Papers 3: considerable improvements, but still beta

I have recently been asked to prepare one of the Oxford Bibliographies. This required sifting through, organizing and annotating a large number of references and so I decided to give Papers 3.0 another try. I have previously been disappointed by various deficiencies of this new version. It seems, however, that the programming team has been working hard updating the (still beta) version. So my impression is cautiously optimistic.

First, it looks there is some attention to how pdf files are organized: the evidence is in Help → Troubleshooting which contains several esoteric but re-assuring commands (I tried them all but did not observe any effect – either good or bad):

Papers 3.0.30 Help menu provides commands for manipulating files.

Papers 3.0.30 Help menu provides commands for manipulating files.

To me, these commands indicate that Papers 3 want Spotlight to see files in their library. Very good news! Unfortunately Spotlight still cannot find all of the files within Papers 3 package (but it does find some!). I also tried to index Paper 3 package with DevonThink, but the results are still not reliable.

I managed to achieve some peace of mind by trying FoxTrot search on Papers’ Library. It had absolutely no problem finding all files by any search criteria. I am still not prepared to invest a considerable sum in buying FoxTrot search, hoping that Papers will make its library more accessible for lay search engines.

Other than that I have managed to smoothly manage all my references. I have been pretty impressed by the ability of Papers 3 to connect to my University’s library and smoothly deliver pdfs from publishers’  websites right into my hands. Though Papers 3 has many exciting possibilities, I still do not recommend it for people who don’t like experimenting with their precious bibliographic collections. There are minor bugs here and there and support documentation is not yet available. All in all, it remains a beta version, but the hope for its successful completion is steadily growing.

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About Aleh Cherp

Aleh Cherp is a professor at Central European University and Lund University. He also coordinates MESPOM, a Masters course operated by six Universities.
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42 Responses to Papers 3: considerable improvements, but still beta

  1. David says:

    Hi Aleh

    Do yourself a favour and make the move to FoxTrot. If you keep a lot of material for searching (e.g. 2000 academic papers), there is nothing like FoxTrot for speed, search refinement, previewing. It will show you every search hit on a file in context. One feature you may not have realised is that the search in the internal FoxTrot PDF preview window colour codes each search term. So if you are searching for something that has a common term and an uncommon term, you can quickly scan the PDF for the color of the uncommon term.

    There is a new version 5 in public beta which makes further improvements. Yes, it is a bit pricey. Yes, they should have an education discount. But it is an essential tool for research. I say that as somone who also uses DevonThink and DevonAgent.

    Thanks for the blog posts.

    David.

    Like

  2. Fred says:

    I agree. It seems to have basic functionality now, and a number of big(ger) issues are seemingly resolved. However, quite a few lesser problems remain. Hopefully they can get those fixed eventually (before version 4?).

    Like

  3. Matthias says:

    Hi, Matthias from the Papers Mac team here. We appreciate the constructive feedback! We’d be interested to hear more about the remaining problems. I.e., what are your most pressing issues?

    If possible, please also make sure to report these issues to the Papers support team, this greatly helps us to file proper issues in our ticket system and to prioritize them. Thanks!

    Like

    • Aleh Cherp says:

      Thanks! I think one thing that would help enormously is to shorten feedback times. Waiting for a week or more is not acceptable. There are a lot of smaller bugs I’d be glad to point out, but the most important big thing is still making the Papers package more visible to Spotlight (and/or guiding the users on how to optimize Spotlight search of the package).

      Liked by 1 person

  4. Matthias says:

    > I think one thing that would help enormously is to shorten feedback times.

    Yes, I understand. Since the launch of Papers 3 the support team has worked very hard to get response times down, and they’re constantly working to further improve that.

    > the most important big thing is still making the Papers package more visible to Spotlight

    Thanks for the feedback. I agree that it would be very useful to again be able to search your Papers library files from within Spotlight in the Finder. We had tried to make the Papers virtual disk (which uses OSXFUSE) visible to Spotlight but for technical reasons related to OSXFUSE this didn’t work out so far. I’ll make sure that we look into it, but ATM I cannot promise you anything.

    Like

    • philipvinc says:

      If I may add, It would also help if you could fix the search field: I am an undergraduate student who used Papers to handle the bibliography of my thesis ( about 30 articles ), and there are some authors and papers which will never show up in search results.

      Like

    • Aleh Cherp says:

      Re: spotlight search. Apparently FoxTrot can beautifully search Papers package. Can’t you make use of their technology to make it visible to Spotlight?

      Like

  5. Chris says:

    I too am giving papers a second look. I left papers and used Sente for my last semester of course work this spring. The thing I liked most about Sente was the annotation workflow. Specifically, when I highlight text, a note is generated with the highlighted text as a quote with a title and comment field. The comment field is especially helpful for helping me to remember what I thought was interesting, controversial, or important about the highlighted text.

    The other part about Sente that was helpful was Rob Trew’s script that allowed me to export my notes (individually) with a citekey for a given article as rtf files to be imported into devonthink. Unfortunately, the script has become unreliable and I really am not comfortable with my workflow depending on an unsupported applescript that could break at any time. Without that script and with a few other annoyances I have with Sente, I am back in the wilderness.

