There was activity here a year ago re Papers, as it transitioned from Papers3 to a ReadCube product. I have carried on using P3 since, but it is no longer supported. Iam considering what to do now. Has anyone transitioned to the ReadCube product, and if so what are your thoughts?
An intriguing alternative I have just found out about is Paperpile (https://paperpile.com/welcome) which is embedded in the googleverse. Any users out there?
Gosh how timely!!!
I am just doing a knock-down, drag-out evaluation between Papers3 and Bookends. I can state categorically these findings so far:
Certain functions that Papers3 once had as best in class are now no longer reliable. Find similar does not work. Matching does not work. I suspect (and have heard in passing somehow) that Papers/Readcube has lost/dropped their rights to access certain Web portal databases that gave them the data they needed to do these two functions.
Papers3 does far better than Bookends at allowing you to set up group searching methods on internet searches. Consider ((au: somename) OR (au: someothername)) AND ((all: some term) NOT (all: someterm)). You can do this in Papers3. You cannot do this in Bookends.
Papers3 has a far better approach to searching multiple resources on the internet. In Bookends, you must run each resource one at a time. First PubMed. Then Google Scholar. Then … Then … Then … In Papers3, they are all run at once.
Papers3 allows you to merge duplicates (sometimes poorly though) while Bookends make you think “What the heck am I doing … I don’t want to REMOVE duplicates, I want to compare/combine/merge them”? And when you are going to “remove” them in Bookends, you have again to do the process in a tedious one-at-a-time, move to a hit list first approach.
I am still struggling with what I consider to be a complex or cumbersome or counter-intuitive layout of the menus and preferences and terminologies in Bookends. For example, I would be looking for a menu or preferences simply saying (Set) Search Engines, not looking for a menu File : Import Filter Manager (which, since “import” is also a verb, could be taken to mean “import the filter manager as a file”).
Neither Bookends nor Papers3 are well-enough equipped to set up group searches on content that is already in your database. You CAN run complex REGEX searches in Bookends, but only on the meta-content to an article. This is useless when you have an article from 1966 that did not import well and therefore only has the title “A New Finding in Physics” that is supposed to be handled by the search on the same grouping list that I gave above. At least Papers3 also searches the document with some levels of simple groupings on internal searches. But its internal search panel only allows you to think sequentially with ALL or ANY, not in groupings with booleans.
The iPad version of Papers3 just a viewer for your entire database. The iPad version of Bookends is nicely done to split the database to “bite size chunks” as needed.
I am heading to a point where I am almost convinced that I will
Use Papers3 to do complex searches over multiple external databases. Bookends is a recalcitrant mule by comparison to the Papers3 rarin’-to-go race horse for this need.
Use Devonthink to search my Papers3 database (as an INDEX resource) for collections of ideas in various ways. Neither Papers3 nor Bookends offers the strength of grouped-term-level search capabilities that I need to get this done without spending more time constructing hack-around-folder hierarchies than actually just constructing group expressions and getting the results.
Extract my findings from Devonthink and export them back to a “Share” Bookends library to allow me to review them on my iPad. This stage of my workflow is still a dream/hope to be tested.
Right now, I am culling my Papers3 database for duplicate files. My cursory review of my Devonthink index on the Papers3 database shows that I need to do a lot of pruning. I need a good Duplicate Cleaner (and will go searching here … @anon41602260 had a reliable recommendation that I lost in an upgrade of my SSD a few months back).
Update: BeyondCompare in this thread.
As for Readcube/Papers … I tried it briefly. The UI is nicely done but the Web app is all that exists and that has far fewer of the core features that I absolutely need from Papers3. I would stay with Bookends over the newest Web-only version of Readcube/Papers.
As for Paperpile … I do not like Web-based apps to manage my citation resources.
Summary: I am probably going to stay with Papers3 until it truly just dies (has anyone tested it under Catalina???). I will not upgrade to Readcube Papers until it is a desktop app and only then when I am convinced that it has not dropped the features I need to do complex searches on external databases.
One other side note. I am convinced that the medical field must be the ones who need these tools compared with science/engineering folks. Why for example do either Papers3 or Bookends not have an entire section in their user’s manual devoted to how to run IEEE searches as they already do with how to run PubMed searches? Maybe the sci/eng folks pay for EndNote instead???
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JJW
Thanks for the long well thought out reply. As for Papers3 and Catalina, I dont know, but it doesn’t come up in the Go64 app sweep of apps that won’t work. Will have to wait and see.
Like you I will keep P3 until it (inevitably) dies. I might try the trial of Paperpile but also not keen on the web only part.
I’ve recently switched from Zotero to Bookends. I didn’t like how non-native the former was, but Bookends has required a lot of learning… It does seem extremely well-supported, however.
Yes. Support for Papers3 is non-existent by comparison to the support available for Bookends.
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JJW
I fall into this camp. The majority of folks in my field use document managers like Endnote or Mendeley because they allow inline citation management while you write (so called “cite-while-you-write” capability).
I also tried PaperCube, and while the UI is very pretty and nice, it’s not worth the price because of the lack of sophisticated inline citation ability (maybe that’s changed since I last tried it out).
I’ll look into Bookends, but it would have to amazing compared to the other two I mentioned.
Doesn’t Bookends have cite while you write? I accidentally hit Option twice sometimes and it pops up a search box to insert a ref.
