Small update of the reference manager overview, now including comments. Also added JabRef as one example of a BibTex application (Bibdesk is one alternative for the Mac). - Martin Fenner

Martin, thanx! BTW, several online tools, at least CiteULike and Connotea, output BibTex and thus support LaTex too. - Egon Willighagen

I'm totally into Zotero right now. - Karen James

Most of these tools, and many online databases, support import/export of BibTex and RIS files. This means that you can move your data around between all these tools, but import/export is a little bit too much work for a regular reference management workflow. - Martin Fenner

Import/export is also tough because there's no standard way to handle keywords/tags, so sometimes they'll be transferred, sometimes they wont. - Mr. Gunn

Nice summary! MIT provides some tips about using Zotero with LaTeX: http://libraries.mit.edu/help... - Jodi Schneider

Am I too old? Today I downloaded Mendeley for the second time and Zotero for the 3rd. I still don't see how I can use either of them. Mendeley was only 50% (at best) successful in gathering citation info from my PDFs. Whereas I tried importing my endnote library into Zotero and it's been stuck in "Progress" for an hour. - Steve Koch

Assuming I can get Zotero to work...what does Mendeley provide that Zotero doesn't? - Steve Koch

The social features (sharing, groups, etc.) are more mature in Mendeley compared to Zotero. That might change in a few months. - Martin Fenner

Steve: The latest Mendeley release should automatically retrieve the correct metadata for all arXiv papers - which other databases are you using? One of the differences to Zotero is that Mendeley also extracts cited references from papers; the next Mendeley release will also include a PDF viewer with annotation capability and improved LaTeX integration, as well as an online PDF viewer and a shared group/lab working space. - Victor / Mendeley Team

Hey, I can't wait for the next release. I really can't. - pn

Hey Victor -- What I tried was importing my PDF library. Many articles had problems. I can fix these by hand, but then I lack confidence in my database. When I clicked on the PMID lookup (or DOI), nothing seemed to happen. I also didn't see any citulike option, but I then gathered that this hasn't been rolled out yet. - Steve Koch

The online PDF viewer is intriguing -- will that allow me to share PDFs with my group so that we can all take notes on the same version of a PDF? I like to use sticky notes and highlighting on my PDFs and it would be cool if I could share these marked up versions and our whole group could access one version without having a bunch of our own personal copies. But doing that online in PDF format sounds complicated - Steve Koch

Steve: Could you please give me examples of DOIs or PubMed IDs for which metadata retrieval didn't work, so we can fix it (I assume that you entered some before pressing the lookup buttons)? CiteULike synching hasn't been rolled out yet - but should be in the next release (~5-6 weeks). - Victor / Mendeley Team

Re:PDF viewer - don't know yet whether we manage to do the *shared* annotations you've described already in the next release, but that's exactly the idea! For starters, annotation will only be available in Mendeley Desktop, not in the online PDF viewer in Mendeley Web though. - Victor / Mendeley Team

Victor: I put a screenshot on the following page. When I click on the "lookup" button it doesn't do anything. None of those three buttons do anything for me. http://openwetware.org/wiki... - Steve Koch

Man, an error on Mendeley? What gives? - pn

It happens in the best families, Paulo! Steve: Thank you for taking the screenshot, I'll give it to our support guys. - Victor / Mendeley Team

Paulo, what do you have so much against Mendeley that you want to make the world to know that? - Egon Willighagen

Steve: I tried looking up the PMID in an empty metadata form (after pressing Add Document > Manual Library Entry), and it retrieves all the metadata correctly. In your screenshot, all the data that could be retrieved is already filled in, so perhaps that's why it *seems* nothing is happening? Which is a UI problem, of course, it should be telling you what's going on. - Victor / Mendeley Team

@Egon: I'm just joking now, having some fun. Isn't that what internet is all about? I wish that they have success with their application. - pn

Thank you, Egon, and thanks, Paulo! We're taking it in the spirit in that's intended - Paulo had a not-very-good experience with one of our first public betas and rightfully complained. And since one of his friends (Ricardo Vidal) joined us as Community Liaison, he's been poking a little fun at us... - Victor / Mendeley Team

Well, there was just today a comment here on science(2.0?) being sort of a game... I agree that fun should be part of it. But in science there really is something at stake: the future of mankind. I have been pondering about using Mendeley, and tried the beta... it looks nice, but I have not found a compelling reason to replace my other tools with it. And being closed source, my preference goes towards equally functional just less polished open source versions... Poking is OK, but it smelled like more... - Egon Willighagen

So, I was curious about pro's and con's about Mendeley... - Egon Willighagen

I'm curious about collaborations between different tools that would make sense. Papers / Refworks has little overlap. Maybe JabRef / Zotero. Connotea and CiteULike would work great with most of the other services. Of course we already have Mendeley / CiteULike as well as Web of Science / Endnote and Scopus / Refworks. - Martin Fenner