papers2 review

March 11, 2011 at 6:12 pm | | literature, software, wild web

Scientists have many options for organizing, reading, and syncing PDFs of articles: Papers, Mendeley, iPapers, Endnote, BibDesk, Zotero, and more.

My favorite is still Papers. It’s clean and simple and beautiful. It works awesome on my iPad: reading PDFs is more enjoyable on the Papers iPad app than on my laptop. Syncing to the iPad over wifi is simple and practically bug-free. Syncing libraries between my home and work computers is also possible by putting the Papers folder in Dropbox. (Although Dropbox syncing isn’t technically supported by Papers, many folks use it to sync across computers. I’ve been doing that for half a year without a problem.)

The major downside with Papers is that it works only on Mac OS. Papers2 is now on Windows, too. On my PC, I use Mendeley. Mendeley is nice because it is free and has native syncing to the web and between computers. The reason I’m not completely sold on Mendeley is that it’s just not as clean as Papers yet. Mendeley is not as buggy as it was a year ago, but it still doesn’t seem to find metadata as well as Papers. But, if you’re starting from scratch, Mendeley is a great option. (Edit: And I like the syncing to iPad/iPhone that Papers offers.)

And now Papers2 was just released! Honestly, Papers2 is a little disappointing, so far. But I suppose I was expecting a lot. But I still have high hopes for it. The support staff is working very hard to fix bugs and add functionality that users are screaming about on the discussion boards.

Some of the cool features of Papers2 include:

  • A quick way to add citations to Word (or any other application on your Mac) directly from Papers
  • Easier keyword tagging
  • Automatic metadata importing (although I haven’t seen this work, yet)
  • Linking supplemental info to the paper it corresponds to
  • Searching multiple databases (e.g. Pubmed and arXiv) simultaneously

The automatic metadata grabbing might be nice, if it ever works. Mendeley tries to do that, too, but I’ve never been impressed. I really liked that Papers1 made manual matching easy (by highlighting the DOI, for instance). The new interface and searching mechanism seems much clunkier in Papers2, and the support staff has already acknowledged as much.

There are several other issues, that make Papers2 feel very beta. Given that it’s brand-new, that’s not exactly surprising. But Papers1 was so refined, that Papers2 seems very clunky in comparison. But I think Papers2 does have a lot of potential.

For those worried about trying Papers2, have no fear: the new version doesn’t overwrite your Papers1 data and PDFs, so you can use both versions side-by-side until you’ve made up your mind. During the 30-day free trial, for instance.

For the Mac, Papers1 has been the cleanest, coolest, and bestest PDF organizer. Hopefully Papers2 cleans up nicely and becomes my new favorite. But right now, Papers2 is not clean enough for me to recommend anyone using Papers1 switch over to the new version.

UPDATE: In the last two weeks, Mekentosj has provided two updates to Papers2 that have made it significantly better. Papers2.0.2 has fixed a lot of the bugs and annoyances in the version I reviewed above. For instance matching is much much better. Like I expected, the folks behind the program are working really hard to make it the best program, evar!

UPDATE2: I use Papers2 daily and I love it. It still has some things on the wishlist that I look forward to, but I think it’s a great program. I guess it just had some bumps at the beginning.

UPDATE3: Papers2.1 is now out at better than ever. Definitely better than Papers1. I can recommend without hesitation that you get this software!

UPDATE4: A bookmarklet for JSTOR.


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  1. If you use Firefox, Zotero is pretty awesome. It does all the things you mention – syncing, cloud storage, and it has a pretty good meta-data grabbing ability.

    The only thing it wont do is work on iPad… but, I don’t have an iPad, so this is not a deal breaker for me.

    Comment by azmanam — March 12, 2011 #

  2. I don’t like Zotero because it’s Firefox only. I don’t use Firefox. So there.

    Comment by sam — March 12, 2011 #

  3. Well… FINE then! :)

    Comment by azmanam — March 12, 2011 #

  4. I’m surprised you’ve had trouble with Mendeley’s data grabbing ability; I feel like that works really well. (But, I can’t compare with Papers since I use Windows/Ubuntu but not Mac OS.) I just save the pdf to a Mendeley watched folder, and unless it’s a very old paper, it usually imports all the data just fine.

