The most successful post: Paper versus Mendeley, Zotero and stuff.

I am really surprised. When I started this blog, I wanted to share my thoughts about science, about being scientific, about research… and also about Mac in research. When I began to use Mac, it was difficult to me because I didn’t knew so much about software, tools, and so. And then, once, I wrote a post, almost like a review, about software to manage papers and references.

To date, it is the most visited post. I can imagine that many people are looking for information about which software is best for their needs. I never intended to make an explicit publicity on a specific software. I just wanted to express my experience about using those softwares.

Now, I want to make some updates to that post, and about managing references in Mac.

1. About Mendeley: I consider myself a reasonable person, specially being a scientist. Therefore, when a new version of Mendeley is released, I install it and try to use it. But, a few minutes later, I send the program to the Trash. Even more, when a fellow ask me about a software to manage papers and references, I ask: “Mac or Windows?” If the response is “Windows”, then I answer: “Give a look to Mendeley. Give it a try”. Almost every time, my friend returns, days later, and say to me “I uninstalled Mendeley. It ‘s just… complicated”.

It seems that, for many people, Mendeley is slow, complicated, and inefficient. Besides, it’s a huge program, considering the lack of remarkable features inside it. I really want Mendeley being a good software, but the opinion of my friends is the same as mine.

b) About Papers: I love Papers. It’s my software to manage my articles. But I feel that, since a long time, the team behind Papers just relaxes. There is no real improvement in every new version of Papers; only the typical “a bug is fixed when you make that-thing-that-you-do once every two years”, and no real improvement in metadata retrieval. I paid for Papers, and if a new version with real improvements in metadata retrieval from the journals, a good system for managing a bibliography with integration woth Word and Pages, and with new tools for making annotations in the articles, I will be glad to pay for a new release. But, in summary, I feel that Papers just got delayed in time.

c) About Zotero: One day, I received that message: “A new version of Zotero….” Of course, as an obedient fan of Zotero, I installed the new version… And I never could use Zotero again. I needed a new version of the Word toolbar. It didn’t work. I tried to go back to the old version of Zotero. Nothing. Also, the Word for Mac is awful. Then I got a huge amount of work, and I never looked back to Zotero. I need more time to solve the problem, but my feelings about Zotero are not optimistic.

That’s all I have to say about this topic at this moment. If you want to know more about bibliographic management, you should read this post.

34 Responses to “The most successful post: Paper versus Mendeley, Zotero and stuff.”

  1. 1 Dr. Gunn May 21, 2010 at 2:30 pm

    Hi Pablo. Thanks for the honest feedback. I think you’re probably right in your comment on your other post about the “genome” of the computer making a big difference to the user experience.

    I wish I could spend a little time with you personally to find out why Mendeley just isn’t working right for you, because the basic user experience is supposed to be very simple. The program should just find the PDFs you’ve put in your watch folder and automatically import them. It’s true that the Mac version lagged a little behind the Windows version, but you gotta give them a little credit for having a version that works on all major operating systems. Papers doesn’t even work on the PC. Papers also doesn’t have collaborative annotation & sharing features, nor online sync.

    I think if I spent a little time with you personally, I could convert you into one of Mendeley’s biggest fans, but the most important thing is that you’ve found something you’re happy with and you’re using the right tool for the job.

    Best of luck with your research and check back in on Mendeley from time to time, it’ll only get better.

  2. 2 mihai tur June 19, 2010 at 1:10 pm

    I’ve used Zotero for 2 years and it’s the best, except 2 month when i’ve had a macbook, with ms word 2008. The word for mac sucks. Also the mac osx snow leopard. I returned to windows 7.
    Sorry for mac lovers. your problems with zotero are your problem with osx, but you don’t know yet…

  3. 3 pabloastudillo June 30, 2010 at 12:10 am

    Actually, the osx is not the problem. The problem is the Word for Mac. It really sucks, as every Office application, either for Mac or PC. I am not willing to go back to Windows just because of Zotero, and I would advice to Mac users to try another application instead of Zotero.

  4. 4 pabloastudillo June 30, 2010 at 3:29 pm

    Dr. Gunn:

    I am a fair guy, so I go back to Mendeley from time to time and see if it got better. I download the latest version and give it a try.
    My basic complains (in Mac) are as follows:

    1)It is a slow program. That,s annoying, because Mac users love speed. Even Endnote runs faster than Mendeley.

