Papers or Mendeley?

When it comes to bioinformatics, I acknowledge that I am a naive and basic user. Nonetheless, I always try new tools and softwares. Some time ago, I became interested in tools for management of papers and data. I discovered Papers, but I was a Windows user. When I moved to Mac, the first thing I did was to try Papers. I was amazed by the software. It was very, VERY easy to use, and it was very valuable to organize my papers collection. I usually have several folders with papers, and when I want to read one, I get lost in the sea of folders. With Papers, all the papers are copied in a single folder, renamed (no more “374645432.pdf, or 1234_2323_349.pdf or names like these), and you can organize your papers into specific collections. Also, you can read the pdf file inside the Papers itself, very useful when you are looking for a lost paper… you don’t have to open every single pdf file… you are actually seeing it when you scroll over the list.

A screenshot of Papers.

A screenshot of Papers.

I felt in love with Papers. But it wasn’t free. You have to purchase. But the web page claimed that, if you are a student, you can get a discount. When I see something like that, I think “well, surely you have to send several papers, letters, signed and with the US Embassy approving..”. But this time it was easy: just to scan your student ID. In hours, I had my discount. Today, I am very happy with Papers. It is really useful to me, specially now that I am writing my PhD Research Project.

But then, Mendeley appeared. My Windows-user friends told me “Jaja, you spent money in a Mac and purchasing Papers, but Mendeley is free”… Well, after several post around there, I tried Mendeley. And I have to say, I was disappointed. My aim is not to post a negative opinion about Mendeley. Sure if you are a Windows user, you will value the existence of Mendeley, and if you are a Mac user, the chances are you have Papers. But I have to say some points:

a) Overall, if you don’t have much time to spent learning to use a program, Mendeley is not good… It is not as easy-to-use as Paper is.

b) If you have a slow Internet connection (or if you have a huge collection of papers), also Papers is your choice. I am still seeing messages with tasks being in operation with Mendeley. Mendeley allows you to have a backup of your collection in the web, but when you have a high number of documents, it becomes slow and, at least in Mac, the software shuts down.

c) You can’t read the pdf inside Mendeley (I already explained why this can be so useful).

I have a backup of my paper’s collection (in progress, though) in the web with the program Labmeeting. I think this tool is the best in the web nowadays. You can:

a) Manage a paper collection, and you also can organize it in several folders, synchronize the metadata, and share the papers.

b) Set up a Lab Page, where you can share data, protocols, notify about meetings, seminars, etc.

c) Get in touch with colleagues.

A little screenshot of the main page of Labmeeting.

A little screenshot of the main page of Labmeeting.

Labmeeting is a good combination of Social Science Networking + Paper/Data Management. I tried to get my lab’s colleagues to test Labmeeting, but I guess scientists are not so interested yet in these tools. Nonetheless, I think the use of this kind of softwares can be very useful to improve communication and performance of a lab group.

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52 Responses to “Papers or Mendeley?”


  1. 1 Alejandro May 7, 2009 at 12:09 am

    c) You can’t read the pdf inside Mendeley (I already explained why this can be so useful).

    These sort of improvements are being introduced in the latest versions of Mendeley. I don’t know if Papers has anything like this, but Mendeley has set up a whole community (and websites) for people to comment and make suggestions to improve the software (see http://feedback.mendeley.com/pages/4941-mendeley-feedback).
    I think it’s way more ‘community-oriented’ than Papers (the scientific community, that is) and, in the long run, it will have more useful options than it’s Mac counterpart.

    Cheers.

    • 2 pabloastudillo May 7, 2009 at 8:23 am

      I totally agree with that… it seems that Mendeley is getting better faster than Papers. But still Mendeley has several bugs in Mac. For Mac users, for now, Papers is still the choice. About the community-oriented scope, it is at discussion if these works are reallly working. There is a forum about this topi in Nature Networks:

      http://network.nature.com/groups/socialnotworking/forum/topics

      Nice to see you here.

  2. 3 Alejandro May 7, 2009 at 10:03 am

    But still Mendeley has several bugs in Mac.

    in PC too… the MS Word plugin is little over a joke, but it’s getting better.

