Papers 3: moving in the wrong direction?

NB: Since this entry was written, 
file management in Papers 3 has improved. 
Follow further developments in Papers app on Macademic.

I have started trying the beta-version of Papers 3, an update of Papers 2, my favorite citation, bibliography and pdf management app. Papers 3 has an entirely new user interface which takes some time to get used to. Nevertheless, I have gradually started to appreciate the smoothness of its many  features, such as search for new references, editing authors, assigning  keywords and collections, and annotating by underlining text. However, I also have a major concern, so serious that it may force me to stay with Papers 2 or switch to another reference management software.

Let me explain. One of the great features of Papers 2 (and its main competitor Sente) is its logical and accessible handling of files. The user has high degree of control over how PDF documents are named and stored in Papers 2. This is how I manage  reference files using Papers 2:

  1. When I save a pdf document (e.g. a scientific article) attached to an email or download such a document from the Internet, I tag it (Mavericks, the next version of OS X, has built-in tagging compatible with OpenMeta);
  2. The document is then automatically imported into Papers using  a Hazel rule triggered by a tag (“papers” in my case).  (Alternatively, Papers can  automatically import all files added to a particular folder).
  3. If the imported document has a DOI (as most scientific articles), Papers automatically matches it with an online database such as Google Scholar or Web of Science and assigns all bibliographic information (author, year, title, journal, etc.). In other cases, I enter the bibliographic data (most importantly author, year, and title) manually.
  4. When the document receives its proper bibliographic information, Papers 2 names and stores it in accordance with the Library Preferences which I set as follows:

    Library

    Library preferences in Papers 2

  5. Now my files are not only available in Papers for reading, annotation and citations, they are also accessible to other applications. For example, I can index them with DevonThink (this is great for relating pdf documents to notes, emails, images, web-pages, and other content which is tagged similarly or is otherwise related), find and tag them through Tags, PathFinder or Spotlight, share them through the Dropbox, etc.
Articles_and_Scholars

Reference files in a Papers2 library

If in the future I decide to use another reference management software (or discontinue using reference managers at all) I will still have access to all my files neatly named and arranged.

All this seems to be gone in Papers 3, at least in the current beta version. All documents are stored together  with meta-information in a bundle not accessible to other software. You can open this package in Finder but it’s pretty difficult to locate the file you need. Moreover, Papers 3 does not seem to name files logically when moving them into its library bundle (for the Dropbox-synced files). For example, yesterday, the file originally named “WEF 2012 New Energy Architecture” was re-named when imported to FCFB7D16-677C-4F58-805F-B0014DF73155.pdf. Imagine confusion of my colleagues whom I sent this file by email!

Update on October 19, 2013

Responding to my query, Papers 3  staff confirmed that switching on the Dropbox synchronization (a new feature in Papers 3) removes user control over how the documents are named and stored. They added:

We are looking into a way how we could re-introduce the file organization with Dropbox syncing but we can’t guarantee if/when it would be available.

[addition on December 20, 2013. This entry describes the implementation of file access in the first official release of Papers 3]

If the Dropbox synchronization is not switched on there is still a possibility to control naming and storage of files, much like in Papers 2. However, the files are still kept in a bundle not accessible to Spotlight. The support staff says that Spotlight index will be added in future versions.

Moreover, I have noticed that if you switch on Dropbox synchronization once you won’t be able to restore control over organizing your files even if you later switch the synch back off and move your library to a local folder. This behavior is  unexpected and I hope it can be corrected in the future. Otherwise an accidental click on a button in the Preferences may cost people their whole libraries!

***

I hope Mekentosj can reconsider these changes or mitigate their negative impact. The ability to work with the same data using different software is really invaluable in academic work on a Mac (consider for example plain-text note-taking where different software can interplay because the content is kept in a simple and logical format). Files referenced in Papers should be accessible to other programs and thus be stored and named in a way that is generic, logical and understandable.

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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.
This entry was posted in Bibliographies, Workflows and tagged . Bookmark the permalink.

183 Responses to Papers 3: moving in the wrong direction?

  1. Csaba Pusztai says:

    I briefly fired up Papers 3, too. I noticed the it received a nice flat GUI, which I also like. If they decided to integrate the database with the bundle, that is pretty bad. From my perspective, being able to access the pdf files from outside Papers (thru Finder) has been important because I never trusted Papers 2. It kept confusing and losing pdfs. I basically had to do double accounting. Import to Papers and save a secondary copy in a different place.

    Like

    • Sedris says:

      Papers 3 is still loosing documents quite randomly…

      Itmight have been a nice piece of software, except that it’s totally unreliable, making it totally useless for professional purpose.

      The Mekentosj (now belonging to Springers) support never replied to my requests when I was talking about Papers 3 loosing documents. They prefer to keep silent on this point, it seems.

      When Papers 3 decides to loose documents, the documents completely vanish from the library, leaving no tracks neither in the trash bin nor the archives; the documents disappear totally from Papers 3.

      I think it happens when one modifies some data in the host source of the document (perdiodical / conference info) or the book for a book chapter.

      Also, if you delete a book (not sure about the conferences or the periodicals, I don’t want to fire up Papers 3 anymore, even to check this, wasting enough time with it) that has some chapter attached (as separate entries), they disappear alongside with it. And weird enough, the books are not considered as sources.

      Another highlight of the inconsistency of sources management in Papers 3: if you link chapters to books, they are accessible from within the book entry. But, if you move the chapter entry into another Collection, the chapter remains in the book but is not accessible anymore (the link to the chapter is not updated when moving the chapter entry).

      I think if all of this appear since the beginning, it means there are some severe flaws and inconsistencies in the very architecture of Papers 3, making it totally unreliable, and it seems their support is not very responsive to those concerns. I’m afraid this software has no future.

      Like

  2. Yojimbo says:

    Damn, that’s a shame. I was considering upgrading from Papers 2 to 3, and at first I was glad that they were using Dropbox, rather than asking you to pay a subscription for their own cloud service, which seems to be the route a lot of the other biblio software is taking. But this non-standard naming (I think Zotero does the same, unless you install some special plugin) is really annoying. All the biblio software already locks our data in to a massive degree (migrating never works well), so to add an extra layer of non-interoperability defeats the point of using Dropbox.

    Like

  3. I completely agree. I love papers. It is my go to application for managing journal articles, but the new database situation is a no go for me. I made a comment about this issue in my feedback for the beta. I sure hope others speak up as well. I cannot imagine this new way of storing documents is vital to its functionality, but who knows. Thanks for the post!

    Like

  4. Che-Min Chou says:

    I am considering move from Papers 2 to 3. I also found this problem, too.
    But I find this problem seems only when I use Dropbox as the Library.
    If the Library is placed in the local folder, both the naming rule and setting database structure are functional. I think you can try it. However, this would lose the ability to sync between Mac and iOS, but the current “Sync” in Paper 3 for iOS is also a tragedy.

    Like

  5. Pingback: Update on file organization in Papers 3 | Academic workflows on Mac

  6. Bob says:

    I tried to restructure my Library to be arrange it by Category, Author as you showed above. Any clue why it only did some of my papers, if left many in Year folders; they are still in Papers 2 library but now I have both Author and Year folders under the Articles category (but I checked, no duplicates). I tried rebuilding the library data base. Any clue why this is happening?

    Also, in this file structure, do papers from first authors with the same surname end up together (I tried to compensate from this by having Last Initial in the filename).

    Like

  7. Aleh Cherp says:

    Bob, did you use Papers 2 or Papers 3 to re-organize your library?

    Like

    • Bob says:

      I only have Papers 2, and I changed the library by changing the preferences as you show in your post.

      Like

      • Aleh Cherp says:

        I have not experienced anything like this. But now I checked my folders and indeed under Articles there are a few year folders. They do not contain anything of interest though (just some empty folders) – all of my pdfs are arranged as required. Concerning the authors with the same surnames, yes indeed Papers 2 puts them in the same directory, which is not a big deal for me as I rarely have such cases. You can however specify subdivision by author’s initials rather than only surnames.

        Like

    • Bob says:

      I checked several of these folders: each time the paper is also in the correct place by author, they appear to all be duplicates. There are few enough I can do them by hand, I’ve done several years so far and no exceptions, they are not required. I’ll post again if I find exceptions.

      Like

  8. Bob says:

    FYI there were exceptions. Maybe 20% of the papers in question had multiple copies. I would suggest to anyone doing this to go over each one by hand, especially if space is an issue.

    An interesting thing is Papers 2 makes errors with first initials, so for instance papers by Sica R got put in as Sica T and you can’t change them or it loses the paper. But that is minor.

    Like

    • Another deception from papers3. I’ve never seen such a terrible launch like this.

      Like

      • I use a hazel rule sync papers to goodreader through Dropbox. I show the PDF in finder from papers, tag the file as red and hazel copy to my unread files in a Dropbox folder synced with goodreader. After reading, I tag it green and hazel copy it back to papers2 folder.
        But now it is gone… And papers3 sync with Dropbox is a disaster. Files don’t sync back from iOS and large library take unacceptable time to sync. And frequent crashes make it unreliable for a real research.
        It is really sad for a great app like this to become so terrible. Workflows were destroyed and a new UI and design (which I found terrible and looking like a pirate copy of iOS design principles) were a priority, instead of a working and functional app. They focused on a sync based in workarounds with Dropbox that is not the best option for database sync. And it is working terribly by now.
        I hope they may find a solution for this disaster, faster then the patient of their loyal user base.
        I will stay with papers2 for now and don’t recommend the update for anyone, as it is a alpha paid version.

        Unfortunately I was forced to look for other alternatives. Accept suggestions!

        Like

  9. Mikael Bergkvist says:

    I’ve had it with this software, expensive update, reports of corrupt data, priority on facebook functionality rather than database integrity.
    Fail!

    Like

  10. David says:

    very dissapointed with papers 3. Not worth the upgrade in my opinion. The only feature I was looking forward to was the dropbox sync, but as this article mentions you lose control over organization. In my case, the syncing has been anything but smooth.

    Like

    • Hi there

      I was the same! Been using Papers 2 for years and Papers 3 has sent me back to Sente which is working much better and has come on leaps and bounds.

      Like

      • Aleh Cherp says:

        Was it difficult to migrate your collection?

        Like

      • Bryan says:

        Aleh,
        Replying to your question about migrating to Sente. It was very easy, and worked very well, bringing over my notes from my Papers documents and just generally not causing problems.

        Like

      • Csaba Pusztai says:

        Same smooth transition in my case as well. From my perspective, Papers may have a nicer, more ergonomic GUI, but that is all it may offer to me over Sente. Also, Sente is scriptable, which is now very important to me in handling my pdf notes.

        Like

  11. Martin says:

    My take is:

    – Grayish abstract GUI is really boring. The debate on skeuomorphism took things too far in the other direction. Colors please.
    – The excel look of the papers listing just bloats the screen.
    – The grid view and cover flow layout are just terrible user interfaces for recognizing text documents….why aren’t they removed already?
    – Author and conference listings are a bit nicer but still very buggy. You can’t see the number of papers for a specific author or conference. How do you find and merge duplicates? All metadata is not complete.
    – Basic text-editing things like bold, etc, is removed from the note taking section of a paper.
    – Manual ordering of papers in a collection is still not available. Impossible to make priority lists.

    There’s a lot more. Basically I think Papers3 is half-baked and not ready for release. Which I guess why it is still in beta.

    Like

  12. SMoore says:

    I wish I would have read this earlier. I appear to be one of those persons who has lost their papers 3 library. Every time I try to open an article, I now have to go to the library proxy and reupload the paper. I can’t seem to fix the problem. I have tried to reimport my papers 2 files, which I fortunately still have, but I am unable to. I will return to using Papers 2 until something better comes along.

    Like

  13. Bla says:

    I was a avid supporter of papers but enough is enough. In addition to all the comments above the thing that ticks me off the most is that many users have libraries, which are easily bigger than 2GB, thus forcing them to pay for extra storage on Dropbox. It’s not about the 9.99$ for Dropbox with more storage. It’s a matter of principle. You cannot force people to subscribe to other paid services I order to use your (quite expensive) software. Very disappointing. I will be looking for alternatives. Anybody tried Sente?

    Also it really annoys me that the Papers forum has been locked down. No more public posts? I guess they are embaressed about all the complaints!

