network from outside).


---- spoiler ----
However, the biggest drawback is that Z tends to lose already saved proxies after each update of the Firefox add-on...

@ noksagt
"What happens if you forget to or can't export before the ship has sunk? ... They also use sqlite for their backend, so their core data is more accessible than, say EndNote's. But all you will have if something unexpected happens to Mendeley is your data: you will have to start from zero to be able to use that data."

I didn't try Mendeley (yet), but from what I've seen on their site I understood that I can have both the software and my data locally. And should the company fail (and I really wish them success), I'll still be able to continue to use the software and the data. Or export them to Zotero. Or did I miss something about Mendeley?

jonbotyson: there's no doubt Mendeley is a couple of years behind zotero in maturity. But it has a different approach, and is very promising in its own way.

On your specific points:
The pdf help file should be there in your default library. Mendeley's approach to getting metadata is different from Zotero, but actually works quite well once you get a handle on the various methods (web-based bookmarklet + pdf metadata extractor + DOI or PMID lookup). I don't use any of the wp plugins in either zotero or mendeley so have nothing to say about them.

Mendeley does have one big advantage over Zotero as things stand, and that is that the web app has full functions (ie. isn't read-only). This has driven me to use it for a current project, where I need to add to my library from computers I can't install anything (firefox extensions included) on.

@ben58
You haven't missed anything. Your Mendeley data syncs with citeulike and Zotero, is backed up online and locally, and is available for export in a variety of formats. You have plenty of options if something were to happen to Mendeley as a company.

@jimbotyson
There were some issues with the linux and mac versions, have you tried the latest release? The developers are very available via twitter (@mendeley_com and @mendeleysupport)

@zroutik
Mendeley now has RSS feeds for subcollections which you can embed or syndicate as a public collection and there is also a "shared collection" feature which allows you to share PDFs with their annotations and metadata with a selected group. This is great for journal clubs and the like.

I'm available on twitter as @mrgunn as well. I serve as an academic community liaison for Mendeley.

@bdarcus

The open API is coming very soon, I hear. The Zotero sync is currently only available in the dev preview, but it's open to the public and stable on my Windows machine. It's also only one-way sync from Zotero, but that may change soon.

The nest point you raise about there not being a standard for word processor integration is a good one, but not one Mendeley can solve on their own. It's going to be an important issue in the future, so I hope they can work together on this.