    About the community-oriented scope, it is at discussion if these works are reallly working.</i)

    It is. Several ideas put forward by users have been taken by Mendeley and included in new releases.

  3. 4 Juan May 10, 2009 at 1:33 am

    Well, I’m a happy Papers user I must say. It is sad that is only available for Mac, as I consider it is a great program for managing big papers libraries, specially for me that I tend to “collect” papers that I never read (similar to what I do with mp3s…)
    Anyway I think that for the moment Papers is one of the best solutions so far, and they have a great community around them, with some plugins that are not related to the guys that are selling the software.
    In case you are looking for free alternatives, the one that I used before Papers was JabRef (http://jabref.sourceforge.net/), which is free. I reallly liked, specially because I was able to export my library as a bibtex file, to use with LaTEX, which in papers is still a bit of a problem (at least for me…)

  4. 5 pabloastudillo May 10, 2009 at 11:23 am

    Thanks for your comments, Juanu!
    I am searching por plugins now.

  5. 7 Hans July 21, 2009 at 2:59 pm

    I totally agree. Labmeeting.com is “the best in the web nowadays”. You upload all your PDFs, then they are linked to PubMed records more or less automatically. Uploading takes some time, but then it is fun to actually work with them. PDFs can be organized with tags, used for full text search. More PDFs are easily collected directly with the PubMed connectivity or through sharing with collaborators.

  6. 8 David M. Morris August 15, 2009 at 4:27 am

    I love your reviews, can someone invite me to labmeeting please. davidmmorris at hotmail.com.

    Thank you.

    David.

  7. 9 Mr. Gunn November 21, 2009 at 8:24 pm

    Astu, the question about whether scientists aren’t interested in online tools or they just haven’t found the right tool yet has been discussed quite a bit. I think they just haven’t found the right tool yet.

    Labmeeting, for example, isn’t quite there, but Mendeley Web does all the things Labmeeting does, with the right approach – letting networks develop around content, and over 100000 scientists and academics have signed up. Clearly, scientists are interested of you do it right.

    Your earlier criticisms of Mendeley were quite correct, but they’ve listened to user feedback and the Mac version has come a long way. Mendeley now has a built-in PDF viewer, plugins that work in Open Office, Word, and Google Docs, and handles Bibtex with no problem.

    Comments like this are extremely valuable to Mendeley, as it is this that allows them to continue to make the software that users want.

    Feel free to get in touch with me via twitter (@mrgunn) or Mendeley if you have any questions.

  8. 10 Proman December 21, 2009 at 9:09 am

    What about Zotero – I think at this point in time mendeley and zotero (in v2.0b7) are almost equally gifted – + Zotero will be free for ever, ’cause it’s open source, which mendeley is not!
    Is papers – as mendeley and zotero are – able to import citations and pdfs directly from the website in your browser?

  9. 11 Hyo December 27, 2009 at 2:01 am

    Question about Papers.
    I am a Mendeley user with Windows and Linux. I’m thinking about buying a Mac and Papers is one of a big reason.

    I find Mendeley is great, but I still have some problems.
    The biggest thing is that it only supports one note per article.
    Does papers support users can write multiple notes on an article?
    And I understand that Papers is basically desktop based. But, is there way to sync? Cause, I want to use it on my laptop and desktop and I wish there’s an easy way to do that.

  10. 12 pabloastudillo January 27, 2010 at 8:08 am

    Hyo,
    sorry for the lack of answering. I have been off the blog for a while, but I am planning to come back these days.
    About your question… honestly, I don’t know. I only have a laptop, and I never asked about sync with a desktop. I know that SENTE (http://www.thirdstreetsoftware.com/site/introduction.html) has sync options between computers. And also pdf highlighting and note taking (notes in Papers are still poor developed).
    By the way, if you own an iPhone, Papers has a version for iPhone so you can have your papers everywhere. Nonetheless, there are a lot of good reasons for change from windows to Mac!

  11. 13 pabloastudillo January 27, 2010 at 8:09 am

    Proman,

    yes, Papers can import directly from the browser. You can browse directly from Papers; even, you can search Pubmed directly from Papers, which I use for downloading papers.

