Papers 2 is here!

My earlier post on Papers and Sente said that the biggest disadvantage of Papers is that it does not allow working with bibliographies. This has changed in Papers 2 immediately bridging the gap between pdf file management and scholarly referencing. As a result I switched to Papers and am now in the process of transferring my library. Although I am not yet prepared to discuss the use of this product in detail (I need to write a couple of articles supported by Papers), here are four of my favorite goodies:

  • Press Ctrl twice without opening Papers and you can search your Papers library (not only filenames, but the full texts too!);
  • Press Ctrl twice while writing (in Scrivener, Pages, Byword or whatever) and you can insert a citation;

  • my Hazel workflow for adding newly downloaded files to Papers library is back! Thus I am pretty assured that all scholarly articles I downloaded can be found through Papers; (for geeks: I am using OpenMeta tag “papers” to toggle the addition);
  • I love highly customized ways I can match a pdf file with its bibliographic reference.

About Aleh Cherp

Aleh Cherp is a professor at Central European University and Lund University. He researchers energy and environment and coordinates MESPOM, a Masters course operated by six Universities.
This entry was posted in Automation, Bibliographies, Files, Writing and tagged , , , , . Bookmark the permalink.

30 Responses to Papers 2 is here!

  1. Pingback: Using Sente and Papers to handle references and bibliographies | Academic workflows on Mac

  2. Pingback: Byword – an ideal tool for plain text writing on a Mac | Academic workflows on Mac

  3. Bryan says:

    I’ll be eager to hear of your results writing papers, Aleh. I’m very interested in Papers; I keep coming back to try it out, and honestly, I want to like it, but, I’m really struggling that I can’t get it to format basic social science reference lists correctly, in terms of capitalizing article and book titles. Have you run into this problem? APA title format uses “sentence case” for references; so, a title would look like this, with only the first word, the first word after the colon, and the proper noun “APA” being capitalized:
    This is an example title: How to format titles in APA
    Conversely, another typical social science format, MLA, capitalizes each major word; so, a title would look like this:
    This Is an Example Title: How to Format Titles in MLA
    For the life of me, I can’t get Papers to convert the capitalization when I change reference list formats. It just gives me whatever the capitalization was when I imported the file information. Needless to say, this creates a bunch of extra admin work that other bibliography software packages seem to handle OK.
    Thanks for all you do here!


  4. Aleh Cherp says:

    Bryan, thanks! Well, at least to some extent it works for me. Here is a clip from a ByWord document cited and formatted in Papers2
    This is the citation: (Ostrom, Janssen, & Anderies, 2007)

    Here is the bibliography in APA style

    Ostrom, E., Janssen, M. A., & Anderies, J. M. (2007). Going beyond panaceas. Proceedings of the National Academy of Sciences of the United States of America, 104(39), 15176–15178. doi:10.1073/pnas.0701886104

    Here is the bibliography in MLA style:

    Ostrom, Elinor, Marco A Janssen, and John M Anderies. “Going Beyond Panaceas..” Proceedings of the National Academy of Sciences of the United States of America 104.39 (2007): 15176–15178. Web.

    I did not check capitalization after a semicolon but I will and come back.


    • Bryan says:

      Fantastic, Aleh, at least in the sense of helping me identify that it really is an “operator error” on my part, and not a missing feature in the software. I’ll investigate why it’s happening. Thanks again for your work here.


    • Bryan says:

      Aleh–Just updating: I deleted my original library, imported a test reference, and it worked flawlessly. Thanks for the encouragement to revisit Papers. I’m pretty happy right now!


  5. Pingback: Citation modifiers in Papers2 | Academic workflows on Mac

  6. Csaba Pusztai says:

    The funny thing is that I remember the early days when Papers (beta) came out and discussed stuff with the Mekentosj guys, they were so firm on making/positioning their product as a pdf management app and not citation software. They did not perceive Papers as a potential rival for Bookends and whatever was around back then. But years have gone by and I guess by popular pressure they did steer development toward building in proper citation capabilities. For our benefit. After all, what sort of user collects hundreds/thousands of pdfs (journal articles) without the intention of citing them some time??? Wise move. Survival of the fittest! 🙂


  7. Csaba Pusztai says:

    I had some time to take a peek at Papers2 and, if I am not mistaken, note taking features are still limited. I really like how Sente lists all ‘quotes’ and notes in a particular document. I like to see all my annotations at a glance rather than having to go through the whole document. Papers2 may be stronger in many other aspects, but this is a ‘deal breaker’ for me.


  8. Aleh Cherp says:

    Csaba, why do you need note-taking in your pdf-management/citation software? Is it to link a particular set of notes to a particular pdf?


  9. Csaba Pusztai says:

    As I read, rather than copy/pasting interesting pieces of text into a separate document, I would like to keep them with the pdf: have them highlighted for future reference. So when I revisit a piece of writing (say a book), I would not have to flip through the pages to look for what I have highlighted.


    • Jenny Groarke says:

      Hold cmd and double click and you can add a sticky to a particular paragraph.
      Also hold cmd and highlight to ‘highlight’ sections of text.
      and you can add notes to the hole paper by clicking notes on menu below the paper.


  10. Pingback: Three stages of the academic workflow and Mac software | Academic workflows on Mac

  11. Roy Kamada says:

    Csaba, I was just about to go ahead and purchase papers2 because I like the interface so much–also it seems to be much better at automatically finding matches for my old PDFs; but the list of highlighted quotes is a game changer for me!

    Aleh, I take it there’s no corresponding function in papers2?