    Like

  14. Bla says:

    Forget Sente, way overpriced subscription model

    Like

    • Oliver says:

      Sente recently changed their pricing model:
      “Effective immediately, a Premium upgrade will cost $59.99 and will come with a total of 5GB of permanent sync space (instead of the old 1GB).”

      http://www.thirdstreetsoftware.com/blog/2013/10/price-change.html

      At least that’s what the blog says. That’s a one-off payment of $59.99, not a subscription fee (The upgrade page is confusing because it at certain points it talks about 1gb of space, and 5gb is still offered on a subscription basis). My library is currently 2gb, I don’t have a paid Dropbox subscription, so for my needs anyway, Sente would be cheaper than Papers 3.

      If I remember, the first release of Papers 2 was messed up too, with lots of missing features. That was when they first locked the forum down and made it non-public. On the plus side, they were pretty good about adding lots of features (back) in to Papers 2, and I think Papers 2 still has the edge over the competition (although in many cases that’s not saying much)

      Like

  15. Bla says:

    I have been searching for a while (on and off) and there does not seem to be a viable alternative.
    Sente: overpriced subscription model
    Papers 3: see above
    Zotero: too little storage space
    Endnote: to expensive
    Mendeley: Elsevier

    Mind you, I am not opposed to paying for good software. After all I was a Papers2 customer.

    But there is a bigger point to be made here. I am sick and tired of having to make account everywhere. One reason for using papers2 was that you could wifi sync between your devices without going through some external servers. If you wanted you could still place the library on say your main computer into e.g. Dropbox. But the sync worked simply device to device. Granted it had/has to be done manually. But who cares. Why they would kill such a nice feature in Papers3 and force me to buy Dropbox storage?

    I guess I will go on using Papers2 for a while. Maybe I have program my own software ;)

    Like

  16. Pingback: What is going on at Mekentosj with Papers 3? | Ruminating...

  17. Sebastien says:

    Let me preface this by saying that while I am as annoyed as most of you about the lack of editable file structure, writing a proper syncing engine is one of the most difficult things in programming and I can understand why it would work better for the papers team to have their current implementation. (Also, the likely reason for the crazy naming of the filenames is that they are using a hash function that uses a complex formula to produce a unique code for each file in order to avoid syncing duplicates. This also reduces syncing errors and makes resolving errors easier.)

    That said, I have a workaround for Mac OS that seems to work for me, but please USE AT YOUR OWN RISK. This method does not have the securities of the built-in sync (e.g. the lock files and the annoying coded filenames) so to avoid conflicts you should avoid running Papers on two computers at once. Also note that this is not compatible with the iOS app (though you can still access all the files through Dropbox on iOS or Android. You won’t get all the annotations and notes).

    I’m using beta 9. I don’t know if they changed the filenames in Dropbox, but I’m not interested in trying.

    1. Disable Dropbox syncing in Papers.
    2. Quit Papers.
    3. Open a finder window and locate the Library.papers3 in your Dropbox folder. Drag the Library.papers3 file to a new home somewhere outside your Dropbox folder. For example, you can put it in the Documents folder. Also MAKE A SECOND COPY as a backup in case something goes wrong, e.g. on the Desktop.
    4. PAUSE DROPBOX SYNCING.
    5. Open a terminal by going to Applications>Utilities>Terminal (or type “terminal” into Spotlight (CMD-space))
    6a. Type “cd” (without the quotes) to make sure you are in your home directory
    6b. Type “cd Dropbox” to go into your Dropbox directory.
    6c. Type “ln -s ~/Documents/Library.papers3″
    7. This will have created a symbolic link (aka alias, shortcut) in your Dropbox folder that points to the library that is stored on your local drive. You can open a Finder window to verify that Library.papers3 is present in your Documents folder and also in your Dropbox folder (the one in your Dropbox folder should have an arrow on the icon). Note you cannot simply make an alias using the Finder as this will not sync to Dropbox.
    8. Open a Finder window and navigate to your Applications folder.
    9. Hold the “option” (or “alt” on some keyboards) key while double-clicking the Papers icon. This will bring up a dialog to change your library.
    10. Click browse, then select the Library.papers3 file in your *Documents* folder (not the one in Dropbox!).
    11. You should see all your papers etc. Open the Papers preferences and make sure Dropbox syncing is still off. In the “Libraries” tab you should have access to the organizational structure preferences again. Set them as you wish, then wait for Papers to do its changes.
    11a. ADVANCED: If you would like easier access to these files, I recommend you enable the “Category” option as the top level in the subfolders. Then see below.
    11a. TO ACCESS THESE FILES IN THE FINDER, go to the Finder and locate your Library.papers3 file. Right click, and select “Show Package Contents”.
    12. Turn Dropbox syncing back on, and wait for it to sync everything (it could take a while). Thank Dropbox for syncing symbolic links.
    13. Test by importing some files into Papers, and opening the library on a different computer.
    14. To access the files on an iOS or Android device, use the Dropbox app (or your favorite 3rd party client)

    Phew! Hopefully that works!

    ADVANCED EASIER ACCESS
    If you created the subfolders for categories, your PDFs will be grouped into a small number of folders, one of which is Articles. (NOTE. In my installation, there were lots of folders that were not moved into the Articles folder. These almost all contained old files that had duplicates in Papers already. However, you will want to check all of these. It’s tedious, but data loss is worse). You can make this folder one-click access (instead of having to right click and reveal the library contents each time) by opening a terminal and doing the following:

    cd
    cd ~/Documents
    ln -s ~/Documents/Library.papers3/Articles

    This will create an Articles folder in your Documents folder with direct access to all your papers. If you want to place this somewhere else or create a different name for the folder, you can generalize the commands:

    cd
    cd ~/Desktop
    ln -s ~/Documents/Library.papers3/Articles Papers

    This will create a folder called “Papers” on your Desktop containing direct access to your library. Change the names above to match your specific situation.

    IOS APP TROUBLES

    Now, if you have the iOS app, I wish you luck. It seems that syncing with iOS wipes the database file in the Library.papers3 file, so not only do you have no papers showing up in the iOS app, but it resets the desktop app so that it thinks you have no papers left (though this didn’t happen in beta 9 at least). I’m assuming this is some precaution the developers took while setting up syncing.

    Anyway, this is what I ended up doing THAT DID NOT WORK. So don’t try it if you don’t want a headache. Also BEFORE YOU DO ANYTHING, make sure you duplicate your entire library file somewhere safe (e.g. your Desktop). You really only need the database file, but it doesn’t hurt to copy everything else.

    1. Delete the iOS app without opening it first.
    2. Go to the App store and redownload the app using either the purchases tab or the search function.
    3. Go to the app settings, and hit “unlink from dropbox”. If it asks, delete all the files.
    4. Relink the app using Dropbox.
    5. Hit the synchronize button (I had to do this a few times) until it starts syncing (or asks you to select your Papers library, in which case select it)
    6. Hit the synchronize button
    7. Watch it not do anything except ruin your desktop setup and then thank Dropbox for storing previous versions of your documents on their servers and yourself for making a local backup.

    Like

    • fmg says:

      Question for Sebastien: If you set up the link from dropbox to Library.papers3 as you suggest, does dropbox see this as a monolithic file, or as a directory? That is, if the papers3 program changes some files inside the package Library.papers3, does dropbox update the whole 1 gb or whatever Library.papers3 or does it just update the changed files inside Library.papers3?

      Like

  18. smrs says:

    OK, i’ve been going back and forth between Sente and Papers, because I’ve just had it with Sente. Two years ago I posted on the Sente support page that you can’t add citations or scan a document with “track changes” turned on (um, what?? you mean like when you are working on a revision????!) and you STILL can’t! I’m so darn frustrated. I’ve also had it with Sente’s clunky attempt at citation handling in word documents. Looking over a manuscript I had submitted for publication, I can now see that for some reason Sente had stripped about 10% of my citations out on that last scan. What??! Why?? I’m so embarrassed that I submitted this and the reviewers thought I had just ignored the literature. Sigh. I am having trouble getting the hang of citing papers in my word document…

    Like

  19. smrs says:

    I hope this isn’t thread hijacking, but I’m pretty thrilled to find other mac academics to ask these questions! I’m done with Sente, now debating merits of Papers 3 vs. Mendeley. Unfortunately, neither seems to have anything even close to Sente’s ability to connent directly to my library resources and import references and PDFs right into my database. What are the major bonuses/drawbacks of either Mendeley or Papers3 (aside from nasty file management from Papers3)?

    Like

    • Aleh Cherp says:

      I think Papers can seamlessly import resources/references directly from remote databases.

      Like

      • smrs says:

        I have now figured this out, the process was not transparent at all. I am used to explicitly connecting to my library resource though the software (e.g., Endnote, Sente) but it works differently in Papers3. I added my library OpenURL info in the preferences, and when I use the search feature, if you look really quickly, you can see it connecting through my library proxy to the search engine. Still would prefer to have my library URL listed as a “search engine” in the search window.

        Like

  20. Peter says:

    Hi Gang,

    Great discussion. I’ll cast my vote (for now) for Zotero (and sync with Devonthink for searching) but clunk along without in-app pdf reading and annotating (I use Acrobat for that). I was considering the switch to Papers 3 but after the negative reviews here I’m starting to wonder. If Devonthink would include better reference management it’d be a no brainer. I’ve tinkered with Mendeley but I’m a little old school and prefer to keep things out of the cloud for now (even though I know they have a desktop version). I’m also wondering if there have been any advancing in terms of cross-app pdf annotation searching (with e.g. Devonthink). i haven’t kept up with tech dev for about a year.

    Like

  21. Annie Yu says:

    Thanks for the post. I’m wondering does anyone here has the sample problem with me. my papers2 kept crashing just right I open the app. I’m not sure whether it caused by my new OSX 10.9. It’s a bit annoying because it kept asking me to send out report.

    Like

    • tobias hanrath says:

      I’ve had the same problem with papers 2.6.4. Contactd mek and initially got a reply about the library being ‘corrupted’ this has been going on for 3 weks now, customer support from mek is irresponsive. sad to see how fast this software has gone down the hill.
      since mek is irresponsive, if anyone else has suggestions on how to get papers 2 functional, please let me know.

      Like

      • ashok says:

        you can do a dump of the database. It is an sqlite3 Db. Open it up in sqlite3 and then dump it as a text file. You will have to modify the sql script it generates to remove the update commands and dump it back to sqlite3. I will post more details if you need them

        Like

  22. Tim of Canberra says:

    Bookends + scrivener + mellel + devonthink for me – stable robust and quick.

    Like

  23. Todd says:

    Regarding SYNC:

    I’ve been using Papers2 with SugarSync to sync between my two desktops and laptop. SugarSync can be sometimes wacky, but has been stable for the last 8 months. I use it because it offers 5GB space on free account.

    Has anyone used BitTorrent Sync? I started months ago to sync large Illustrator files to work on wherever and it works phenomenally for this purpose. It is peer-to-peer syncing (no cloud) and therefore no limits and incredibly fast. But because it is so new I have been hesitant to use with a database file that if left open could become corrupted (I think).

    I do not use an iPad with papers so perhaps my usage is more straightforward.

    Like

  24. Csaba Pusztai says:

    I just gave a third chance to Papers (Ver. 3). I started from scratch, I thought I would build a library for my ongoing projects rather than use my big ol’ library (actually built in Sente). I filed 30 PDFs last night, matched the ones that needed bib info, added keywords, did some highlighting. Neat. Today I added two further PDFs. I noticed they were not automatically renamed and moved to the correct sub-folder (Articles/year/author). I could not get Papers to do the job, verified the library from within sent, it restarted and said it could not re-load the verified library. I try to point Papers to the library by going into Preferences, would not work. Actually it still remembers the path, but only loads an empty library. That is the so-called verified library. Papers may have the nicest GUI, clean looks, but —excuse my French here— is a large pile of crap. I am happy that it did not happen to me with a larger library. I have the PDFs, so I will just go back to Sente. Or I don’t know. It is kind of frustrating. Humans have managed to build spaceships to fly to the moon, but we don’t seem to be able to get a reference manager work properly.

    Like

  25. Csaba Pusztai says:

    I have been trying to figure out where Papers3 stores its database. If I open the file (folder) with the extension “.papers3″, I can find my PDFs, but there seems to be no database file there, even though I just added a reference, so Papers has created the file some place. Hidden files are made visible, but I still can’t see anything relevant.

    Like

  26. Aleh Cherp says:

    Check this comment http://blog.macademic.org/2013/10/18/papers-3-a-step-in-the-wrong-direction/#comment-7390 – it worked for me to get the files in Papers 3 in some sort of an order

    Like

  27. Csaba Pusztai says:

    This came from the Papers team today, but I just realized that the update at the end of the post does say the same thing. Funnily enough, I did not have Dropbox syncing ON when all this happened. And when I tried to look up the potentially deleted .papersdb file through the Dropbox website, it did not log anything related to Papers being deleted.