  12. 14 Thieme February 17, 2010 at 5:18 am

    I paid for Papers and used it for a while, but switched to Mendeley. I have been waiting for an upgrade for Papers, because it crashes all the time.

    I am still quite hesitant about which way to go, both software tools are quite good I think.

  13. 15 pabloastudillo February 23, 2010 at 6:53 pm

    That’s weird to me. I have never see Papers crush in my macbook; I am using the 1.9 version. But I have crashes with every version of Mendeley that I have tested so far.
    I guess sometimes the computer’s “genome” can make a big difference in terms of performance between softwares.

  14. 16 mat July 16, 2010 at 3:12 am

    Hey there,

    just stumbled over this review and I’d like to add some points. I just came across Mendeley while being a long time papers user (practically from the launch). Let me just quickly give You the reasons why I consider moving to Mendeley at least partly:

    – The paper reading and annotation feature in Mendeley is GOLD! imagine highlighting and commenting a paper and then sending it around for discussion not only to Your lab mates but to Your cooperation partners on the other side of the globe… papers is still missing the annotation feature completely!

    – the citation plugins for Ooo works really fine. It became really close to what Endnote does with citations, left alone that now you have the pdfs right where Your citation library sits- neat!

    Currently the only things missing for me are sub-folders in the main tree and integration with more word processors like pages and Mellel… apart from that I am really enjoying to work with Mendeley… it might be valuable to make an update to this review ;-)…

    cheers, mat

  15. 17 Pratik Desai July 23, 2010 at 12:55 pm

    I have been using Mendeley, but I am unhappy with the fact they they don’t have any feature to organize pdfs! This is in a software whose primary purpose is to organize pdfs. Users have been requesting tags/subfolders for years, but they have not done anything. They appear to be very slow. Just came across sente and it seems very appealing. Any significant negatives of sente? They don’t seem to have a ‘hot folder’ where you drop all your pdfs and it will import, or a web plugin for importing. Any problems other than that? I am happy to pay for a software that works, rather than messing around for a year providing feedback.

  16. 18 Dr. Gunn July 23, 2010 at 4:20 pm

    Hi Pratik!

    Tags and PDF organization into subfolders has been a feature of Mendeley almost since the first release. Perhaps page 8 of the getting started guide would be a good place to start: http://www.mendeley.com/getting-started/

    Just to make sure we’re starting from the same place…the instructions there refer to Mendeley Desktop, not Mendeley Web.

  17. 19 pabloastudillo July 24, 2010 at 12:37 am

    Thank you for your comments and feedback.

    Dear Pratik, Papers is outstanding in their capability to organize papers into folders. Besides, the feature that allows to create collections is also excelent. A single pdf can belong to several collections, and that’s how I have collections by theme (“Regeneration”, “Developmental Biology”…) and Authors.

  18. 20 mat July 25, 2010 at 1:41 am

    @Pratik- I never tested sente because you are requested to hand over significant amount of money (89$) in order to get a license… but everyone of us compromises in a way I guess… astu with highlighting and sharing, you at least with the sharing capabilities and me using Mendeley with subfolder organization and the native paper search through interfaces like Pubmed or google scholar plugins I really liked in papers… and I guess everyone of us has his workarounds… astu could use skim for annotation and highlighting for instance… I am curious to see which of these solutions will make it out on top first… I doubt the price tag of Sente will ever reduce, though;-)

  19. 21 Jessica Hall November 27, 2010 at 5:13 pm

    I was dying to find a “Papers”-like program for my PC (since Papers is not compatible with PC) and finally found it. Phew! It’s called PDF Stacks. I’ve been using it to organize and manage my PDF files and research papers on my PC. So far, I’m very impressed. Hopefully this post will help.

  20. 23 Hazel Jackson December 2, 2010 at 2:57 pm

    Hi there,

    I am a Mac user, and as a PhD student, need software which will allow me to insert citations and bibliographies in my documents. I have been using Mendeley for a couple of months now, and am completely fed up with it.

    It continually has issues with inserting citations correctly into a document, sometimes its correct, sometimes not, sometimes it changes the citation after you inserted it correctly. If you try to change the citation in the document it cuts the sync with mendeley (which defeats the object of using it!).