    Mendeley also updated their iPad app pretty recently so that you can read all your PDFs in app. Unfortunately, it’s not syncing the annotations yet, so for “important” things where I want to make notes I end up doing the actual reading/note taking in GoodReader instead, but I have my Mendeley folder in my Dropbox, so that everything syncs wirelessly between my computer and my iPad.

    Comment by mary — March 14, 2011 #

  5. PS I also like Mendeley’s features for sharing references with a group. We’re now using that in the lab to send new papers to each other, in addition to our meatspace bulletin board. Does Papers do sharing?

    Comment by mary — March 14, 2011 #

  6. i’ll continue giving mendeley a chance every few months. the fetch does seem better than a year or two ago. papers matching is via pubmed (or whatever databases you want), which is generally very good. but it has been mostly manual. i think papers2 is trying to introduce automatic metadata fetching. maybe it’ll work. but i’d rather have manual matching that works perfectly than automatic fetching that fails part of the time.

    papers1 doesn’t do sharing. papers2 might.

    Comment by sam — March 14, 2011 #

  7. The recent update makes matching better than ever!

    Comment by sam — March 17, 2011 #

  8. I completely agree. If Papers2 winds up being able to do everything it claims and restores significant lost functionality, then it will be excellent. Papers2 is not there yet. Given how long we waited for it, it’s a disappointing release. It seems like every time I open it I find some new element that doesn’t work properly anymore. Why did it take so long to take a step backward?

    Comment by Joe — March 19, 2011 #

  9. Papers2 is great, but unfortunately the sync to iOS devices (one of the killer features) is completely and utterly broken. Tech support were all over the place at first, and have now gone silent on the issue — gives the impression that there are big, time-consuming problems at the technical end. It looks like the v2 upgrade was rushed to market too soon, which is a pity, because if it worked as advertised it would be hands-down the best citation & research tool for the Mac.

    A lot of people are going back to Papers v.1 for the meantime. New users should certainly look at Papers v1 if they need iOS capability – otherwise Papers2 is fine.

    Comment by Daniel — April 2, 2011 #

  10. sync to my ipad works fine after the newest updates of papers2 and papers for iOS. update both and try it again, Daniel.

    Comment by sam — April 2, 2011 #

  11. I’ve been using PDF Stacks on my PC and Papers for MAC.

    On my MAC, I like Papers v1.94 than Papers v2. More fine-tuning is needed as there are still bugs present in v2; however, I like 1.94 very much!

    I’ve tried Mendeley on my PC but it’s too cluttered and not an easy workflow. For those seeking an alternative to Mendeley, PDF Stacks looks promising as I have been using it for some time now!

    Comment by Poonam Shah — April 6, 2011 #

  12. would love a tutorial on all of the features of Papers 2 with more detail than their website. Any recommendations

    Comment by Eric — May 1, 2011 #

  13. Eric, I recommend downloading Papers2 and trying the trial version.

    Comment by sam — May 2, 2011 #

  14. Papers 2 is not ready. All the missing features greatly counter-act any of the new cosmetic features. I am back using papers1 which is more mature with functionality. I can not believe the lack of professionalism of these developers! They launched a skeleton of a product, and a page full of promises of how great will it be when they eventually (who knows when) include all the good functions of the previous product.
    Matching button, author merging, blue buttons easy search criteria construction – these are essential for my use of the product and they are all missing.
    I will support this new product when its functions include and improve those of the previous version. Right now it is just work in progress.

    Comment by Cristian Rios — May 29, 2011 #

  15. Papers 2 are released way to soon. It lacks the Library Import function, so all pdf files from the library in Papers 1 have to be imported manually 1-by-1 (though I don’t think it’s an issue if you just update from version 1). I have had it for a week now and it had crashed +10 times… Also there is know way to control how the Authors are displayed in the overvew. I prefer the first-authors last name and not initials followed by last name and then et al.
    If you have papers 1 – no need to get papers 2 yet

    Comment by Casper — September 12, 2011 #

  16. Casper, I use Papers2 daily and I love it. But maybe you’re right that it was released too early.

    Comment by sam — September 12, 2011 #

  17. Hi,

    I’m a french student, and apologize for my poor English.

    I was using Papers2.0 for organising my bibliography and searches, but not the searching tool in Papers.

    I tried it, but i’m a little confuse, as a student I can’t spend a lot of money in publications. So I was wondering, is it possible to select only the free articles in pubmed while using the paper’s searching tool ?

