ReadCube Papers Beta – organising references

The ultimate purpose of academic work is to advance and disseminate knowledge. This means constantly identifying, absorbing, engaging with and eventually challenging prior academic work. There are several Mac apps that can support this process. Ideally, such an app would help to find scientific publications online, download and organise the relevant files (usually in pdf format) on local computer as well as related bibliographic meta-data (e.g. author, year of publication and title), annotate these files, and finally insert citations and bibliographies referring to this work during academic writing.

Earlier on Macademic, I wrote many entries on Papers, in my view the best academic reference and pdf management software for a Mac. However, a few years ago Papers was discontinued and started to be less compatible with new versions of macOS. As crashes became frequent, I searched for a replacement.  For a while I used Mendeley – it worked ok, but I always had a feeling that it is not an app developed with a user in mind. I also tried Sente, Zotero, BookEnds and EndNote, but nothing was comparable to Papers in its ability to organise, annotate, share and cite.

Eventually, I started working with the new re-incarnation of Papers , which is now developed by ReadCube. It is still beta, but I have already used it in several manuscripts and in daily work, so I can share a few first impressions.

The first (and the most dreadful) hurdle in switching to a new reference manager is transferring your existing library. ReadCube provides a special utility to import Papers 3 libraries. At the time, I had some 3,000 Papers documents and these were imported without significant problems. Of course, I kept a backup of my old library, but so far I have not used it. ReadCube can also import pdf files or reference libraries such as BibTex (in case you want to import from Mendeley or other software).

Papers is available as a browser, macOS, and iOS app. All synchronise pretty seamlessly (except the iOS app does not sync hierarchical collections yet) and you may need to work with all of them for different purposes. The macOS/browser app has many amazing functions of the original Papers, here are five that I use most often:

  • adding a pdf from a designated ‘watch’ folder (if you download a pdf from the Internet in this folder – you’ll then find it in your library);
  • organising pdfs on your computer (e.g. in folders corresponding to authors) so that you can always locate them (e.g. for sharing with others);
  • organising your documents by tags (for example on a specific topic) or collections (for example cited in a specific publication); a lovely recently added feature is the ability to search for tags as shown in the screenshot below; it’s also possible to flag, rate and color-tag your references;
Screenshot 2020-05-03 at 20.46.51

Main screen of ReadCube Papers. The sidebar on the right shows different methods of organising the references: by flags, tags, collections, etc. Tags are searchable, as shown.


  • sharing your libraries with collaborators;
  • searching for new references on the Internet and quickly adding them to the library.

There are still serious omissions, which make me hope ReadCube will improve their product to match the original much loved app:

  • to download pdf files behind the paywall through your university proxy you need to use the browser, not the desktop version of the app;
  • to simply email a reference and the related pdf to a student or a collaborator (something I do a dozen times per day) is not possible with one click, as it was in Papers 3; one has to click on the Share through email button, then locate the file in Finder (right-click the entry in the reference list and you’ll see this option) and then drag the file onto the email;
  • managing authors is worse than rudimentary; once the authors are entered it is impossible to edit them or change order, all you can do is to delete everyone and enter anew; furthermore there is no general author list (as in Papers 3) which I used to find duplicates, spell the names correctly and consistently, etc.
  • earlier one could match the metadata from the Internet to avoid manual entry, now this feature has miraculously disappeared.

I will review citation with ReadCube Papers in one of the next entries and meanwhile hope that ReadCube will keep improving this promising product.


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 Bibliographies, Writing and tagged , . Bookmark the permalink.

22 Responses to ReadCube Papers Beta – organising references

  1. A K says:

    Hi Aleh, I’m wondering if you’ve come across Polar Bookshelf.



  2. Simon says:

    I’m still using Papers 1 (yep one) now 26,000+ pdf’s. 10 yo mac now grinding under workload but STILL works.
    Searching by tags or authors√
    downloads metada after loading √
    filing into subfolders√

    Thanks Prof. sounds promising.

    It would be nice to upgrade before this old mac dies and not lose 20 years of reference articles.


  3. Thanks. I’ve also long waited for “Papers4” (now ReadCube Papers). The betas did not do it for me for a long time, but finally the “real version” (still feels like beta, though), tested again this March, managed to import my 10k library; I assume the progress here was a working restart/continue functionality of the importer. We then moved the whole group to Papers4…
    Overall, I agree with you: there is no other tool that comes close in terms of usability and productivity, the new one is better than the outdated Papers3, but is is also missing many things (aka features) and has many bugs (e.g., go from PDF to library – it’s there in the sidebar, but not the list/table, try OPT-x in an input, …). But, for you, there is the “refresh metadata” which works fairly well for me.
    The shared library for my group finally provides this feature – promised maybe 10 years ago – in a reasonably well working way, It’s definitely fairly seamless.
    The biggest problem, however, is the intransparent bug-tracking and feature-request system they have! If that would actually show reported bugs, requested features, and discussions thereof, I would be a lot more optimistic and happier.
    Still, an important step forward – nice you report on it (although the current version is formally not beta anymore:-)

    Liked by 1 person

    • Aleh Cherp says:

      Thanks Jochen, I’ll keep working and testing and posting updates – hopefully next time on citations and bibliographies. Your tips are highly appreciated!


  4. Sotirios says:

    Hey Aleh, I’m very happy to see new blog posts. My colleagues and I have learnt a lot from your blog! Cheers 🙂


  5. Peter Sands says:

    Can you compare directly with Bookends?


  6. petesands says:

    Can you compare directly to Bookends?


  7. Victor A Cazares says:

    Hi Aleh, thanks for your post. I’ve followed your blog for quite a while now . It’s helped me a lot over the years (since I was a grad student, and I am starting my faculty appointment this summer!).