    ———–
    Hi Csaba

    I’m afraid that if you use Papers 3 for Mac to sync with Dropbox, you no longer have an option to organize your files by, for example, author, title, year etc. This is because we can’t technically guarantee where the files referenced in the Papers library are at any point in time. In order to be able to offer reliable syncing of PDFs across different devices we have to disable custom file renaming when the library is stored on dropbox and have Papers control file naming.

    We are looking into a way how we could re-introduce the file organization with Dropbox syncing but we can’t guarantee if/when it would be available.

    I’m sorry for the inconvenience.

    Best wishes,
    xxxxx

    Like

  28. Quick access to PDF file is a requirement for academics and other knowledge workers. In my book, _Cognitive Productivity_, I described several strategies to do that–some involving LaunchBar. Unfortunately, Papers3 breaks some of these strategies.

    – The Mekentosj Papers3 upgrade procedure preserves neither the original folder structure nor the file names. This breaks LaunchBar shortcuts. E.g., I have a *very* large number of papers (in my Papers2 folder) that I could quickly access with LaunchBar shortcuts. I normally get around this problem by creating a symbolic link from the old Papers folder location to the new one. Unfortunately, my old shortcuts are still broken, but I will try reverting my LaunchBar index when I have the time. That *should* revive the old shortcuts.

    This problem exposes a weakness in ObDev’s LaunchBar. LaunchBar could be designed to robustly handle cases where users move files and folders. They could, for example, store redundant index information in metadata (extended file attributes); or they could use more sophisticated techniques. However, really Mekentosj should by default preserve the same folder and file names from Papers2 to Papers3. Many of us used Papers2 exactly because files were stored in a predictable, accessible way on the file system

    Also: Launchbar doesn’t have visibility of papers in the Papers3 folder. Users need to add each Library.Papers3 subfolder’s name manually to the LaunchBar index. (Articles, Books, Custom, Media, Patents, Reports, Styles).

    I hope that Mekentosj addresses these problems soon, before exiting Beta.

    Liked by 1 person

    • I’ve managed to get Spotlight to index my Papers3 library (Library.papers3). I did this by adding Library.papers3 to the Apple → Preferences → Spotlight Preferences → Privacy pane, and then removing it. This was based on a tip from Francine Schwieder on https://discussions.apple.com/thread/1217221?start=0&tstart=0

      Otherwise, I would have used the mdimport command from the command line. That should do the trick. cf:

      https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/man1/mdimport.1.html

      Luc

      Like

      • Aleh Cherp says:

        Great idea! But I can’t add Library.papers3 to Spotlight privacy pane (it’s not selectable). Any tips?

        Like

      • Hi Aleh,

        1. Open Spotlight’s privacy pane.
        2. Open the Finder folder that contains your Library.papers3 folder.
        3. From the Finder, drag and drop the Library.papers3 folder directly to the Spotlight pane.

        That works for me. I just tested it again. I’m using the latest Mavericks release. If that fails, there is also a “+” button in the privacy pane you can use.

        If that fails, there is the mdimport command.
        1. Open terminal.
        2. type mdimport -r
        3. Drag and drop the Library.papers3 folders into this Terminal window. That will copy the pathname after the “-r ” argument. **Be sure to leave a space between the “-r ” and the path.
        4. Hit the ENTER key in that folder.

        I’m quite busy next few days but I will likely post a blog article on CogZest.com that describes how to work around these Papers3 issues. Papers3 has issues; but in many ways it is an improvement. I’m inclined to stick with it at this point.

        (The problem here isn’t just Papers. If Dropbox and BitTorrent provided a good PDF search tool, we wouldn’t need Papers for iOS so much. iOS Syncing technology is still very primitive. )

        Like

      • Aleh Cherp says:

        Thanks for the tip! I still can’t see the results (i.e. Spotlight searches do not seem to reach inside Library.papers3). I hope it will also open the package for DevonThink indexing ;/ Anyway looking forward to your post on CogZest.com and good luck with what you’re doing now!

        Like

      • Aleh, my apologies to you and your readers! The effect of what I did was to make the results show up in LaunchBar _not_ Spotlight. I.e., (1) I added the folders inside the Library.papers3 folder to the LaunchBar index; (2) I did the spotlight manipulation. I know the spotlight manipulation had an effect, because I could see the OS X metadata processes using “top” (and hear my MacBook’s fan go wild). I did this test twice. I know that LaunchBar uses Spotlight information when it can. But the PDFs still don’t show up in Spotlight itself.

        So where I’m at now: I can search Papers3 PDF’s by file name using LaunchBar. I can search for the content of Papers using Papers3’s search tool.

        I will investigate more when I have a chance.

        Like

      • Aleh Cherp says:

        Yes, same for me. I wonder if I need to create a duplicate of every reference file – one for tagging and indexing and one for storage in the Papers3 database. I was seriously considering such a workflow for Hazel, but one problem is that then I will need to manually name at least one of the files, which is annoying. (and of course it’s super annoying to keep 2 copies of the same file).

        Like

  29. Papers3_Fail says:

    Thanks for providing this review. Papers 3 is a joke – I tried it recently and it does not even return simple search results, even for Nobel laureates! Devs have stopped allowing comments in public forums and do not respond to support requests effectively. Papers 3 is a massive fail. Don’t upgrade.

    Like

  30. Aleh, I meant to write “Hit the ENTER key in that window” not “in that folder.”
    I’m basing this on the MAN page. I also gave it a whirl, but by this point my folder was already indexed. (My papers folder is a big one. It takes a long time to index).
    See also http://www.macosxtips.co.uk/index_files/terminal-commands-for-improving-spotlight.php

    Like

    • Finally got back to this. A very simple solution occurred to me to get Spotlight to index the Papers3 library. But it’s a “use at your own risk” work-around as it involves defeating Mekentosj’s treatment of the Papers3 folder as a package. So be sure to have backups if you try this. So far it works for my Papers3 library; but there could be side-effects.

      This tip assumes that the folder containing your Papers3 library is indexed by Spotlight. It assumes that Dropbox syncing is not enabled.

      Here’s how it goes:

      1. Quit Papers3
      2. rename your Library.papers3 folder to a temporary name, e.g., Library.tmp (yes, change the extension).
      3. Create a new Library folder (I called mine Papers3Library.)
      4. Move all the files in the Step 2 folder (Library.tmp, in my case, i.e., all your managed by Papers3) to the Step 3 folder (Papers3Library). Spotlight should start indexing this folder (Papers3Library), which may take a while.
      5. Delete the empty temporary folder created in Step 2 (Library.tmp, in my case).
      6. Using Terminal.app, cd to the folder that contains your new Papers3Library folder (where your original Papers3 library resided, cf. Step 2), and then create a symbolic link to it. In my case, I issued:
      ln -s Library.papers3 Papers3Library
      This will make the effects of Steps 2-5 opaque to Papers3.

      Now, launch Papers3 to ensure that you haven’t messed anything with it. Exercise a few of its major functions. Take corrective measures or recover from backup if you did.

      That’s it. Basically, what we’ve done here is to put all the Papers3 PDF files in a regular folder that will be indexed by Spotlight. And we have forced Papers3 to access the new folder via a symbolic link. It might also work to use aliases rather than symbolic links, but I haven’t tried that.

      Troubleshooting tips. In the unlikely even that you’re also having problems with Spotlight:
      1. you might need to tell Spotlight to reindex your drive. See: http://www.macosxtips.co.uk/index_files/terminal-commands-for-improving-spotlight.php
      2. You might also need to use mdimport -r to bring in the new folder (Papers3Library).
      3. You might want to try adding the Papers3Library to the Apple menu/Preferences/Spotlight/Preferences/Privacy tab, closing the Preferences window, and then removing the Papers3Library from the Privacy tab. This can trigger Spotlight to index the folder.
      4. If you are a LaunchBar user and if you have changed the path of the Papers3 library, you might need to update your LaunchBar index.

      Note that it can take Spotlight a while to index a folder or drive. (Several hours in the case of a large drive.)

      NB: I previously tried just creating a symbolic link to the Papers3 folder. While this link enabled Launchbar to index the package contents, it didn’t cause Spotlight to index the folder. Apparently, there’s no way to tell spotlight to index a package folder.

      Before doing all of this, I issued the “lsregister -u” command on Papers3. It did deregister the .papers folder extension but didn’t cause Spotlight to index the .papers3 Library. It may have had a pertinent side-effect but I doubt it affected the outcome of this procedure.

      Like

  31. Everyone should check out beta10. There is a new feature that allows you to access your library through finder via a virtual disk. I can confirm that the virtual disk is indexable for Devonthink – though I had to click around a bit to get the papers to show up in Devonthink. I have not yet figured out what this means for spotlight indexing. In any case, I like that they’re listening. And I very much like where the iOS app is now. Search and import are amazing – and the annotation is superb. There have been a lot of complaints about papers 3, but I’m pretty excited about what they’re doing.

    Like

    • Joetoe says:

      It does sound exciting. Do you know if Papers PDF annotations are searchable/indexable? This would be a game changer for me.

      I have Zotero but considering Papers as a possible alternative. Zotero works well for me but I like the idea of viewing and annotating pdfs in the reference manager (RM), which Zotero doesn’t do but Papers (and several others) does. As far as I know however, no RM makes pdf annotations searchable/indexable in Spotlight / Devonthink so I haven’t switched. (I might as well as keep Zotero which is free and has great support. I can annotate in Skin and run a script that exports them to Devonthink.) However if Papers PDF annotations are now searchable/indexable this would be a game changer for me.

      If any of you have other workarounds for making PDF annotations searchable (unflattened) I would love to know!

      Like

      • No. There used to be a Rob Trew script that would extract highlights and notes as RTFs to Devonthink – his site seems to be down. I’m sure it would need to be updated to

        I think there’s a way to accomplish what you’re doing using papers. From papers, you can open whichever pdf you are viewing in any pdf program. So you can do your annotations in the papers iOS or desktop app. From there, if skim is your default viewer, you can just hit option+command+o to open the file in skim. Then select File–>convert notes, and your annotations will convert over to skim. Then in skim you can run your script. In fact, I think this is what I will be doing for now.

        But are these pdfs even visible to spotlight?
        Right now I am having trouble getting spotlight to pickup the library. The pdfs are aliases in a virtual drive. I am hopeful that this will work eventually though – I imagine spotlight functionality was their intention with this feature.

        Like

  32. Aleh Cherp says:

    Great news, thanks, Chris! But how do you get beta10? I have built 9 and when I check for Updates it says it’s up to date.

    Like

  33. Csaba Pusztai says:

    I have the Rob Trew script, but I can’t get it to work.

    Like

  34. Rosina Lippi says:

    I spent some time looking at Papers 3. To do that properly I imported my Papers 2 database, and I do not like what happened. Just one of many glitches: all my work on authors (correcting, merging) was gone. Instead of one version of an author name I suddenly had three or four (again). Papers has never been good about documentation, and that’s a real issue when there are such fundamental, large-scale changes. And something that has never made sense to me: why do they have a ‘public’ discussion forum where every thread is private? Talking to other users is really useful for a whole lot of reasons. I’m going to go have a look at Sente.

    Like

    • Csaba Pusztai says:

      Papers was my first purchase in terms of reference managers….back at 1.0. I then switched to Sente, but I keep an eye on how the competition evolves. I gave Papers 2 a try, and Papers 3 as well. Honestly (from my personal point of view), Papers excels in its GUI….nicer, cleaner than the others. And that is where it ends in my opinion.

      Like

  35. Pingback: Papers 3 is here | Academic workflows on a Mac

  36. Joetoe says:

    Does anyone know of recent comparison reviews of Papers, Bookends and Zotero? (I’ve heard negative things about Sente’ business model.)

    Thanks Chris B for the workflow tip exporting annotations to DT via Skim but sure wish there was a way to avoid that step.

    Are Papers’ tags searchable from spotlight, etc? I haven’t been about to get DT see my Zotero tags so I’ve had to re-tag in DT alt Leap.

    Like

    • David says:

      Just got this from papers:

      Since the beginning Papers has had the ability to organise your files for you. We’ve now taken this further in Papers 3 with a new file browsing feature. You can view your library using Mac OS X’s Finder or any other application using your chosen file organisation settings as before (available as “All Papers” in the screenshot below), but also navigate to your PDFs via the same criteria like authors, keyword, collections, sources as you can when using Papers itself. Once you’ve set it up, you can view your library just like any other folder on your computer!

      Like

  37. emzed2 says:

    Hi all – Matias from Papers here. Just to complete the story on the file organisation feature changes in Papers 3 — the new system introduced in 3.0 offers a lot more power than what was there in Papers 2 and before. During the beta we temporarily took out the customisable file organisation for Dropbox organised libraries, but the file organisation feature is now back, and more solid than before.