Edit: https://www.sonnysoftware.com/bookends/floatingcitations/floating_citations.html
I’m old-school. I use LaTeX and manage bibliography->citation links with \cite{} keys. Granted, it is a studied habit that requires great diligence compared to the “cite-while-you-write” in MS Word approach. As I might say … Robust habits learned over a few decades are not easily given up just for the sake of shiner things on the road.
I would use Bookends entirely for my local database were it not for the difficulties that I have with the architecture and corresponding restrictions within its local search forms as well as with the oddities of its menu/UI language/layout. At the back end, I already know that Bookends integrates with DevonThink Pro and exports BibDesk files cleanly for my LaTeX documents. We’ll see where my ventures with it finally land.
FWIW, I have not found any citation manager on the iPad the can compete with what I see being offered in Bookends. I had hopes once for PaperShip, but that ship has sailed.
I have worn myself thin with using Mendeley to do anything with my citations other than to share them with my research group.
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JJW
It might have, it’s been some time since I’ve looked anything past endnote.
I’m tempted to switch to endnote for everything - currently on papers 3 for reading and endnote for citations (easier to share with my research group via endnote web).
Do you find Endnote to be worse for reading than Papers3?
How do you keep the two citation managers “in sync”?
(FWIW, I am currently importing my Papers3 library for a trail run of EndNote).
I am also especially curious about the iPad experience with EndNote. My goal is to be able to read (and annotate) any and all of my PDF files seamlessly and entirely on the iPad regardless of their home application.
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JJW
Further findings:
Paperpile does not search the PDF content. That is perhaps a deal breaker for me (see below).
Paperpile is working on a desktop-only version of their app.
Papers3 beats EndNote X9 hands down in the complexity with which you can construct complex searches on external databases.
Papers3 beats EndNote X9 in the number of external databases configured out of the box for search (Google Patents is my prime example missing in EndNote and Bookends both).
EndNote is tied with Papers3 and both beat Bookends in the intuitiveness of their UI and application approach (I grant that some may see this ranking as being subjective for a given user).
All else the same, EndNotes searches seem to be faster and the returns more reliable/consistent compared to Papers3.
Nothing beats DEVONthink Pro for being able to create complex searches as well as to clean up duplicate or mis-named files in the database.
I still think I will end with Papers3 + DEVONthink as the best of all my needs. When Paperpile has its desktop only app, I may test it also in combination with DEVONthink.
I still want to test Bookends as my iPad citation reader tool, interfacing it through DEVONthink or from Papers3.
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JJW
The iOS app for Endnote has come a long way (though I wish sync was a bit more automatically inclined) and has nice annotation capabilities.
From my review in the last few days Paperpile does not do annotation. It seems to have some issues importing a library, where a completely different paper shows up when you click on read. I’m a little concerned re the rate of progress on the app having browsed the forums. The labelling is horrible (very google webmail, which I don’t like aesthetically).
ReadCube Papers actually looks quite good. All my tags were imported. They have an ios app and soon to release a desktop app. The subscription is a little more expensive than Paperpile. I’m trying the 30 day trial.
Have you considered Zotero?
There is a solution to import from Zotero to Devonthink - that gives you the best of both worlds for acquiring references and searching for them.
I have to back off this statement a bit. No application can search for text in a bitmap PDF file. It is not the fault of Bookends.
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JJW
If you index the PDFs with DEVONthink (which I think should run ABBYY FineReader on them?), you should be able to search the full text in Bookends, correct?
(This thread is a bit long, and I may have lost details and the point by now 
)
I wouldn’t yet give up on Papers!
I just got invited to the new ReadCube Papers desktop beta which is the desktop version of the Web app:
Here is some more info concerning this.
But I too got quite frustrated by the old Papers version - mainly because it could hardly handle my large collection of papers.
Thus I bought Bookends - it really takes a while to get used to it but after long digging, trying, searching in forums I was able to find most of the functionality I need. Nevertheless, it really has a poor interface and is definitely not appealing to look at.
(Btw: If you need to search for multiple terms you need to click the “advanced…” button in the search window)
Unfortunately, I can’t comment on the beta yet since I am currently too involved in finishing a rather long manuscript and need a reliable system until I’m done…
Just digging out from Fall NIH cycle!
I haven’t really tried endnote for reading. I just use them for different tasks out of historical purpose. My endnote library started in Endnote 3 and I’ve just always kept citations there since that is where my old ones are. Papers was similar, started with papers 2 since someone said it was better than just folders of PDFs (which is what I had prior, and before that paper). I just keep them in sync as needed. Students add citations to endnote if needed for manuscripts, and I add them if needed for proposals (typically just copy the title from papers and search in endnote).
Part of why I’m exploring what to do is that there wasn’t any thought behind my arrangement, just inertia.
Ok. So I’ve been through endnote (kind of pricy for students), tried zotero and some others, then landed on Bookends. Bookends had some errors and had issues. Then next was Papers 3, which allowed me to just drag a pdf into it for import and it would grab the metadata, allowed better searching for references online, better management of imports, duplicates, etc.
NOW, Papers have moved to another model (Online app) that follows the revenue-stream subscription crowd, and it will allow you to drag in references, but otherwise, it is not very functional at all. I will probably use Papers 3 until I have no other choice but to move on to another.
I use Mellel (word processing) and am looking for a citation manager (app, not online) that will allow me to embed citations and keep track of them in my document. Be really wonderful if it works with DEVONthink. Any ideas?