    Thank you

    Comment by Jbaba — February 8, 2012 #

  18. not that i know of. you should post this on the Papers help discussions.

    Comment by sam — February 10, 2012 #

  19. hello – Ive just read your review – I am about to DL papers. Is the general recommendation in this community, stay with papers1 still. its March 11 2012. Current version is papers2.0.17

    appreciate your perspective

    Comment by purelight — March 10, 2012 #

  20. hi – little segway off topic

    is there any research paper application “add-on”, that links with papers or doesn’t link, that enables:

    1) enable me to fix the page numbers in the PDF file to match my personal book copy, so my auto citations numbering is then accurate. the numbers are different, as to how the pdf was created.

    2) enable me to proof read pdf – so have 2 version side by side — one version is of “original” and other version is “marked up”

    3) split a 2 page layout (book style) that is really on 1 page physical pdf, into single pages pdf, so can be easily read


    Comment by purelight — March 10, 2012 #

  21. purelight: as of today (March 21, 2012), Papers version is 2.1.17. I would go for Papers2 without hesitation. I’ve used Papers for years and had the occasional frustrations with 2.0.x. By now, most of my beloved missing features (e.g., merge authors) have been restored or even improved. BibTex export is also working like a breeze (vs. Papers1). So, in a nutshell, Papers2 all the way I shall strongly recommend.

    Comment by Nico — March 20, 2012 #

  22. Papers2 is great. No reason in my mind to stick with Papers1. I agree with Nico.

    Comment by sam — March 21, 2012 #

  23. UPDATE: Papers is now available for Windows PC, hence alleviating some of the limitations mentioned by some users.

    An important note: as far as I know, one license can be used on both Mac and Windows.

    For users juggling between computers and OS (e.g., Windows and Mac OS X), they can use Papers on both with a single license. As importantly, they can share the same library (i.e., sync between the Mac and Windows versions) using, for instance, DropBox.

    All-in-all, some great news for multi platform users. just missing Linux now but running Papers on Windows through VMware (or similar) can do the trick for Linux users

    Comment by Nico — April 25, 2012 #

  24. Thank you so much for the comparison. I will definitely go with Papers2.

    Comment by Tango — May 7, 2012 #

  25. Huh…I just bought Papers2 (2.2.10) a few days ago for the first time. Since I have been using it, it has run slowly and crashed multiple times. Yesterday, it crashed again and reverted to an old version of the library with only half my data in it. I have wrote to technical support over a day ago and still not a word on how to recover my library. While Papers2 seemed like it would be great, it has been nothing but crap so far. I asked two colleagues that both use Papers2 and they curse it daily.

    Comment by SMA — May 23, 2012 #

  26. Jeez, that sucks, SMA. I hope you find your data. I never have problems with Papers2. Maybe it didn’t install correctly, try a complete uninstall (including preferences files) and reinstall? If you’re having problems with Papers2, maybe you should transition to Mendeley. I have only used Mendeley infrequently, but it seems to have blossomed into a great piece of software.

    Comment by sam — May 23, 2012 #

  27. Been using Papers2 for about a year now. Used Endnote before and Reference Manager before that. A number of updates have improved Papers2 over the time I’ve been using it and I really like Papers2.

    Trouble is: on several occasions I have seen my citations go haywire. One time, a couple of weeks before handing in my PhD, a number of references were mixed into other references. Probably a result of cutting and pasting some paragraphs which included citations. Things like this has happened to some of my colleagues as well. The worst thing is that you might miss these incidents because Papers2 doesn’t warn you. We did not seem to run in to similar issues with EndNote. I have written to Papers2 support about it and are awaiting a reply.

    Bottom line: I would really love to keep using Papers2 but I need to know what caused these issues or the App is to “dangerous” to use!

    Comment by Torben — June 12, 2013 #

  28. I’ve been using Mendeley for citations, because it’s easy to collaborate.

    Comment by sam — June 13, 2013 #

  29. I’ve been using paper for windows for about a year now. I have come to loathe the program. Every time they update it, something new and unexpected breaks. Updates have corrupted my library twice now. Searching my library is broken (rebuilding the spotlight index doesn’t fix it). Citations are broken on update and require me to manually extract the citations to get them to work.

    Citekeys are frustrating and difficult to edit by the end user, making what should be a very nice feature not.

    I hate this program and I paid money for it. Don’t get it.

    Comment by Zak N — February 7, 2014 #

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