    I’m soooo fed up with it. I love papers, however I need software which like I said, will insert citations/reference lists.

    Can anyone help me out here…I have used Endnote before, but didn’t find it hugely user friendly…

    Any recommendations appreciated

    • 24 Alejandro Montenegro-Montero December 2, 2010 at 3:04 pm

      Hey Hazel,

      A citation editor for Mendeley is coming, and while Mendeley isn’t quite there yet in terms of citation integration, it has been moving fast. I guess what I’m saying is that many of the issues you mention will be overcome in future releases.

      Now, what I’ve been using until now, is Mendeley for organizing my PDF library and Endnote for citation integration. As you can export your reference list from Mendeley to Endnote, this is fairly simple and has worked perfect for me.

      Endnote is simple once you get the hang of it. In the end, you just use a couple of functions.

  21. 25 Mr. Gunn December 2, 2010 at 3:07 pm

    Hazel – I’m sorry to hear you’ve been having trouble. As we’re still a free beta product, there are occasionally issues that crop up, but I’m sure if you emailed support they could sort you right out.

  22. 26 Hazel Jackson December 2, 2010 at 3:15 pm

    Hi Mr Gunn

    I’m afraid I have tried emailing their support and writing on their forum…no solution yet. Its very disappointing as I love the idea of the software..i just need it to WORK!!

    They simply keep advising me its because i have office 2011, however, the problem started when i had 2008, and i have spent the last 3 days trying out the new tester pluggin for 2011. Still it keeps going wrong…most frustrating.

  23. 27 Mr. Gunn December 2, 2010 at 3:27 pm

    Thanks for clarifying that, Hazel. It does work for us in testing, so the best thing I can suggest is to tell support the steps they need to take to reproduce the problem so they can isolate the cause and see why it works for them but not for you.

  24. 28 pabloastudillo December 3, 2010 at 9:25 am

    Hi Hazel, Alejandro and “Mr. Gunn”.

    Thank you for coming to the post and discuss.

    Hazel, I recommended previously using the Papers+Zotero combo. I don’t know if Zotero works in later versions of Microsoft (I’m still using Office 2004, because I don’t want to spend more money in a crap like Office, and iWork is getting better and better in every new version), but so far my Papers+Zotero combo works fine to me.

    I agree with Alejandro that Mendeley is getting better, and I am waiting to see a huge improvement of Papers in the next version because I have the feeling that they are frozen in time. Citations and insertion in documents is the “mother of all battles” in this field because Papers and Mendeley have done a very good job about reference management (altough they have differences, intended for different people).

    Have you used Zotero? I have a post:
    https://astuscience.wordpress.com/2010/06/30/references-management-in-mac-new-guide-on-using-zotero/

    Best regards to all of you.

    • 29 Hazel Jackson December 6, 2010 at 10:44 am

      Hi pabloastudillo

      I had not heard of Zotero…but am in the process of using it now! Great bit of kit, many thanks for the recommendation!

      Thank you for your help.

      All the best

      hazel

  25. 30 enature December 31, 2010 at 3:20 am

    I was a big fan of Papers when they came out a few years back. But Papers virtually stalled for about two years and its competition not only caught up but surpassed Papers.
    Recently I was very pleasantly surprised how Mendeley works. Not only it is free but also it provides social integration with other researchers and, what is even more important to me, it lists relevant papers and provides useful statistics on the number of readers.
    And Mendeley does what Papers so far failed to deliver for Mac users. With Word plug-in now it is rather easy to insert citation in Word of Office 2011 on Mac without using Endnote.
    These features convinced me to switch to Mendeley.

  26. 31 Tiem February 5, 2012 at 7:24 am

    I’ve just stumbled upon your blog after reading a few reviews of Papers and other referencing software. Thanks for your honest reviews! Very helpful in terms of Papers2.

    Reading through the comments on the present entry, they sounded like they were recent comments. It’s early 2012 and I’m not sure how much things have advanced, at least when it comes to inserting citations. Earlier tonight I spent over an hour trying to insert 23 citations using Mendeley. I’m only part way through too. I hadn’t realised this would be so trying because I only just got the software to insert a single citation without crashing. Now it works but takes from 30 seconds to several minutes to finish inserting a single citation.