    Papers 3 does seem much better now and I am inclined to go back to it. A feature that I, and I am sure others, would especially appreciate is the ability to attach a comment specifically to a highlight. That and the ability to export notes individually with citekeys, and perhaps full references, would be amazing.

    In terms of responsiveness from support, I made an inquiry yesterday about adding magic citations support for the foldingtext text editor and received a response within hours. So that’s promising.

    Like

  6. Aleh Cherp says:

    I don’t see the ‘Published’ field when I am editing a reference to a book. Only “Start date” and “End date”. Very annoying because it means I can’t cite books. Sent a query over 2 weeks ago. Another problem is citing in ByWord – it always asks to change file permissions every time I try to insert a citation.
    I agree relating notes to highlights would be really great. Exporting that into an rtf would be a dream.

    Like

    • Chris says:

      I see the field on the iPad, but not in OSX. Strange. Yeah, that’s a pretty basic thing that needs to be right – at a minimum.

      Like

    • Matthias says:

      > I don’t see the ‘Published’ field when I am editing a reference to a book. Only “Start date” and “End date”. Very annoying because it means I can’t cite books.

      I agree that’s a very nasty bug that must have happened in the last version. I’ll look into it.

      Re. that ByWord issue, I couldn’t find anything in our issue database. If you haven’t done so, please file a bug report about it. Many thanks!

      Like

    • Matthias says:

      Re. the display of inappropriate fields for type Book: I’ve fixed this issue. The fix should hopefully make it into the next beta which will be out soon. Sorry again for the trouble!

      Among other things, this next beta will also add support for scriptability. This should allow for instance to write a script that exports all annotations to individual text files.

      Like

  7. Pino says:

    Sorry Mathias, It is not possible you are making profit with a still “beta” version, that’s unacceptable for a company.
    I used to use papers and still keep papers2 while I am moving to a different alternative, after my bad experience with papers3.
    You are not a small company any more, you are part of Springer, big company making already lot of profit. There is not justification to sell a software that has almost a year with a lot of problems. That’s simply not acceptable.
    Best,

    Like

    • msteffens says:

      Hi Pino,

      I’m just participating here in order to get feedback, but I understand your frustration. I apologise for the trouble you were facing with Papers and you should, of course, choose the tool that best suits your needs!

      Best, Matthias

      Like

      • Les R Becker says:

        Matthias,

        I’m jumping in here. Apologies in advance.
        Though synchronization has improved, it remains quite unpredictable. Entire folders I have created on OSX simply do not sync to IOS. And, it would seem that unless one is recognized as a blogger or superuser, responses to help requests are so slow as to be nearly useless and no one has been willing to assist with my sync issues, not all of which are mentioned here out of courtesy to readers.
        TY.
        Les

        Like

      • Matthias says:

        Hi Les, I’m sorry for the trouble you’re facing! I’ve asked support to look into your issues. Matthias

        Like

  8. Mark says:

    I am following this conversation with a lot of interest since I am curious to know who much Papers has improved. Sadly, after reading this blog and other comments, it sounds like there is still work left to do. I too tried Papers a few times over the years, but each time there was just too many “beta” behaviors to justify the cost. In short, I got tired of waiting to see things fixed or features added.

    I moved to BookEnds about 5 years ago and it has been a very good experience until somehow Thomson Reuters and Web of Science completely messed up how BookEnds taps into that database through my university connection. All evidence pointed to the problem being with Web of Science, and even after having an IT librarian specialist and the creator of BookEnds chiming in, Thomson’s response was basically, “sorry, we are aware of the problem, but don’t plan on fixing it.” Luckily, most functionality is there with Google Scholar.

    BookEnds has a steep learning curve and one does have to swim through a very large manual to occasionally find answers and the interface is not pretty and not always intuitive. However, the creator of BookEnds understands that those of us in academics have precious little time to deal with software problems and I’ve had him respond directly to me on a Sunday when I had a grant proposal due the next day. I will take the warts of BookEnds for such stellar support any day.

    Like

    • David says:

      I also use Bookends and have done so for many years. I tried Papers and Sente. The latter is good, but did not support citation formats in the humanities very well. The former has always looked fantastic but never proved powerful or reliable enough.

      Bookends on the other hand mostly looks bad, but the support from the developer is incredible. I too have had responses within an hour, on a weekend, often with patches made the same day or corrective files sent to me. It is clear that he gets what academics are up to with these tools and how we work. While the app is ungainly in parts, the overall power and variety of functions is excellent. I have never found that I could not do what I wanted.

      If you use Mellel, the integration with Bookends is especially good. I used it with BibTeX as well.

      David.

      Like

  9. Carl Casca says:

    I’ve been following this very closely. Thanks a lot Aleh for keeping people up to date on how papers3 is progressing. I’ve been a papers2 user for a long time, but am nervous about upgrading. They’ve been sending around grandiose sounding “much improved” emails, but I’m not very trusting of them lately. Any chance you’ll soon take another look and report back on how it’s coming along? I’m not enough of an expert on the nitty-gritty software details of it to decide for myself if it’s really getting better. Thanks for any insights on how it’s progressing.