    During the beta process for Papers 3.0 we temporarily removed the file organisation for Dropbox synced libraries because we could not guarantee for libraries synced on multiple devices that the library metadata and PDFs remain consistent — this was a hard limit of the combination of technologies that Papers builds on, and not giving chances for losing your PDFs had to take priority. Meanwhile we then implemented this new safer, more powerful (I hope you agree!) system, and will be rolling out updates to it in future Papers releases of course — what you see is 3.0.

    The ability to do Spotlight searches for files on the Papers volume using Finder and other applications is definitely something high up on our personal wish list of features, and we hope to put it together. I can’t make a promise of if or when that would happen, but we’ll do our best.

    Like

  38. Les R. Becker says:

    I upgraded yesterday. Thus far, a big mistake. I will maintain my Papers2 install for a while.

    LRB55

    Like

  39. James Mickley says:

    Those of you complaining about Papers 3, just know that this is unfortunately standard behavior for Mekentosj. I’ve been using Papers since ~2007 and while I depend on it greatly, I’m thoroughly displeased with the way the developers handle things.

    During the era of Papers 1, users were “promised” features such as in-text citation, highlighting etc. repeatedly. They were “almost finished” and “just around the corner” or “in the next update” for a good 2 or 3 years. If people complained about being strung along in the forum their posts just got deleted. Meanwhile, one of the reasons for the wait clearly seemed to be the developers focusing mainly on the iPhone and later iPad apps. Those people who’d been using Papers for Mac for years got highlighting etc more than a year AFTER the iPhone did.

    Then Papers 2 was released and as a paid upgrade, almost as much as the software itself. They saved all those nice features for Papers 2. Papers 2 was really half-baked at the beginning too. Only some of the new features were there at the start, many of the old features were gone and Papers 2 was fairly buggy to boot. The release happened too soon, was terribly managed and seemed to have everything to do with profit and very little to do with users. It also coincided with a new OS version (Snow Leopard) and Mekentosj forced a lot of people to upgrade by dropping support from Papers 1 for the new OS.

    Now they’re just doing the same thing with Papers 3. To their credit, I expect some of the old features will come back in time, but I don’t think Mekentosj is reliable at all with doing this in a timely or non-deceptive way.

    My personal (and controversial) 2 cents: Find a cracked version. Don’t pay unethical and underhanded developers. Especially if you want Papers 3.

    Like

    • emzed2 says:

      Hi James — I can see how it can be frustrating that it takes us time to deliver some of the highly requested features such as annotations which arrived in Papers 2.1. I am in fact one of the authors of this annotation feature you mentioned and it’s an interesting case to bring up — I implemented it together because I too had wanted it to be there since Papers 1 and due to the much improved framework we had built as part of Papers for iPad where annotations were brought in first, and during the Papers 2 cycle it became possible to put it there at Papers 2.1. We did a *lot* of groundwork to get to that stage, and it’s very much the same situation with also for example full bidirectional syncing between Mac versions — it simply took time to get the application into a state where this could be done, and could be done in a reliable way that meets the kind of requests we get from our users.

      Meanwhile all these technical things happen, in order to develop the product further us the Papers developers also need to eat, pay rent, so there is a business model behind the product which involves occasional paid updates which bring new functionality. The Papers model is really simple: you get a 30-day free, full featured demo during which you can decide whether you like the app or not, you get free updates to that for several years (for Papers 1 this was the case for some four years). We do our best to respond to support requests be that from demo users or paying customers, and we support the older versions even once the newer version is out. I can understand your frustration but I simply do not understand suggesting using cracked versions of the software. Not only are you suggesting something illegal depending on the country you pirate the software in. Set aside that, certainly by mine or I bet by many of the readers’ definition of ethical behaviour, it does not qualify. If being ethical is a consideration for you, there are alternative products with different business models out there, I’d suggest trying out some of those. On the ethics of Papers development, I assure you both myself and every other developer and support person in the team are listening in and responding to feedback we receive the best we can, and we try to make it very clear when responding to feature requests that we can’t know for sure if or when we’ll be able to ship it… unless we are very certain that the feature is ready to go out.

      Like

      • Aleh Cherp says:

        Matias, I think Papers is an amazing product (and I have already paid for Papers 3 ;), so I believe it’s worth it). But there are two points which I can’t over-emphasize:

        1) Mac (or PC) editions should be prioritized; it is there most heavy-duty serious academic work happens; true, we make notes and occasionally read on iOS, but writing, the core academic activity, by and large occurs on traditional computers. That’s why I was disappointed to see that Dropbox syncing (an iOS-focused feature) nearly wrecked file handling;
        2) We need access to our pdf files not only through Papers, but also through Finder, Spotlight, Leap, GoodRead, DevonThink and tons of other applications. In the same way as text editors should keep documents in an interchangeable formats (plain or Markdown) a pdf-management software should preserve access to pdfs.

        Like

      • macbee says:

        I’d like to add that a lot of my work, even when away from desk, is done in areas and environments where wi fi or other such services are simply not available, unreliable or too expensive to access. Transfer of large files using Dropbox or other cloud services is simply not practicable.

        In addition to Aleh Cherp’s comments about academic workflow, when doing field work, I need the facility reliably to back up my databases and other files on a regular basis between my main and secondary computers. Annotations, notes, local files, manuscript updates all included – not all my Papers usage consists of search and match.

        I think the Papers 3 interface, and its improved editing etc, is pretty good and a vast improvement over Papers 2; however, syncing for backups need to remain local – note that I’ve already paid for the upgrade, although my patience is finite.

        Like

  40. labrat says:

    I hate the new interface. I loved the side bar on the left with all the folders I needed, organzied and the already set “My papers” That is all gone and with it the easy access. Why is there this trend to destroy perfect programs (almost perfect), see also Apples miserable attempt to “upgrade” keynote… I am going back yo Papers 2.

    Like

  41. I have been a Papers user since v1. And I have been very satisfied with Papers 2. However, I have held off on Papers 3 because I anticipated a number of problems. The same thing happened when Papers 2 was first released. It was basically unusable for the first few months, but after that, they finally got it together and it worked beautifully. I expect the same will happen here, I just don’t understand why Mekentosj insists on releasing new versions with so many issues, as it needlessly hurts the company’s reputation.

    Like

  42. Roy Smith says:

    I have also been a long term Papers user and rely heavily on it for keeping many academic projects in order. But having easy access to the PDF files with other software is absolutely critical. For example, I use unison for file synchronization between various Macs. If the library appears as a single file then it will need to be copied in its entirety with every paper addition.

    I haven’t upgraded to Papers3 yet, but can anyone shed some light on whether or not Papers3 will have the backup and access problems that I’m concerned about?

    Upgrading from Papers1 to Papers2 was a painful process, taking months to get back to the same functionality. I hope that Papers2 to Papers3 is more smooth, although having been bitten once I’m waiting until I’m sure that these issues are sorted out.

    Like

    • Sebastien says:

      Roy,

      The library appears as a single file to the user in the Mac Finder, but it in fact contains every individual PDF. A similar thing happens for applications. If you go to the finder, right click on an application, and select “Show package contents”, you’ll see all the files present inside, even though the app file looks like a single file. I don’t think there would be any problems for syncing/backup, as long as Papers isn’t open on both computers simultaneously.

      Sebastien

      Like

      • Carl Joseph says:

        This is quite remarkable. Why encapsulate all the PDFs like that? With Papers2, I just put my Papers library into my DropBox folder and it syncs perfectly well. With Papers3, it seems as though if I do something similar, it will sync the entire massive combined file each time there is a minor change. What a waste.

        Like

  43. fmg says:

    Roy, You can access the contents of the package Library.papers3 as Sebastien instructs, or also via soft links pointing at subfolders of Library.papers3. The two synchronization tools that I have used, namely Chronosync and Dropbox seem to work fine with Library.papers3. The former can be set to “dissect” packages. The latter actually treats the Library.papers3 package as an ordinary folder. (Just to be clear, I am NOT using the official sync method built into Papers 3.) It would not be hard for you to do a trial of Papers 3 and test whether Unison is able to to a sync without copying your whole library each time. Please report back.

    Like

    • Roy Smith says:

      Thanks fmg & Sebastien. Knowing that it is a package rather than a file is helpful and may make the sync work. I don’t sync my Applications folder so I don’t know how Unison will handle these cases. I’m already careful about not having Papers running on both machines when syncing via Unison so that issue is unchanged. I’ll report back on Unison syncing when (and I guess if) I test out the upgrade. After the Papers1 to Papers2 transition experience I will be waiting for some time yet before deciding about the upgrade.

      Like

  44. KSB says:

    Long-time user of Papers 1 and 2. Tried out Papers 3 and found it to be extremely unstable. papers2 was working perfectly so I just went back to that. Now I’m noticing that recent updates to Papers2 have coincided with more errors in that software. I never had any significant issues, but now find papers missing from the database and search functions that are ceasing to work. Simple search for an author name no longer returns any results. Not certain if this is coincidence or if v2 is being crippled to force upgrades to v3?

    Like

  45. Larry Hinman says:

    I made the mistake of upgrading to Papers 3. I’m going back to version 2, and now have to figure out how to export three week’s worth of work into a format that I can then import into Papers2. Not exactly how I want to spend my time!

    Like

  46. johnres says:

    Well, you can use Long Path Tool…….

    Like

  47. Morrison Hodges says:

    I’ve used Papers since v1. Version 2 worked for me. Version 3 doesn’t work for me (can’t properly import version 2; can’t get metadata for new PDFs; no response from Mekentosj when I complained about this). How can I go about getting my money back?
    Morry Hodges

    Like

    • Morrison Hodges says:

      After I made the post above yesterday, I went back online to the Mekentosj website, and found that they are now part of the Springer group, a giant publishing house. Quality of product is now trumped by making money. The only thing that could be worse is if they had been acquired by Elsevier. I have asked my credit card company to get my $39.50 upgrade fee back. I would advise others to not upgrade or buy the program. Sad….Papers, I hardly knew ye……
      Morry Hodges

      Like

  48. rkopietz says:

    Thanks for this post. I cannot believe that they changed it and that they have not a single piece of information about this substantial change on their website. I send them feedback via their form. Let’s hope they fix this soon.

    Like

    • Larry Hinman says:

      While I have no love for Springer Verlag, and I am deeply dissatisfied with Papers 3 and will be going back to Papers 2 for the foreseeable future, I wouldn’t dismiss it just because Springer has purchased the company. The challenge for those working on Papers3 will be to turn this into a sufficiently rich source of revenue for Springer while at the same time developing a product that we as users find increasingly useful.
      That said, I’ve been increasingly puzzled by the inflexibility of the Papers team in terms of the categories for classifying entries. Not only is there no option for working papers (a glaring omission), but I have no idea how to classify a lecture on YouTube, for example. The categories are all 20th century. Even if there were a few user-defined categories, that would be a help. For example, how does one categorize a particular art exhibit, rather than just a single painting or the exhibition catalogue. These are, at least for me, crucial omissions that I would think could be remedied relatively easily, but after making this suggestion for almost two years, I’ve seen no movement. I even requested a map of all the categories and subcategories, something that would help many users. From what I could farther in the response, they don’t even have such a paper. How, if you are writing software to organize information, do you not have a map of your own categories? This is not an issue of corporate influence, at least in any obvious sense.

      Like

      • Aleh Cherp says:

        Larry, thank you for this clever input. I totally agree on all counts. It’s hard for a small company to survive and develop, so the acquisition by Springer may be a logical move and it may even play out well. I am also frustrated by the lack of the “Working Paper” category (was looking for it yesterday).

        Like

  49. fmg says:

    Categories: the problem is not necessarily that the available categories are 20th century, but that the developers have not though of, and cannot possibly think of, all the categories which their users might want. I want a category for course notes or lecture courses, not exactly a 21st century idea. Users should be able to define their own categories.

    Like

  50. yjm says:

    Papers 2 user working out when/ if to upgrade to Papers 3.

    I wanted to ask whether 3.0.15 (and whatever the latest version of the iOS app is) improves on any of the issues people have been highlighting above.

    I’m not so concerned about having human-readable pdf names, just core data integrity, stability, usability and so on. It took a while before Papers 2 was fit to use. Is 3 still beta-ish or is it ready for daily use?