    I really like Mendeley, but wonder if fixing this super slow citation problem is actually on their list of things to do. The problem has been around for a few years now.

    I’d like to try Endnote, but I don’t think it is compatible with Lion 10.7. Perhaps worth a try anyway.

    • 32 Alejandro Montenegro-Montero February 5, 2012 at 10:29 am

      I’ll also repeat what I said before. I use Mendeley for managing the PDF files, reading, making notes, highlighting, sharing articles with labmates, etc, (which is great!), but Endnote when it’s time to get them into MS Word. Mendeley is definitely not quite there yet for that, although they claim they do.

      You can simply export your reference list from Mendeley to Endnote (you can also do it the other way around), and you are ready to go. No need to go fetching for the information once you already have it Mendeley. It works great for me. Some people argue that Endnote is a pain in the a**, but I’ve never experienced any sort of problem. It works.

      Personally I never got into the ‘in-browser’ Zotero style, but that’s just me.

      The new player on the field of reference managing is ReadCube (which contacted me for feedback), but they are more focused on managing the PDF files than in inserting citations. ReadCube is based on Adobe Air.

  27. 33 mat February 5, 2012 at 9:42 am

    Well, some time passed on the papers vs mendeley front- and both weren’t idle with their development: Papers 2 arrived with a handful of quirks and regressions compared to v1, but eventually, things have MUCH improved too the best:
    – you can highlight, annotate and cite into virtually any word processor thanks to the universal and global citing system- which makes exporting your database to some citing manager superfluous

    -You can wonderfully sync your iOS devices- since I moved to the iPad for reading I didn’t ever print one publication and never looked back- now I am highlighting/syncing and the processing my library during writing stuff together- just wonderful to have it all in one system!

    So, to renew the recommendation: for the Win world and collaboration Mendeley still is the best system, if You’re on a Mac, eventually even owning ad iPad for reading/annotation, there’s no way around Papers 2 in my opinion.

    What do You guys (that follow this thread) think?

    • 34 Proman February 5, 2012 at 10:08 am

      I can only repeat what I said before: Zotero!
      It now on version 3, has a stand-alone version is able to plug-in not only to firefox, but also chrome and safari.
      there are also apps for android&iOS: http://www.zotero.org/blog/zotero-apps-go-mobile/
      Plug-ins for word-processors are also featured.

    • 35 Alejandro Montenegro-Montero February 5, 2012 at 10:30 am

      I’ll also repeat what I said before. I use Mendeley for managing the PDF files, reading, making notes, highlighting, sharing articles with labmates, etc, (which is great!), but Endnote when it’s time to get them into MS Word. Mendeley is definitely not quite there yet for that, although they claim they do.

      You can simply export your reference list from Mendeley to Endnote (you can also do it the other way around), and you are ready to go. No need to go fetching for the information once you already have it Mendeley. It works great for me. Some people argue that Endnote is a pain in the a**, but I’ve never experienced any sort of problem. It works.

      Personally I never got into the ‘in-browser’ Zotero style, but that’s just me.

      The new player on the field of reference managing is ReadCube (which contacted me for feedback), but they are more focused on managing the PDF files than in inserting citations. ReadCube is based on Adobe Air.

    • 36 matrhein February 5, 2012 at 1:26 pm

      Wow thanks for the replies! Actually, I was planning to check out zotero, got the files and probably run a test next week- @Proman: does it actually support citing in pages? The comparison wiki wasn’t clear about that… With papers supporting pages citing, I really got hooked for the functional and fast interface of pages….

  28. 37 Isaac September 3, 2012 at 10:51 am

    Hi
    the best of Mendeley is that’s cross-platform. I have my Mac for personal use, but in my work I use PC. So… after some time I had built TWO independent libraries of pdf files, one in my mac and one in my pc. Mendeley has made a cloud (I think it’s a cloud technology) sync available so I finally integrated two huge pdf libraries into one universal, available online, available in my PC, my Mac and my phone all in Mendeley, and for free. I was also a Papers fan, but as of 2012, I think Mendeley is totally better.

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