    Liked by 1 person

  10. Martin Wagenmann says:

    I really like Papers and used it from the very beginning. But the major – and really only reason – that keeps from upgrading to Papers 3 is the fact that the only way to sync is through Dropbox.
    I work in a university hospital (Düsseldorf) that blocks access to Dropbox for security reasons. With Papers 2 I sync my Papers library between my Macs with ChronoSync (set up so that only new or changed entries are synced) and that works reliably since years. (My library includes more than 6.200 papers and with 6,7 GB copying the whole folder is no option).
    But this is no longer possible with Papers 3. Until now, I didn´t find a solution for this problem. Since I can imagine that many researchers in university hospitals face similar problems with access to the cloud, I don´t understand why the Papers team doesn´t offer a solution to this problem.
    Best

    Like

    • Marcos says:

      I also work in a university hospital in spain and face the same problems as Martin , any suggestions?

      Like

    • gth17 says:

      I completely agree on this point. My library is larger then my dropbox account, and this has made me move back to Papers 2. Which is a shame, because otherwise I am happy with Papers 3. Why on earth isn’t syncing allowed without using dropbox?

      Like

  11. emmalalalala says:

    Aleh! Very helpful blog. Thank you. I have joined word press just to follow it. I too have been on the papers boat since version 1 and as a complete papers 2 devotee and was totally devastated to read your first post, but I am lifted to see that things have changed a bit. Feeling much better seeing Matthius’ contribution to this discussion. I don’t want to switch apps…… and like many others and hoping I wont have to. I want papers to continue improving and Im willing to be apart of that process, but I need to know they wont flake out on me! I have just started a Phd- and the method i begin with for my referencing is crucial. I am still on papers 2….. and I’m debating …..do I wait to see how Papers 3 steps up….do i jump ship or do I support the improvement cause and buy in? The others are right, papers in no longer the underdog– I hope I can expect to rely on them!!!

    Like

    • Aleh Cherp says:

      Emma, thank you. My advice would be to go for Papers 3. You need a professional-grade app to support your PhD studies and Papers 3 will do the job. At the moment, there are also ‘exit strategies’ to other reference managers.

      Liked by 1 person

  12. Yohan Farouz says:

    Nice blog here. I am happy to see that there is kind of a community that still wants to give Papers 3 a try. Personally, I feel like they resolved most of the initial bugs introduced with the Dropbox Syncing… Except the Android app availability.
    It seems like Papers is actively working on their Android version, according to their career webpage. Well, it’s been six months like this and I couldn’t wait any longer. I wanted my 2000+ papers listed and sorted on my Android, immediately. I tried switching from Papers to Mendeley, but it messed everything up. In the end, I chose to develop my own app that actually downloads the Papers library that is stored on Dropbox.
    Since this week, you can check it out on the Google Play Store: it is called EZPaperz !

    https://play.google.com/store/apps/details?id=net.ezbio.ezpaperz

    Hope you’ll like it.
    Any feedback is more than welcome, as I’ve done that between immunostainings and cell culture ;)
    Spread the word

    Like

  13. ctwomey says:

    Thanks to all the contributors here; this is extremely informative as I ponder migrating from Sente, but also simply thinking about the different ways one might use the software/workflows.

    Like

  14. delfin says:

    Hi there! Great to read this discussion on Papers 3. I’ve also used Papers since the very beginning with versions 1, 2 and recently upgraded to Papers 3. The main reason being I decided to get an ipad with the idea that I would read and annotate my papers with it and keep my Papers library synchronised with my mac book pro (which I upgraded to Maverick). Papers 3 is still very new to me and I find it hard to get used to it after Papers 2 but after reading your post I would like to give it a try. However, one main feature I haven’t been able do is to get all my pdfs on my ipad. So far synchronisation with dropbox only synchronises the metadata. On my ipad I can download the pdf one by one but…. I have about 2000 articles. Is there a way to download all the pdfs at once and keep Papers 3’s pdfs synchronised between my mac and ipad?

    Like

    • Aleh Cherp says:

      Have you tried Papers 3 for iPad?

      Like

    • Les R Becker says:

      Perhaps you are describing normal behavior for the app, at least according to my experiences. A sync between desktop and iPad results in a placeholder for the paper (the metadata) being transferred to the iPad. When one accesses the article on the iPad, the actual download seems to occur and thereafter the paper is permanently on the IOS device.
      I’d be interested if others have observed this behavior or perhaps can offer a more accurate explanation.

      TY

      LRB

      Like

      • delfin says:

        Yes I think this is exactly what it does. My issue is I would like to have all my papers downloaded and stored on my iPad so I don’t have to worry about internet connection when I’m searching for an article in my Papers’ library and want to read it, let say when I’m travelling in a plane with no internet…

        Liked by 1 person

      • Les R. Becker says:

        I agree that this would be a great feature. At risk of sounding like an apologist for the software developers, my best guess is that earlier post-version 2 iterations of the app (they were terrible) attempted to accomplish this and that is why sync lagged on forever and ultimately failed.

        Like

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