    One bug with Papers 2 and the old iOS app which never got fixed (despite at least 2 bug reports from me), is that the notes field for papers that did not have a pdf attached to them (ie books, the non-electronic variety) did not display correctly in the iOS app. Each book you looked at would display the same notes field as whatever the first one you clicked on to had, so it looked as if all of your books contained the same notes. It looked like a terrifying instance of data corruption, but I think it was just a display problem, as on the Mac app the books still had their correct notes attached to them. Does anyone know if this has been fixed in v3? (not that I should have to pay for a bug fix…)

    Like

  51. Larry Hinman says:

    I upgraded to Papers3, almost went back but decided to tough it out, and now regret that decision. Unfortunately, that means six weeks of research have to be exported from version 3 back to version 2, but the risks simply are too high. Dates have gotten scrambled in ways I still don’t understand. One NHYT article from 2014 was listed as being published in 2002 in the citation, others appeared as “yesterday” or “last week.” Truly bizarre. Moreover, when I “send to Papers3,” Papers receives the article. Usually, if it’s a scientific journal such as Nature, it does just fine. However, if it’s from the NYT or some other newspaper and that article contains references to scientific papers in, say, PLoS, then it pulls the reference to that paper instead–mostly, since it does not change all the metadata. This is the kind of stuff that should only be happening in an early beta release, and I don’t know what else it is messing up. That’s what really scares me. I want a program I can trust, not one that I continually have to spend time monitoring. Today I noticed keywords were scrambled on some of my articles (I don’t know at what point that occurred), and I deselected the incorrect keyword on one article and, before I could select the correct one, the article has completely disappeared. How knows where it went? The inflexibility of their categorizing system, etc., is something that I can grudgingly live with and certainly something that I can anticipate. But this kind of stuff is simply make me feel that I cannot trust Papers3.

    In other words, if you’re thinking about making the jump, don’t.

    Like

  52. Albert says:

    I just moved to P3 and regretted it. I have had tons of problems including errors and failure to register. It’s has now been sorted but I wished I didn’t move to P3. Matching articles is more unwieldy in P3 than P2 and it seems that there is no automatic importing like P2 when you add articles to ‘Add to Papers’ folder. Also, I missed the ability to copy a reference and manually edit it like in Endnote. I find this helpful when dealing with book chapters. Also I wish Papers has a Preview Pane like Endnote.

    Like

  53. ionas says:

    I have been using Papers for years. I made the mistake to update to Papers3…. Suddenly the database got corrupted… really annoyed and disappointed…

    Like

  54. sdv says:

    I just tried to update from Papers2 and it deleted almost all of my pdfs. Now I have none of my articles anymore. The time it will take me to find them all again is ridiculous – not to mention I don’t have subscription access to all the journals anymore.

    Like

    • Carl says:

      Going forward, make sure you keep backups of anything you wouldn’t want to lose. Never trust a single program or hard drive with important data.

      Like

  55. Carl says:

    I have found the direct access through the file system an indispensable feature of Papers 1 & 2. I store the files in DropBox so I can then easily access them on my iPad through PDF Expert. This change means I absolutely will not be upgraded to 3. I remember these sorts of growing pains in Papers 1, and it’s sad to see them in 3, but the change to file system management is the step I just can’t support. Looks like I’ll be running Papers 2 into the ground then kissing mekentosj good-bye. It’s been a good run, though, and for that I’m thankful.

    Like

    • fmg says:

      Carl: I have a softlink in my dropbox folder pointing at my papers 3 library, which is located outside the dropbox folder. On the dropbox site on the web, my papers 3 library shows up as an ordinary directory with subdirectories and files. I can access pdf’s from my library on my iPhone, for example. Should work the same on your iPad. I presume this will work the same if you just locate your papers 3 library in the dropbox folder.

      Another possibility for direct access is to edit the info.plist file inside the papers3.app to make the library into an ordinary folder rather than a bundle. I tried this, and it worked, but then I undid it because I don’t want to mess too much with things I don’t understand well.

      Like

  56. François says:

    Hello,
    For the syncing with Dropbox, I use it for some years with papers 2. Very simple to do. No problem with the names of the files. You put your directory in dropbox, change the preferences, and it’s done. When you do the same thing in your second computer, the work is done!!!

    But I still have to sync with the iOS program. That’s one of the reasons I don’t like that app on my iPad.

    I hope that it wasn’t a mistake to reveal to the world that way to use the old version (papers 2), I would be very disappointed if it became impossible…

    P.S. for the update to papers 2, I also was very disappointed for at least 6 months… It was … terrible.

    (sorry for the mistakes, I live in Belgium, and I speak french…).

    Like

  57. I just switched to Mendeley (ecology/natural science papers, about 1GB of PDFs at last count) after **really** thoroughly not enjoying the Papers 3 downgrade in functionality. I’ve started working recently with Markdown and pandoc to produce documents rather than either Word or Pages, and Mendeley works quite well in that context. It’s ability to correctly identify downloaded PDFs is also superior to Papers 3, where I had started to experience the need to correct or assist it most of the time, DOI or none. Had a great run with Papers 2 for 5-6 years … but not sentimental now about moving on.

    Like

    • Aleh Cherp says:

      How do you cite with Mendeley in markdown documents (e.g. in Byword)?

      Like

      • Lawrie says:

        At the risk of appearing to be an unreconstructed geek … I’ve found that I enjoy the transparency of working in Markdown (various flavors) and (i) keeping the formatting as simple as possible, (ii) hand coding what formatting there is, and (iii) citations are just another link, in this case to a bibxtex file that is constantly updated by Mendeley. I’m going backwards away from black box WYSIWIG, and using Markdown/Pandoc as a simpler way of getting LATEX style typographical formatting with very lightweight and uncluttered text files as the backbone of the writing project (in my case my PhD thesis). It’s less of a slick approach than how Papers 2 magic citations work, but therefore much more flexible/manipulable. In converting to HTML or PDF or indeed DOCX, Pandoc can reference a citation style file of your choice to render the final form as you’d like it (or as the journal may mandate).

        This resource may be a useful way in – https://github.com/scholmd/scholmd/wiki/citations

        Like

  58. Peter says:

    ReadCube http://www.readcube.com is getting some attention. Has anyone here tried it out? I’d be curious to hear what people think.

    Like

    • Csaba Pusztai says:

      I did accidentally come across it a couple of weeks ago, so I downloaded and tried it. The GUI is very trendy, but in terms of its functionality it is still in its infancy. Itcan download papers from online repositories, but basically that is it. No way to edit metadata (reference details). Only very basic features are available.

      Like

    • Peter — I spent a couple hours with ReadCube today, and it is very promising. I agree with Csaba that it has some way to go, but it is *far* better than both Papers and Endnote at getting the correct metadata. To test it I imported 900 pds all at once, and it handled the import without a problem. Of the pdfs it did not find metadata for, 90 percent were articles from newspapers, magazines, online or similar non-journal type material. It also can’t handle chapters of books. This is to me the biggest area for improvement. If metadata is incorrect you can, in fact, change it, but it takes a couple steps. What’s really great is the ‘enhanced pdf’ feature — which is only available on a small number of my imported articles. The reference links are live on the enhanced pdfs, so you can click on a reference and go to the article itself (through a university proxy, of course) and download it immediately. Just playing around with it I found two articles I had somehow overlooked but needed to read. So it’s not ready for prime time — it couldn’t serve as a primary reference and pdf manager — but the bones are very solid, and I can’t wait to see where it goes from here.

      Like

    • Storytelling says:

      Peter — I spent a couple hours with ReadCube today, and it is very promising. I agree with Csaba that it has some way to go, but it is *far* better than both Papers and Endnote at getting the correct metadata. To test it I imported 900 pds all at once, and it handled the import without a problem. Of the pdfs it did not find metadata for, 90 percent were articles from newspapers, magazines, online or similar non-journal type material. It also can’t handle chapters of books. This is to me the biggest area for improvement. If metadata is incorrect you can, in fact, change it, but it takes a couple steps. What’s really great is the ‘enhanced pdf’ feature — which is only available on a small number of my imported articles. The reference links are live on the enhanced pdfs, so you can click on a reference and go to the article itself (through a university proxy, of course) and download it immediately. Just playing around with it I found two articles I had somehow overlooked but needed to read. So it’s not ready for prime time — it couldn’t serve as a primary reference and pdf manager — but the bones are very solid, and I can’t wait to see where it goes from here. Also: ReadCube has a really good support structure, far superior to Papers.

      Like

      • Peter says:

        Another advantage of ReadCube is In-line clickable references.

        Might it be possible to use as a ReadCube as a kind of front end PDF reader- annotator for Zotero or some other more developed ref mrg, for instance by syncing the libraries, at least until Papers gets its act together. Perhaps that would ease metadata editing (i.e. reference types) in the interim, which could be done in Zotero (alt whatever).

        Like

      • Peter says:

        Apologies Storytelling: you did mention the clickable reference function…

        Like

  59. panchap says:

    I have a papers3 library in dropbox from my old computer. How do I import its contents to papers installed in my new computer? After importing this library, I would like to delete it from dropbox and use the usual sync option.

    Like

  60. Alex says:

    I’ve been annoyed by another change between Papers 2 and Papers3: the unique number that the application assigns to each paper (you can see this number in the library view by adding the column “No.”) Not yet having reached the enlightened state of a paperless office, I still have a lot of printed papers with important hand-written notes and highlightings. I enter these papers into Papers2, write the unique number on them and file them in boxes. After importing my Papers2 library into Papers3, I discovered that there still is a unique number for every paper – but it’s not the same as the one Papers2 assigned! According to tech support, there is no way of getting the Papers2 number into Papers3, so now I have to decide whether to stick with Papers2 or whether to go with v.3 and re-number all my printed papers.

    Like

  61. some scientist says:

    I like papers1. I loved papers2. I really wanted to love papers3, but it was like one of those good-relationships-gone-bad that you know you just have to leave. My first hint that it wasn’t going to end well was the the papers3 store was (and still is) broken so that I could not pay by credit card and was forced to use PayPal. My second hint was that the support team did not seem at all concerned about this issue – they told me to just use PayPal like it wasn’t a big deal that even their store is broken. Really, I suppose I shouldn’t have been surprised that the program is even more broken.

    I definitely don’t want Facebook and papers interacting, and I’m not sure why anyone would.

    The dropbox situation is, as discussed above, also totally unacceptable. My collection of papers wouldn’t fit on dropbox, and I need the dynamic capacity of dropbox for moving data around between collaborators, not static long-term storage of pdfs.

    The only good part of my papers3 experience: it was really easy to get a refund from the apple store for the iOS version of papers3 (see here for info on how to do it: https://sites.google.com/site/appleclubfhs/support/advice-and-articles/app-store-refunds)

    Any suggestions about what to try next? I loved the combination of citation manager, pdf organizer, and pdf reader with notes, and it was crucial that I could use my iPad and laptop interchangeably.

    Like

  62. Mario Negrello says:

    A problem with readcube is that it is not independent. It is associated with big publishing houses (no names here, one can easily find them), who are backing it, and no doubt can find means to abuse us in the future. I recommend against reinforcing the power of the publishing lobbies, and the walls they build around information.

    Like

    • wjr says:

      I totally agree with you on Readcube. I want control of the PDF and I don’t want to have to “Mother may I” to the publishers.

      Like

  63. Mark Brandon says:

    Luc P. Beaudoin post on December 13, 2013 at 6:52 pm contains a clever way to allow spotlight to index and search the library folder for Papers3. I agree with Luc, that searching from finder is a real time saver when trying to recover a file from the Papers library. I used this option all the time when using Papers2… Hopefully we will see it return for Papers3. I have tried Luc’s work around, and it appears to work very well. The only problem I had was with step 6, which had some confusing wording and an error in the recommended ln command. The full 6 steps are included below, with edits included.
    BTW, I would be interested to hear from others about their experiences with this work-around.

    1. Quit Papers3
    2. Rename your Library.papers3 folder to a temporary name, e.g., Library.tmp (yes, change the extension).
    3. Create a new Library folder (I called mine Papers3Library.)
    4. Move all the files in the Step 2 folder (Library.tmp, in my case, i.e., all your managed by Papers3) to the Step 3 folder (Papers3Library). Spotlight should start indexing this folder (Papers3Library), which may take a while.
    5. Delete the empty temporary folder created in Step 2 (Library.tmp, in my case).
    6. Using Terminal.app, cd to the folder that contained your original Library.paper3 folder (and now contains your new Papers3Library folder), and then create a symbolic link. Assuming the same names, this link will be named Library.papers3 and will point to PapersLibrary. The command in terminal is:
    ln -s Library.papers3 Papers3Library
    This will make the effects of Steps 2-5 opaque to Papers3.