    Ive been a Papers user since the begging. I felt that Papers2 was the best. Like you, I also really lost hope when Papers 3 got so buggy. I’ve recently upgraded to ReadCube papers and I think there is a good chance that the developers bring back the Papers functionality that you described and many of us loved. One (potential) positive of the subscription model is that if they don’t improve the program, they lose subscribers more rapidly.
    One major gripe is that last I tried (~ 2 weeks ago) I was unable to use the citation/referencing functionality, their so called “Smart Cite”.

    Anyway, wanted to say thanks again! I really appreciate your blog.


  8. Oliver says:

    Thank you for the review! I did try out Papers3 at one point and liked the usability. After buying it too quickly I discovered that it didn’t record book series for monographs or articles in edited volumes. This is absolutely necessary for humanities. I asked the developer then because I didn’t think this was possible and they told me they probably wouldn’t add this field. Did they include this now?


    • Aleh Cherp says:

      There are fields for book series in Papers, but frankly I have not managed to display them correctly through the citation styles available. Which citation style are you using?


      • Oliver says:

        That sounds somewhat promising and I will check it out but I have to finish another project first. I can rarely use the built in citation styles as they don’t fit what is expected in German theological literature so I need to adjust them. Sometimes, there is an SBL style I use but I don’t remember if that was useful in Papers. Thanks for checking and replying!


  9. FM says:

    I was a big fan of papers since my residency/masters years and been through papers 2 and 3. I wanted to love readcube but it just wasn’t working for me. I’m not an academic but I use reference managers to organize important references in my speciality and to keep up with new studies (I like to have them organized rather than dumped in my downloads folder). I have recently switched to paperpile and have been extremely happy with it. The only downside for me now is that it only works on chrome for desktop but they are working on apps which is something I’m looking forward to. The PDFs get saved to google drive so I can still access them on my iPad.


  10. Florian says:

    I’m so glad you’re finally writing again. I can only repeat the other comments: I/we have learned so much from you. And the fact that you then also take up the really most difficult topic – reference management – is again very grateful. The last years often brought me to despair in this respect. Your trust and your adherence to ReadCube Papers amazes and encourages me after these years of suffering. I would be very interested in your opinion of newer products like Sciwheel and PaperPile, but also of the old, but very stable Bookends.

    Finally I would like to ask you to update your very valuable page Essential software for academic work on a Mac with your experiences of the last years.

    Thank you very much for your blog.


    • Aleh Cherp says:

      Thank you, Florian! Your message goes directly to my ‘Feel good’ folder! (Do you have one? Highly recommended!). I will try to update as much as I can, but I can’t realistically test all the excellent software due to time and budget limitations. So if you or anyone else have valuable experience to share – I’d be more than happy to give this platform for a guest post.


  11. James Rudd says:

    Great review. Have you noticed any improvements? I’ve been with Papers since the start and am clinging on to Papers3 for now. But I’d love to make the jump to this new app. Any updated fixes for the issues you mention?


  12. LI Zhu says:

    Thanks for the review. I have been used Papers2 & 3 for a long time, and then switched to Mendeley. Recently, I switched back to the new Readcube Papers. Overall, I am satisfied with it. But there is an issue that really annoys me.

    The periods (.) are missing from the journal abbreviations when I use the SmartCite. For example, it should be “Phys. Rev. B”, not “Phys Rev B”. Of course, I can modify them from the metadata in the Papersapp. But I don’t want to manually edit them thousands of times. And it seems like the developers don’t think it’s a bug. But I never have this problem in Papers 2 & 3. I don’t know if you have the same problem?


  13. Art Pericles says:

    Thanks for blogging on this again. Your old posts on Papers were what drove me to it. I migrated from Papers3 to Readcube Papers last year. I find, like someone said above, it still feels like beta.

    A number of features from Papers3 are still absent, and we have no sense of when or if they are working on them. Take Magic Cite, for instance. Or Spotlight integration. Or the way PDF annotations work (you’re not able, as with Papers3, to underline part of a highlighted text— only one annotation per text). The iOS and iPadOS apps are quite far behind. As opposed to the desktop app, you don’t have a panel showing annotations— and this was really crucial for me to navigate documents, particularly for books.

    I was still willing to stick to it, but there is one major shortcoming. Citekeys from Papers3 don’t work. The tool (SmartCite for Citekeys) is unstable. Beyond that, and crucially, it is simply not compatible with Papers3 citekeys. Three main reasons:
    1) Paper3 syntax isn’t supported. Manuscripts I wrote which use syntax such as {Barendt.2014, p.14} are not parsed.
    2) In fact, as confirmed by Readcube support, there is simply no way to add page numbers using citekeys. You have to do it manually. No modifiers are available.
    3) Finally, even if you have citekeys with no pages, the Smartcite for Citekeys doesn’t parse anything within footnotes

    And what’s more: they are not doing anything about it. I wrote them a number of times on this. Their final word is they have no plans on working on citekeys. They even offered a refund.


  14. I used Papers for years. I stopped in 2021 but will have another look. Regarding “to simply email a reference and the related pdf to a student or a collaborator (something I do a dozen times per day) is not possible with one click, as it was in Papers 3; one has to click on the Share through email button, then locate the file in Finder (right-click the entry in the reference list and you’ll see this option) and then drag the file onto the email”: if you invoke a PDF in Hook (our app), you can do ⌃⌘\ to share it via email. If there’s demand, we can enable a global shortcut for that.

    Hook was compatible with Papers 3. We’re having a look at the latest version of Papers (I’ve been exchanging emails with the ReadCube folks)


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