  12. Peter says:

    I tried papers2 and it was quite nice, but finally decided just to go back to endnote as it is more compatible when you have to share your files with PC users. Endnote used to really suck, but now its actually pretty darn good and the features list is overall pretty comparable to papers 2, at least for the things I need, including maintaining pdf files of my articles. The only thing I don’t like about Endnote is that its expensive and that they gouge you about once a year with their upgrades.


  13. Csaba, If you use to read PDFs, you can see all your notes in The Skim Notes pane of the window on that PDF file. You can also easily copy your notes out to another document from within skim (just click on a note and do “select all”). You can even open the Skim.notes file (which contains your notes) in its own window. Skim is scriptable so you could get your notes automatically, too.


    • Aleh Cherp says:

      Scrivener is also available for PC. Byword and OmniOutline are only available for Mac and iPad/iPhone but I am sure there are simple text editors and outliners for PC as well.


    • Sofia says:

      I miss that same feature in Papers2 that Csaba has pointed out. I have just made up my mind for Papers2 after using/shopping around for other reference managers. While I read, I like to take notes for FUTURE reference too. Consequently, I’d like to not only be able to re-read my notes without having to open them individually in the pdfs, but also (and most importantly) to be able to apply search options to the collection of notes taken over time. I really wish that was possible in Papers2.

      Luc, is the suggestion of using Skim an alternative to Papers2, or can the two be integrated for a nice paperless workflow (I use Mac and IPad)?
      Any other suggestions?

      Thank you!


    • Sofia says:

      I miss that same feature in Papers2 that Csaba has pointed out. I have just made up my mind for Papers2 after using/shopping around for other reference managers. While I read, I like to take notes for FUTURE reference too. Consequently, I’d like to be able to not only re-read my notes without having to open them individually in the pdfs, but also to apply search options to the collection of notes taken over time. I really wish that was possible in Papers2.

      Luc, is the suggestion of using Skim and alternative to Papers2, or can the two be integrated for a nice paperless workflow?
      Any other suggestions?

      Thank you!


      • Sofia, Skim and Papers2 can indeed be combined. Tip: select a paper in the Papers2 library, from the Paper menu , select Open PDF with menu item, which is a hierarchical menu. From there, select Skim. I do this all the time.
        Also, in the Preferences window, select the Papers tab. You’ll see an “Open PDF Files” label. To the right of that, you can select Skim as your default reader.

        Skim is IMO the most powerful PDF reader on Mac and probably on all platforms for scholarly (including cognitive) productivity.

        Fortunately, Papers2 stores PDF files on the file system rather than a database.

        Papers2 unfortunately lacks tags. I have contacted Mekentosj (now owned by Springer) to request that feature. I assume, given that Apple OS X Mavericks will have tags, that Springer will change its course and add tags. This is important because as it stands, several apps have their own tag systems. So tags added in (say) an OpenMeta, Papers2, EverNote, and diigo are all independent of each other. I’ve long called for a unified tagging system. Mavericks tags can provide this uniformity. We need tags also to be uniform on iOS devices.

        However, even today you can tag Papers2 PDF files using CaseApp’s tag tool. Then you can view your tagged files in any OpenMeta browser, such as Ironic Software’s Leap (currently my preferred solution). Ironic Software has published a tool to convert OpenMeta tags to Mavericks tags, so your effort there won’t be lost.

        In my new book, Cognitive Productivity: The Art and Science of Using Knowledge to Become Profoundly Effective, I describe many innovative ways of using Skim for cognitive productivity. I also discuss tags and other ways of organizing research. The book is on LeanPub. . This book is for all kinds of knowledge workers, not just scholars. The book is original as a productivity book in that it has a very strong basis in cognitive science.


      • Aleh Cherp says:

        Thanks, Birgitta!

        Kind regards,



  14. Floor Christie says:

    Hi guys, I’m pretty new to Papers 2 but I like it. Now yestreday it was still working fine for me but today I’m working a way in word and press ctrl 2x and nothing happens! Yestreday that feautre would work fine. Any idea what has changed or what I should do? Thanks so much!


  15. brian says:

    i’ve been trying out papers2 for ipad. As I read I copied chunks of text thinking they were saved in some central place connected to the pdf. I now realize I have no idea where even a single copied text is and how to access it. Does someone know how the copy function works and whether I can copy/paste text somewhere like the notes as I read? thanks


  16. dritchi says:

    Hi Aleh, I was curious to know how you think Papers2 stacks up against Sente. I’ve purchased Sente but it’s been less than impressive and caused me to start to look at Papers2.

    What are the advantages of Papers2 over Sente?


    • Aleh Cherp says:

      I switched from Sente6 to Papers2 earlier this year. The main advantage for me is it’s nicer and friendlier interface – which eventually means quite a lot for productivity. Since I have not actively used Sente for months I am not sure how its more recent versions are performing, but I’ve experienced difficulties with inserting citations in Scrivener before. In general if I remember correctly wordprocessors need to be ‘tuned’ to work with Sente whereas Papers is so versatile it allows you to cite anything anywhere.


  17. Hi Aleh! I’m a Sente 6 user and am in the process of switching to Papers 2. But exporting and importing does not bring in all the PDF:s and certainly not the notes. Any tips on how to go about it? I have something like 850 references with annotated PDF:s in Sente, and I haven’t got the time to do it manually…


  18. Vincent says:

    Hello Aleh,
    great to find another academic dealing with these things. I would like to switch to Papers2 now that it does references reasonably well, and it looks like I can export my library OK, but I also have several writing projects with lots of EndNote references (unformatted) already in them. One of them is a book that will take me another year, at least. Any idea how I might turn EndNote references into Paper2 references? I am fine with a little Word scripting but wouldn’t want to make a huge look-up table with “ref1 -> refA” etc.


  19. Pingback: Papers 3: moving in the wrong direction? | Academic workflows on Mac

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