    Like

  64. wjr says:

    I have been a Papers 1 & 2 beta user for years and I keep several thousand papers on my working 2.7.3 version. I keep going back to Papers 3 and trying it but I just really dislike the reorientation of the application with respect to data. Worse, I distrust it to keep my papers (my livelihood) safely. It’s not so much the PDFs (which I archive) but all of the metadata and search organization that goes along with it. So, I will sit for a while and see if they fix it.

    Like

  65. Mikael Bergkvist says:

    Sorry to see that there is still no improvement, same database corruption issues but facebook integration remains a priority.
    I really don’t get it. And I will certainly not pay for it…

    Mikael

    Like

  66. LW says:

    Thanks for the review and all the thoughtful comments. I feel like the Papers development team has the wrong priorities. What is most important to me are the basic functional requirements where Papers often fails. For example, I want to use it between different computers. This should be mindless, but it repeatedly fails to “sync.” I want to seamlessly “match” or use my library resources, but again, always a hassle. If someone wants to tell me I need to think about a, b and c and work on this or that, I’m sorry, but that’s not the point, It is 2014 and a lot of software just works. I’m too busy working on our research to be the sysadmin of Papers. Dumping a whole new (and confusing) UI in Papers3 is a clear sign someone at Papers doesn’t get it and is taking a superficial visual design approach over delivering solid, functional software. Sigh…

    Like

  67. Lauranne says:

    Hi !
    It’s interesting to see that there is much more discussion here about papers than on the “official” support…. Thanks for this opportunity !

    Well, as many people here I was interested in buying the new papers 3. What I did, after trial on mac. ’till there, no problem. Except, maybe, the fact that we cannot oragnize folder if sincyng with dropbox. But I’m ok.

    My BIG problem began when I tried to install it on windows. Of course I wanted to sync between my mac (home) and PC (work). As we cannot use dropbox if we wanna organize folders, I use Cubby (another cloud storage service as so many) and sync folder between mac and pc. However, I’m unable to easily sync the library because the architecture is really different. So the next idea was to check the Cubby sync folder and automaticaly import new pdf in the papers windows (and eventually copy them in another folder but not necessary…). Well… I’m unable to do it.

    In fact at this time, I’m just unable to only create a library because papers crashes. The fact is that it allways open in my old folder (the one on dropbox) and I’m unable to change the location of the folder containing the library…. Would you have any idea/ advice / other ?! I allready contacted the support via private e-mail but no answer…

    As you can imagine, I’m pretty disapointed !
    Thanks !

    Like

  68. Martin Heimann says:

    Papers 3 is a big disappointment after working long time smoothly with its predecessors. Most annoying for me is the dropbox synchronisation: Every few minutes my entire library gets copied over even if I have not done anything in Papers 3 and it is just “resting” in the background. This blocks my internet and gets very costly when I am using my mobile phone. Does anybody know how to stop this? All I can do for now is to quit the program.

    I also experienced a consistent crash at startup when no internet was available. I could access my library only after I was back on the internet.

    It is also sad, that the former “open” company stopped being open. All feature requests or questions through the help website of Mekentosj could be made public so that one could learn from others. Now all is private, and several of my recent inquiries did not get answered at all. This is very bad user support – I fully paid for the product…

    What are the alternatives?

    Like

    • Bruce says:

      I’m glad I read all of these posts. I currently use paapers1 on intel mac OSX10.4.11. ~13,000 .pdfs works seemlessly, find whatever I want, synch with iOS6 ipad. I have papers 2 on another mac OSX6.0, now mavericks. Papers 2 has been unstable on any operating system I’ve tried to run. Does anyone know if Papers 1 can run on OSX mavericks? Not going to risk all that filing despite wishing desperately to upgrade to OSX mavericks – seems really nice O.S. trouble free on my other computers, but papers2 still “glitchy”. Definitely not going to papers3 after the above.
      I too had noticed these guys had stopped being so “open”.

      Like

      • Wjr says:

        Bruce,

        I run Papers2 on both MacOS and IOS with no problems whatsoever. Both operating systems are most current. Other than an occasional sync hang up that is easily fixed by a re-sync, I have good stability. Papers3, on the other hand, is simply not usable at the moment.

        You have more papers than I have ever heard of – 13,000 PDFs is impressive. One thing that I have found is that all PDFs are not the same. I occasionally find that some publishers produce PDFs with different and less reliable engines or produce such files with an engine whose RIP outputs very obsolete code (keeping in mind that a PDF file is a form of PostScript). So, your problem might be with either some bad PDF code.

        Also, you might consider archiving some of your files. Papers is a pointer system. It keeps metadata in the application which is used to find the PDF data in a set of flat files associated by year (folder) and author. This latter can get corrupted, particularly with auto matching. Bad year tags are common and I don’t know how much room there is for such a large number of pointers to the folder/file construct.

        Like

  69. Bruce says:

    Thank you Wjr.
    Unfortunately do not have time to fiddle with Papers 2 and it is on another Mac which I don’t regularly use. Papers 1 works beautifully for me. Did get reply from mekentosj yesterday who know of only one “success” with Papers1 running on Mavericks. “Some had problems with the inspector-view, and others experienced corruption on start up”. And the disclaimer “we do not support Papers 1 anymore”. So I’m really “none the wiser”. But probably better to stay where I am. Anyone know what the limit for pdf storage within Papers 1 is likely to be?
    This is probably a stupid question for the technologically endowed. I have never exported to “papers Archive”. Could this be used to send current library to another computer ? what does it actually “archive”?
    I am a bit risk averse with now 13,000 .pdf’s…….. “if it’s not broken don’t fix it”.
    Regards Bruce

    Like

    • Wjr says:

      Which is why, with a mere 4,000 papers, I am quite cautious about moving off of Papers2. BTW, I once asked the folks at Mekentosj about the database limit (Papers2) and they did not have a definitive answer. I suspect that there is one but it is good to know that you have so many files!

      I back up not only via the archive but also via a disk image archive and with a bulk copy to a server. Paranoia is good in this case.

      Best.

      Like

  70. kate says:

    Thank you for keeping all these thoughts on here! I’m an academic and have been a papers user since the very start, it revolutionised my PhD. I’ve had a year out from work, appear to have a corrupted papers 2, and was considering upgrading / starting again onPapers 3 – don’t think i’ll bother now having gone through all of these posts and the feedback is still massive disappointment.

    So…. can anyone concisely provide a list of the useful workflow / article / research management tools that they use for storage / working on / retrieving / handling etc. Only all of the 14 colleagues in my department print off articles and store in regular ‘my articles’ on their PCs…. I’m a mac user at home and an enforced PC user at work, but massively out of the game in terms of where paperless office / decent pdf handling / research is at.

    Best wishes,

    Kate

    Like

    • Martin Heimann says:

      I switched to Zotero. You can export your bibliography from Papers3 in RIS format; it will also include the local path to the PDFs (if there is one). The import into Zotero goes then seamless. I converted over 5000 references – worked flawlessly. The logic behind Zotero is a bit different than in Papers, but once you are familiar with it, it works perfectly.

      As to database size: Zotero synchronises the database on it’s servers, but the PDFs only if you allow this. I have Zotero synchronize the PDFs on our OwnCloud WebDAV (about 5 GB). This gives a convenient backup and allows me to access them also from different computers. One can also access them from mobile devices; there are several apps available for this.

      Like

  71. James M says:

    I am another of those who is disappointed in Papers3 and is very concerned about the future of this information organizing tool.

    I have nearly 16,000 references with associated pdfs in my Papers database. I purchased Papers3 and migrated. To my great regret.

    Papers3 disassociated around 5% of my pdfs from their references – that is, when I select such a reference, it no longer has a pdf to open. This seems to be some kind of metadata failure for the most part. If I search in the OS for a string that I know is in the pdf, I can find it maybe one time in 3 and reassociate the pdf with the reference. I have also found instances of a reference being associated with the wrong pdf. And many of my pdfs are just plain gone. This is a problem as I no longer have full text access to many of these references. Fortunately, I archived my Papers2 database before experimenting with Papers3.

    I don’t get a good feeling for the direction that Papers is taking. 3 is very much slower on my system than 2, and I have yet to find any new functionality that helps me. I would have loved it if the developers had simply built in a local synch function in 3 so that when I come home with my laptop, it would update the database on my desktop. I have so large a database that I would have to pay DropBox a monthly charge if I were to sync the way Papers offers. No thanks.

    In the long run, I’m really concerned that the developers are under-resourced and falling into the mobile app trap. I have over 20 years of literature research hanging on the Papers app thread. I’ve started exporting the pdfs to an archive because I’m concerned that the company has too small a resource base to be likely to be around five years from now.

    Like

    • Larry Hinman says:

      I am in basically the same situation, and it’s hard to tell whether Papers 3 will improve or not. I know I haven’t discovered all the instances of dissociated PDFs, but it’s at least as high as 5%. I have vacillated on whether to jump ship or not. Papers 2 did improve significantly over time, but I don’t see comparable improvements in Papers3. The closed format for discussion is terrible, because it makes it difficult to figure out what are isolated problems for me (and a few others) and what is widespread. Moreover, I don’t see the responses to others’ posts, which typically i can learn a lot from reading.
      Also, I find that I can’t get the iOS version to import new papers from Safari. Support has been no help. (This is one of those situations where it would help to know if this is happening to everyone or just a few people.) Furthermore, I estimate that 30% of my papers on the iOS version of Papers have lost their association with a PDF, and when I try to read them on my iPad, I get a standard “404” error message.

      Like

  72. Therefore, we make a layout of the project and co-ordinate with our designing team
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  73. Roger says:

    A Solution to all our problems is nearby in my opinion !

    Firstly I add my voice of discontent for the same reasons and the future seems pretty clear, and frankly hopeless! I came from Sente after using it for many years. For a long time I believed that when I was searching in Sente, I was searching my (pdf) content and was so embarrassed to find out how stupid I’d been. In disbelief I dug into the database (package contents) where I found the accumulated detritus of years of work. It was riddled with duplicate attachments, in some instances I had more than 4 copies of the same pdf attachments. Further investigation showed me that when an attachment was ‘deleted’ in Sente – and the record mirrored this action – in fact this was not actually true and the package ‘contents’ revealed all of these (deleted) attachments were still there; ‘orphaned’ I think is the term. I lost months years almost trying to fix this crap and in desperation tried Papers 2 with a sample database of around 4,000 references.

    I did a search immediately with a topical keywords and instead of the 7 hits I found in Sente Papers 2 provided me with almost 200 hits! I was sold on it immediately and decided to switch to Papers 2 and even more so after I read the preview for Papers 3 which I’m also regretting.

    There is no way I’m putting my work on someone’s Cloud! I can’t imagine anyone developing serious IP in the scientific, pharmaceutic, aerospace, engineering domains or in the legal professions that cross-reference enormous databases of references, depositions and media etc. It would be professional suicide and in some cases irresponsible.

    So I suggest a solution.

    I’m a very new convert to DEVONthink Pro and, using Skim for PDF markup and annotation and variety of AppleScripts has made my work so much more efficient, it’s easy and frankly it’s fun. If I paid myself my usual hourly rate for the time I spent trying to fix Sente over the last couple of years – I’d be $250,000 richer today so I’m happy to pay whatever it costs for DEVONthink because it just works. It works even better than I’m able to appreciate yet but it’s better than seeing the darkness at the end of the tunnel that is Sente and Papers and I’m sad to say that.

    Why don’t we all just petition DEVONthink to produce a reference manager to our combined specifications and see if it floats?

    Like

    • Koenraad says:

      Hi Roger, I have been using DevonThink Pro for many years now and I can assure you it is useless for bibliographic work. I like to use it for scanning my business invoices and bills, and varied materials such as regulatory guidelines and so on. DTPO does an excellent job of finding any string inside such a database because its search method is fuzzy. However, if you try to search inside a database that focuses on a particular topic (say: aspirin), any search on “myocardial infarction”, “stroke”, “bleed”, “platelet”, “mortality” etc etc will essentially retrieve your entire database. It’s totally unusable for this kind of work.

      Like

  74. Pete says:

    Hi, I’m a new student just trying to get my head around Zotero, Papers, Endnote, Bibtex and many others……My friend was using Papers2 and said it was the best he had tried by far….

    Now I hear that Papers3 is a mess and is still by the sounds of all the above comments a BETA which is being improved as and when the developers get round to it and it may never be as functional as Papers2.

    So I guess my question is…..If Papers2 worked great and was fully functional, and it wasn’t broken…….Why change? Can’t someone simply buy a papers3 licence and use it retrospectively for Papers2….If Papers2 does all everyone needs it to do ?