    2) It lacks a full compatibility with word processor softwares. Currently, it supports Word 2008 in Mac, but the most part of Mac users still use Word 2004 (and because that Word was a crap, nobody wanted to purchase the Office 2008), and they turnet into iWork. Pages already support Endnote, which is a big improvement, and Zotero now works very good with Word 2004.
    Besides, the Office 2008 is heavier than the 2004 version. The most part of the Mac users I know are using either Office 2004 or iWork, so choosing Word2008 for integration with Mendeley was a bad choice. At least Zotero made the effort to offer integration with both versions of Word.

    It is impossible to have a good impression with Mendeley if doesn’t support Pages or Word 2004, because you just can`t make bibliographies, and Zotero (also free and cross-platform) does. I am aware that iWork doesn’t support plugins, so we have to wait for an iWork version that allow plugins. But I think that Mendeley should cover Word 2004 into its word processors. Even Sente has more compatibility with word processors in Mac.

    Also, about the online features, several sites also offer such features (I personally love Labmeeting, but it’s not the most popular).

    As I said before, when somebody ask me for a reference manager, I ALWAYS recommend Mendeley. I am not a bad guy 🙂 Congrats for the improvements in Mendeley. I am still far from using it by now.

  5. 5 Mr. Gunn June 30, 2010 at 4:27 pm

    I don’t disagree with you on Word for Mac. We added it because it was easy to do, but I know iWork would be a better choice. The developers are also working on back-porting the plugin to work on Word 2004.

    In general, the Mac version has been getting more and more attention lately, which I think has been reflected in the past release or two, so expect things to continually improve.

    Thanks for your patience, Pablo.

  6. 6 mat July 16, 2010 at 3:27 am

    Very interesting, indeed…let me just comment on the feature that is lacking from papers and is present (and adorable) in Mendeley:

    highlighting and annotating:

    with papers I used to organize and read with skim, providing me with the ability to highlight papers- but the highlights then were not appearing in papers… now I am using Mendeley and it does the highlighting and organizing BEAUTIFULLY- @Pablo, please review this feature for Your own benefit’s sake!

    this does not count in the additional benefit of sharing your highlighted and commented paper with Your scientific community… it is REALLY powerful and I dearly hope that the Mac version will receive further support to improve on the shortcomings..

    • 7 Florian Doster July 21, 2011 at 10:31 pm

      Hey Mat,
      I’d appreciate a comment on if and how you could tranform your highlights from skim to Mendely.

  7. 8 mat July 16, 2010 at 3:42 am

    oh, did I mention that I LOVE the full screen paper feature in Mendeley compared to papers? Papers has these Odd black bars while Mendeley just gives You a full width screen display- did I mention that You can highlight and annotate in full screen?-)

  8. 9 pabloastudillo July 16, 2010 at 10:05 pm

    Thank you Mat for your comments.

    Of course, neither Papers or Mendeley are perfect. Personally, I am fine with the Full Screen mode of Papers. Even more, I like to print the paper, make my annotations, adding post-its (the small ones), and I have my printed papers in folders grouped by theme and author. I don’t use highlighting.

    I agree with you nonetheless that Papers should include this feature in the next version. But, weighting all the factors, I still love Papers and Mendeley isn’t yet an option.

  9. 10 pabloastudillo July 16, 2010 at 10:10 pm

    Oh! I forgot:

    The main feature that I use in Papers is searching in Pubmed directly from the browser inside Papers. So, when I download the paper, is already “matched” in the library, with all the right medatada. Weekly, I updated my library in Zotero, because I use Zotero plus Word 2004.

    I don’t think that sharing papers with highlights is really a big deal (what’s important to me, maybe is not that important to everyone). I usually share papers when my lab mates, and when we think a paper is really valuable, we review it in a journal club session (on Fridays, with coffee and cookies).

    Finally, there is a lot of discussion about distributing papers among people, considering the rights and permissions. I believe that there is no problem, only for academic purposes. But some people disagree.