    The dropbox sharing I dont know whether you had that in papers2 never having used Papers2 before but should be just a case of synching the output folder of where papers2 nicely renamed all your stuff?

    Just wondering?……

    Like

    • Lauranne says:

      Hi Pete,
      just to answer about the syncing. I guessed the same behaviour than the one you’re expecting (i.e. just have to sync folder via dropbox). However, be really careful : you cannot !! Of what I understood (via thousand of tests !), the fact is that papers on mac and papers on PC do not create exactly the same database if you choose to automatically save and rename your documents. Then doing it will make your data corrupted and your only possibility will be to reimport (and re-arrange…) all your stuff.

      If I can give you my opinion : apparently you’re beginning ; probably have you only few papers ? I think it’s the right time to test it by yourself. According to me, one of the best option is mendeley (free, automatic rename, web saving, very good and active support, cross platform, easy to use with word, automatic export of “.bib”…).
      Currently I’m also using bibdesk because writing my papers with LateX. The good point with this software is that the database IS the “.bib”. Then, no need to export anything, and you’re sure that references you entered in your library are well written (I had some problems with mendeley because of export format: it created ” ` ” symbols rather than ” ‘ ” and corrupted all the .bib).

      I hope my answer will help you a little.

      Like

      • wjr says:

        Lauranne,

        The one thing that I won’t do is to hand my literature store over to Elsevier. Cloud based or even internetwork client server based storage is subject to both tampering and data mining. Candidly and given the known bias of the large publishers, I don’t trust them.

        That is why I chose Papers. It is entirely an application, keeps a simple database (based upon pointers) that allows the data (PDFs in this case) to be accessed as flat files in their native form and is not “manageable” by big brother.

        What is the first thing that you hear when Mekentosj is purchased by a publisher? The database is screwed up and encodes your data and, OBTW, it is not being fixed any time soon, it seems. Papers2 is the best application ever done in its class (tried them all at one point or another) and they look to be destroying themselves via Papers3.

        Like

    • ridgeguy says:

      I recommend you use Papers 2, leave Papers 3 alone for now. Maybe it will get better, maybe not. My belief is that Papers 3 suffers from an under resourced dev team and premature/excessive focus on social-mediafying the Papers product.

      I’m on Macs, and I sync Papers 2 between my laptop and desktop systems using CarbonCopy Cloner. I make all new entries to Papers on my laptop. When I get home from work, CCC syncs the changes in my laptop Papers folder with my desktop Papers folder. I can also just trash the desktop Papers folder and copy over the laptop Papers folder for the same result. At 15+K references, I have to connect to my wired Gigabit LAN to get the latter done in a reasonable time. The delta synch using CCC works fine over my wifi. It would be nice to be able to sync over the web, but I have too many references for an unpaid sync repository (Dropbox), and like other posters in this thread, I am extremely reluctant to trust literally decades of my reference mining to a cloud service.

      I plan to continue to use Papers 2 so long as it remains compatible with OS X versions, and to keep a copy of all the pdfs in my entire reference database as a separate resource that isn’t dependent on the continued existence of Mekentosj as a business entity. Web-based businesses come and go rapidly and with little warning. Given the original pdfs, you will always be able to reconstruct the important aspects of your reference collection – so long as they didn’t disappear from a cloud repository.

      Like

      • Wjr says:

        The problem with going with the flow wrt web companies is the metadata work that you put into the database. When you have a considerable number of papers this represents a significant amount of time that would be difficult to recreate.

        Nothing out there now really replicates Papers. My initial hope when they were purchased was that having a large company backing them would give them stability over time and, therefore, the ability to both support the product long term and to enhance their offering with other workflow products.

        So far it is disappointing in the extreme.

        Like

  75. Lloyd says:

    I have had similar bad experiences with Papers 3. Really the additional features are marginally beneficial for me – whereas the less usable UI (grey on white for your main library list, really? with no option to change it?), the poor handling of PDF renaming and folder structure all add up to a large regression. I’ve gone back to Papers 2 – but the problem is presumedly that won’t be around forever.
    I don’t mind paying for a good solution. I’m hoping they will have fixed the many problems by the time I have a look at Papers 3 again. If not, maybe I’ll have to look into Sente, Zotero, etc…
    I wonder what the appetite would be for DevonThink to create a reference manager? Perhaps as a Kickstarter project to see if the interest was there?

    Like

  76. MS says:

    Hi, just want to add my experience as well. I am a full time researcher. I Work with Papers around 10 hours each day. My papers and collections are essentials for all my work. I Changed from Papers 2 to 3. I Had heard about some problems with papers 3 but consulted several friends who did not have any problems (at that time – they do now). To make a long story short, Papers 3 started soon after to crash regularly, especially when searching for new papers within Papers 3. Often I lost the last couple of hours imports, collection, etc at every chrash. Then it went on to say my database file was corrupted. After a long communication with Papers staff, deleting all files from the computing with Papers 3, reinstalling, starting to use a backup version in dropbox from before the first crash (with loss of all the papers imported in between) I started to work from the beginning again. This lasted two days before it started to crash again. Also, very often the “Cite while you write” function did not work with word. Papers 3 recognized some of the citations in word but not all. Thus, the bibliography made within the word document was incomplete and wrong.
    Being a Papers user for several years, I have to say I am surprised by the fact that I had to pay a considerable prize for the update (Papers 3) when already payed for version 1 and 2, and then when having done this I find that I have risked my complete library and collections. To anyone who may have doubt about whether the benefits outweigh the limitations of the update, from my own experience I have to say I strongly recommend not to update.

    Like

  77. Wow, that’s what I was searching for, what a information! present here at this weblog, thanks admin of this web
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    Like

  78. AZ says:

    I completely agree with MS. I am very much disappointed in Papers 3.0. The interface is promising but the back end is very much broken. In an attempt to bring Papers forward, something very fundamental was broken. I have tried every trick in the book (from complete re-install to turning off various other functions). Somehow it seems that the indexing function locks up the entire program and either crashes it or prevent you from doing anything at all. Everything works fine if you have 100-500 entries. But when you get serious, the software breaks down.

    I transitioned from Papers 2.0 and immediately experienced a dramatic and critical failure. I’ve been patiently working to find a solution but no luck.

    if anyone has found a way to make papers 3.0 work effectively (with a sizable library) then I would love to know.

    Like

  79. Lymphoma Lab says:

    I echo what’s been said already. Despite the tremendous promise of Papers3, it’s a bit of a nightmare to actually use. My main issues have been: inability to find papers I know are in the library and repairing the program’s spotlight index does not fix the problem, merging authors in the authors view causes much of the meta data (especially the order of authors) to get scrambled, constant problems matching imported PDFs to the correct metadata (I can find it in pubmed in my brower — tell papers3 to find the same paper using pubmed, no luck), preferences reset themselves to default regularly, customer support for solving problems approaches non-existent.

    I have been researching alternatives. I looked into DEVONthink mentioned above but this does not seem to include inserting citations in manuscripts. Can anyone comment further on this product and whether it’s a true replacement for all the features of Papers3?

    I’ll give the Mekintosh people credit for putting together an excellent website that truly describes what their product is supposed to do (in marked contrast to the DEVONthink site, which is terrible), but the product itself is so problematic and the company seems so short-staffed, I’m extremely concerned the issues will ever truly be addressed, although I continue to use it for now.

    Any other suggested alternatives?

    Like

    • Martin Heimann says:

      As mentioned before: make the transition to Zotero. Works perfectly. And the Zotero client Papership (Mac or iOS), which was initially quite buggy, is now really doing a good job.

      Like

  80. fmg says:

    Martin, Upon export from papers 3 and import into Zotero, bib data is imported and pdf’s are left in place, with a link to their location. That means: (1) old pdf’s will be in one place and new pdf’s obtained in Zotero in another. (2) Pdf’s with obscure names and locations from papers 3 will still have obscure names and locations (3) You don’t dare try to use both Zotero and papers 3 during a transition period because papers 3 will destroy links to pdf’s in Zotero.

    Zotero doesn’t seem to have any means to batch import the pdf’s along with the references to a new location. There is a Zotero add on called zotfile which promises to be able to do batch import and renaming of pdf’s , but has no obvious procedure for doing this.

    I obviously don’t have much knowledge of the Zotero ecosystem, but at first look it seems like it depends on various add ons to accomplish tasks which you would expect the central program to take care of, like organizing and renaming files.

    Like

    • joe says:

      To “batch” import with Zotero all you need to do is select the files you want to import and drag them into Z’s main window. Simple as that. With one click you can also start the auto fetching of bibliographic meta data. I can also report that Z is a fully functional and well supported reference manager with a healthy open source user community. That explains that availability of additional add-ons and plugins more than any inherent lack in the actual app. It’s free after all … geez!

      Like

      • fmg says:

        No doubt it’s very good, especially for a free program. But batch import doesn’t work as you say, when the files are already in a hierarchy.

        Like

    • Martin Heimann says:

      I exported all Papers3 papers as a RIS format library. Then Importing them into Zotero preserves all bibliographic data (at least almost all, since some fields in Papers3 are not also existing in Zotero). With this import, also the PDFs are copied from the Papers3 to the Zotero database. Worked flawlessly. I split first in Papers3 my entire library in chunks of a 1000 entries by making appropriate reading lists and exported each of these separately.

      I had also a large collection of PDFs outside of Papers3. Dragging them into the Zotero window works less well, since Zotero then has to extract the bibliographic info from the PDFs and fetch the missing info from Google Scholar. This leads often to less optimal bibliographic info; and there are often PDFs for which this does not work. For these one has to download explicitly the bibliographic info from the database of choice (e.g. WOS).

      Zotero allows then also to upload the PDFs on a OwnCloud volume (I did not want to purchase more storage with Zotero). Works all in the background very well. My iPad has thus access to the entire library via the OwnCloud database (using PaperShip).

      Like

      • fmg says:

        Hmmmm, thank you Martin. I did exactly as you describe (but only with a small trial collection of references.) Bib data was imported, pdf’s were left where they were in the Papers3 library, not copied by Zotera to its own storage. Maybe there is some preference to set in Zotera to change this behavior?

        Like

  81. Lymphoma Lab says:

    So I’ve given Zotero a trial run. I was able to import my Papers3 library by exporting as an RIS file and then importing to Zotero (Firefox extension version on my 2011 MBP). The PDFs ended up importing to Zotero’s own filing system without problem, so I’m not sure what went wrong for you, fmg.

    Zotero certainly seems flexible and stable, and likely to avoid some of the issues currently plaguing Papers3, but, that being said, I have some deep misgivings on a couple issues of usability that will be SORELY missed in Zotero compared to Papers3, at least for my purposes.

    Papers3 is extremely good about being able to update metadata and attachments, while Zotero essentially completely lacks these functions. To get at what I mean:

    -You import a paper to Papers3 by using “open in papers” javascript link in your browser and get the PDF, either automatically or by clicking the download link. You can click on supplemental info links on the web page version of any paper and they’re automatically saved and permanently linked to that library entry as supplemental data. Metadata needs updating? just tell it to rematch using your database of choice. This latter is a huge issue (for me at least) because I get a lot of articles when they very first come out as E-pub versions. Later, if I want to cite them correctly, I need to update the metadata to reflect the print publication.

    Zotero has no ability to rematch metadata. None at all (I asked on their forums). So if you want to update it, you’ll have to re-import the whole entry from scratch (or edit it manually, clearly not a workable option). You can set Zotero to automatically import PDFs for articles when you add items, but this is the only opportunity to do so without having to download files to somewhere on your computer and then manually drag them to the correct entry in Zotero. That means ALL supplements (≥50% of data for all publications in the life sciences) and all article PDFs you weren’t lucky enough to automatically import when you first added that entry.

    These issues are pretty much deal breakers for me and Zotero for the present. I may have to stick with Papers3 for now and pray for fixes to its many issues.

    I’m curious to hear others’ experiences switching to Zotero from Papers3 and whether they found workarounds for these issues, or about other Papers3 alternatives.

    Like

  82. Scott says:

    I have used Papers 2 for several years now through various versions of OS X (now on Mavericks). I have been very satisfied with how it runs. I store all the files on Dropbox for access from different computers at home and work and that works flawlessly. (The only concern is that if you turn off your computer before Dropbox has a chance to synch, you can run into trouble. Same if you leave it running on another computer. Therefore, best to turn off Papers a few minutes before you turn off your computer) Tried Papers 3 when first came out and it was a mess for me (can’t recall all the difficulties).

    Like

    • Morry Hodges says:

      I said in a comment last January that the sale of Papers to Springer meant the effective end of Papers as a useful program. Nothing has happened since to change my mind. For those looking for a replacement for Papers, I suggest Bookends, from http://www.sonnysoftware.com. It’s a superb program. I think former Papers users will find it to be more than an adequate replacement. It’s written by an NIH scientist—as a hobby, as far as I can tell. Support is prompt and expert. PDF support is excellent. Integration with MS Word for Mac and with Nisus Writer Pro is flawless. And the price ($40, I think) is more than reasonable. I would appreciate it if anyone who tries Bookends would leave a comment here. Morry Hodges

      Like

      • Morry Hodges says:

        Just checked—it’s $60, not $40. But you can try it before you buy. Morry

        Like

      • Martin Heimann says:

        Did not know Bookends, looks indeed very promising. I’ll try it out. Thanks very much for the tip!

        Like

      • Bruce says:

        I use Bookends for bibliography too (love it on Mac) and Papers One merely to store and trace .pdfs without problems. Recommend others to consider also.

        Like

  83. Lymphoma Lab says:

    An update for any still following these comments: For now, I’ve been won over by Zotero and finding it meets all my needs. I’ve found good workarounds for the concerns I listed above. (Ask if you need any details.) I also investigated Bookends, which seems quite good, but I’m sticking with Zotero for now since I’m all set up with it and getting used to it. Zotero also seems to have a bit better integration with word processors for citation insertion. Both seem to have active and very helpful support communities.

    Anyway, didn’t want my last comment here to be down on Zotero since i’ve been won over to it at this point!

    Like

  84. yates999 says:

    I upgraded to Papers3 today – but I hadn’t found this thread before doing it.. and had similar issues to the ones listed here. I also tried the last recommended “Bookends” which works well as a reference manager but when I imported unrecognised PDFs the process to correctly match a reference with a file was painful. It is also quite slow to handle 100’s of PDFs on import.

    I am going to continue with Papers2 in the hope of a good update of Papers3.. very appreciative of anyone that can indicate a competing platform which can also cover the core Papers functions in a reliable / robust way.
    – manage pdf files (even OLD papers)
    – help match files to references online
    – handle references

    Thank you to all and your suggestions..

    Like

  85. slowpokegene says:

    I switched from Papers3 to Mendeley months ago, which worked generally fine. But yesterday I found that the syncing of PDFs between Mac and Windows did not work so that I end up got quite a lot duplicates. I decided to give Papers3 another try, hoping it might get some improvement over the months, but it proved that I wasted myself a whole night and morning — still a mess.

    Like

  86. Avi Ghosh says:

    Have any of you guys tried papers3 for windows and/or papers 3.2 for mac? I’ve been sitting with papers2 for mac until sometime this summer (but had the license for papers3 that I hadn’t been really using until they worked the kinks out)

    Recently (due to getting a windows machine) I needed to enable syncing between the two platforms so have been following Papers3 for mac a bit passively. A few weeks ago Papers upgraded themselves to Papers3.2 for mac and Papers3 for windows which is supposed to be a massive rewrite (and it certainly is on the windows side).

    Papers1.5 for windows was super buggy but I have had no real issues between Papers3 for windows and the new Papers 3.2 for mac, enough so I have kept to this version for the last month or so. That said I haven’t really tried using this for citations yet and really simply as an book/paper database that syncs between computers / ipads etc.

    Like

    • slowpokegene says:

      to Avi: Don’t try Papers3 for Windows! I did it and lost my library yesterday. Fortunately I was working with a small library of just around 100 papers.
      For syncing between Mac and PC, I think Zotero is a good candidate now, following suggestions by people in this thread. You can either sync both data and PDF files with Zotero’s own cloud space, free under 300MB or charged for more spaces, or you can sync only data with Zotero while saving PDF files in Dropbox (with symlink to Zotero Storage folder).
      Papers3 is still the best literature management tool by many means, but unfortunately it is indeed moving in the wrong direction.

      Like

      • Avi Ghosh says:

        I actually realized my mac and pc versions aren’t syncing anymore.. weirdly papers 1.5 and 3 for windows are syncing with each other but the mac version seems to be frozen probably at the papers 3.2 upgrade. I am going to try to move to something more stable .. that said at 3600 papers over the course of years (since papers 1) this is going to be a bit painful.

        Like

  87. Mart says:

    Solution for Spotlight indexing:
    Papers 3 (unlike papers 2) stores all your pdf in a library. OSX spotlight does not search within it, which is a shame. I was able to resolve this problem using Quicksilver. It is an awesome FREE app, or bookmark, or file launcher (just google it) as well as many other things. In Quicksilver’s settings add the Library.papers3 library to its custom search directory. Then change the search options (bottom right corner there is a little i) to search for 4-5 levels deep. Now when you search with quicksilver for an author’s name it will find the pdf or the folder with them inside. Hope this helps.
    Mart

    Like

  88. Kristoffer says:

    I moved to papers3 from 2 shortly after its release. It has improved a lot since, but there are almost always some issue going on. And as pointed out in this thread, the company seems short-staffed and I have rarely been successful getting help using their support-system. Once I had to tweet them to get a response! One issue I have right now, is that some of my papers are listed in the library as being authored by ‘anon’ although the authors are correctly indicated, and I also tried the ‘match’ function to get all the meta data in the correct format, but it doesn’t help. The search function can correctly find the papers, but it becomes a problem when you use papers as a reference tool, since the citation will not have an author name. Has anyone encounters, and solved, this problem?

    Like

  89. Bla says:

    Amazing that this thread is still alive. I’ve commented about a year ago. I have not gone back to papers and made due with Goodreader on my iPad, synching the contents with a free box.com account. box.comm contrary to dropbox (which Papers3 wanted to force me to pay for) offer 10 GB for free. That should be enough for most collections of pdfs. At least it is for me. I have been considering bookends, but thought it was rather expensive. However, if you hurry, there is currently a promotional offer to get Bookends, Scrivener and some other software as a package for 49$, which is an amazing deal (http://deals.macupdate.com). I now use Bookends and it looks pretty good so far.

    Like

  90. Duh says:

    Hi Bla, thanks for your comment and link to the deal. I’ve been facing similar considerations. In my case I’ve been using Zotero, which works well but it lacks things like in-app pdf view and annotation. I’ve never found a good comparison of Bookends and Papers, which to me seems like the best paid alternative to Papers 3 (Zotero being the best free open source one). Sente seems like the runner up. Price-wise, Papers, Sente and Bookend all cost about $60 for a single user (Papers even a bit more), so I’m not sure why you consider Bookends expensive.

    Like

    • Mark Brandon says:

      I am a long term user of Papers (on my Mac), and I have been using Papers 3 since it came out. I agree that the first versions Papers 3 had lots of problems. I also did not like the fact that the library was saved in a virtual disk (using OSXFUSE). This can be fixed by using symbolic links (see comments above by Beaudoin and Brandon). With this fixes in place, the library becomes searchable from the Mac Finder app. The newer versions of Papers 3 are much faster and more stable, but some kinds of edits are still a bit sluggish. I recently found bug in the program where a deletion of an listed entry would cause deletion of files from other entries. I submitted a bug report to Mekentosj several weeks ago, but have heard nothing in reply. Like others, my impression is that Mekentosj is lost the ability to keep up with technical support and to fix bugs and problems promptly. I worry that the Papers 3 is on a path towards being abandoned. But for right, now it is functioning sufficient well for my needs, which is to mantain some order in the ~8800 entries I have in the library. In my experience, there is nothing else available on the market or via freeware that works as well as Papers 3. I am keeping my fingers crossed that the development and management of this program will be back on track.

      Liked by 1 person

      • Martin Heimann says:

        Had the same experience with Mekentosj. Moved now first via Zotero to Bookends. Bookends just does the job in a superb way. And if you have an issue with the program, the developer responds to you within 24 hours – that’s what I call service. I highly recommend it.

        Like

      • Mark Brandon says:

        I tried out Bookends, but I was put off by the task of importing my content from Papers to Bookends. I would move immediately if there were a full import option available. In particular, the Bookends web site indicates the following shortcomings in the import process:
        1) Collection (group) names will not be exported/imported, just references.
        2) If your attached PDFs are not found in Bookends, you must tell Bookends where they are. Either move the PDFs from where Papers or Sente stored them to the Bookends default attachment folder, or in preferences set the default attachment folder location to the folder where they are currently stored.
        I have many collections organized in Papers, and it would take me a lot of time to recreate those collections manually in Bookends. The second note above suggests to me that the Bookend import processes cannot be trusted to be fully successful. These issues worry me in another way: Why is SonnySoftware, the developer for Bookends, unwilling to design their software to do a full import? It suggests to me that they are willing to take shortcuts, and may have done so within the Bookends program itself. By shortcuts, I mean that certain options are offered but never fully developed. My past experiences have left me very sensitive to avoid this kind of problem.

        Liked by 1 person

  91. Larry Hinman says:

    Glad this thread is still active, since the Papers site is so private about all these discussions.

    Somehow, I haven’t yet given up on Papers, but one of the major issues for me is its classification structure. Where, for example, does a podcast belong? Is it audio? Is so, you are faced with choosing either radio or CD. Of course, it’s neither. The categories don’t fit and we are left trying to push round pegs into square holes.

    A couple of years ago I asked Makentosj for a map of the category structure and they said that they don’t have one. Perhaps they don’t, but that’s hardly good news. If this is going to become a good product, it needs a much clearer and perspicuous system of classification than it presently has–or else it needs to let users define their own set of categories. It has great difficulty with groups of items and the individual members of the group (an art exhibition, a specific painting in that exhibition; a radio show and a particular daily broadcast of that show; a conference and the particular papers presented at that conference, etc.) All of these are analogous to a journal and the particular articles in that journal or an anthology and the particular pieces in that volume. The whole-part relationships are often crucial, and sometimes I want to direct students to a particular conference or exhibition without necessarily singling out one particular item therein.

    Like

  92. Patrick TRIEU says:

    As most of you, I use Papers since many years. In my hand, version 3 is quite problematic. My library is located on a portable hard drive and is used on 3 different computers (work, home and travel). The main problem is that when the library is updated on one computer, the other computers did see the modifications. Rebuilding the library etc temporary solved the problem. Desinstalling and reinstalling papers do not change anything. Seems that some file(s) is (are) stored on the computer or is associated with the computer. I never experienced this problem with previous version.

    Like

    • Bruce says:

      ASked this question a year ago no-one knew the answer then trying again. Currently running Papers 1.97 on my OLD mac OSX10.4.11. yep that old. Purely because Papers1 is flawless – 13,000 pdfs stored and filed links with ipad hassle free.
      Would dearly like to upgade OSX to Mavericks but to scared to stuff up a perfectly functiong filing system.
      Anyone know if Papers 1.97 is compatible with Papers 1.97.
      Without some certainty I’ll stay where I am.
      Simon

      Like

  93. Yohan Farouz says:

    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 today, 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

  94. utsira says:

    OK, here are my thoughts on the whole biblio manager dilemma.

    I wrote my PhD thesis with Bookends/ Word, but switched to Papers 2 when I finished, because of little things about BE that annoyed me (I can’t actually remember too many details about what these issues were, and this info is several years out of date, so these might have been fixed, but it was things like not having support for the core text features of OS 10.9 such as a long press for diacritics, not having a proper ddmmyyyy field for citation styles that cite newspaper articles, not automatically grabbing your pdf highlights like Papers and Mendeley do, not having a magic manuscripts style citation system that works in almost any text editor like Papers etc)

    I’m still using Papers 2, and don’t plan on switching to Papers 3 soon, if at all, unless the comments on this site get a LOT more favourable.

    The underlying issue though is feature creep, and our expectation that these programmes do a lot of things, grabbing pdfs and metadata of all sorts of websites, marking up pdfs, seamlessly interfacing with our word processor of choice etc etc.

    And none of these programmes are ever going to do any of those things that well. The browser will never be as good as your actual browser, with all its passwords, VPNs, bookmark(lets) etc. The note taker will never be as good as Evernote or whatever. The PDF reader will never be as good as Skim. And the iOS experience will probably be way worse than just using Readdle or Good Reader.

    Zotero is promising, but it doesn’t have accessible citekeys, which I think is essential to avoid being locked in to whatever word processor they support.

    Mendeley has cite keys, but as a database it has almost no tools at all, no smart groups or anything. I think it’s unusable as a serious research tool.

    Long term, when Papers 2 eventually ceases working, I think the best solution might be to switch to a series of apps that are good OS citizens (ie they have interoperability handles like Applle Script or URL schemes). BibDesk would be the central database, Evernote the note taker, Skim the PDF reader, Pandoc would format the manuscript adding in citations etc, and the whole thing would be glued together with little bits of Apple Script.

    Like

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