  10. 11 aloctavodia September 6, 2010 at 12:52 am

    Mendley is fast, easy to use, and completely integrated with oppenoffice, at least on GNU/Linux (ubuntu) 🙂

  11. 12 aloctavodia September 6, 2010 at 12:53 am

    Mendley is fast, easy to use, and completely integrated with, at least on GNU/Linux (Ubuntu) 🙂

  12. 13 AD October 7, 2010 at 1:42 pm

    What about Sente? Have you tried that software? It’s great for storage, notes, bibliography, etc.

  13. 14 pabloastudillo October 9, 2010 at 6:22 pm

    No, AD, I haven’t. My efforts have focused so far in Endnote, Papers, Mendeley and Zotero. I wanted, but the time is a precious asset for scientists 😉

  14. 15 Nik November 21, 2010 at 2:55 pm

    For Windows, you may also want to take a look at

    Similar to other products mentioned here, but also has good annotation features, collaboration, online sync, powerful OCR, and a bunch of other nifty features designed for academics to get a handle on their PDFs. It’s free.

    All the best.

  15. 16 Roberto Sánchez Torre December 8, 2010 at 8:33 pm

    Hi Pablo,

    I think that you speak Spanish, and my English is not good enough, but I will try to do it as best as possible.

    I’m working with Papers and Zotero, I don’t know why, but the Papers’ integreation with World didn’t work. And like with you, my Zotero’s bar in Word didn’t works, but you can use it with the menu of the Automator for Word. I had to research in the Zotero’s forum, and I found that I had a Spanish version and it was installed in the User Data for the English version, only cut, and paste in the Spanish’s one and to work.. ok is not the most beatiful design but works very well… May be if I make that the integration of papers works with Word it will be the only program that I use.

    I never test Mendeley

  16. 17 pabloastudillo December 9, 2010 at 8:24 pm

    Hello, Roberto.

    I am not an expert, I have to mention. Maybe you should read my last post about Zotero and Papers, here:

    I found out that most of the problems I had in the past with Zotero was because I had the wrong version of Zotero. But I tried hard the last time to solve the problem.

    A friendo told me that if you have Word 2008, you should be fine. But I am still expecting a new, improved Papers version with full integration with Word (and also Pages, but that is a dream so far).



  17. 18 step21 April 22, 2011 at 9:42 am

    I don’t know how it was in the past, but at least now I have to disagree with Mendeley being slow. Especially when I tried papers on my Macbook Air, it was slow and in addition really annoying to use I think. I don’t really remember anymore what annoyed me so much that I stopped using it, but there was something. The latest version of Medeley by commparison is quite nice, and fast most of the time, also let’s you choose whether to manage your papers or not. Though I don’t use the word plugin, so I can’t speak for that.

  18. 19 sensak July 17, 2011 at 2:54 pm

    THANK YOU VERY MUCH! your post change my life at all. I was writting my phd work, and I was using Mendeley.. and It was horrible, too much time to get a cite in the word page… Pages is a very good software! it is a pity that is not for free… but at least, is not so expensive.

  19. 20 Tyra Sturdivant July 23, 2011 at 4:29 am

    GREAT REVIEW! I pretty much agree with all you said in your post, especially at the beggining of your article. Thank you, this info is very valuable as always. Keep up the good work! You’ve got +1 more reader of your great blog:) Isabella S.

  20. 21 Deichscheich October 21, 2011 at 1:58 pm

    Okay people, what about … LibreOffice? It works like a charm with both Zotero and Mendeley. It’s a little unfamiliar at first if you’re used to MS Office, but you Mac guys shouldn’t have a problem with that?

  21. 22 Juan Andres August 7, 2012 at 3:43 pm

    weena compadre… Papers la lleva…aunque la version de IPAD no la uso para nada.
    muy buena la pagina.


  22. 23 Diego Carrasco September 25, 2013 at 6:09 am

    how fast is papers to catch a pdf from the web (whether this be google scholar, proquest, elsevier, or other source)? I notice zotero lags and freeze to do that. I would guess about 20 to 30 seconds (enough to get you annoyed). Mendeley is worst for that case, its lagged when is open thanks to the rebuilding of all the index. How much time papers take to do this?

    Does it problems with memory? I got library of about 8 gb of pdfs. I know mendeley is slower the larger the library. Zotero can handle it (is just laggs when you add a new item). Is there a limit in which papers shows a bug or a design limitation?

    Apparently if papers is so good, sounds better to write from a mac than a pc laptops (could be expensive, but faster).


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