Thinking about Switching from Papers 2 to Sente

Of the four project development variables – scope, cost, time and quality – quality isn’t really a free variable. The only possible values are “excellent” and “insanely excellent”, depending on whether lives are at stake.
“XP Explained” by Kent Beck

For a long time my impression of Papers 2 was rather negative. A lot of really great ideas but a terrible execution. It literally hurt to see great ideas badly executed. But over time, and surely with Papers 2.7.3, these problems seem to be (mostly) solved. It’s stable, it allows me to focus on writing, it assists me.

I love Papers 2.

Given that I work with content outlines, writing the last article with Papers 2’s “cite while you write” feature was a breeze. You create a content outline, write the text and just by pressing ctrl + m you can insert a (magic) citation. That’s how citations should work … simple and easily accessible. Without interrupting the writing flow.

Also invaluable, I can easily sync my literature to my iPad and iPhone. Yeah, sure, you could improve any reference manager or citation software (got a couple of ideas), but, hey, it works.

For now.

Unfortunately, the current version of Papers is Papers 3. After seeing the initial bad reviews of Papers 3 a while ago, I did not upgrade beyond Papers 2. Trusting my references to a buggy software — with errors I might not detect, yet stake my scientific integrity on the correctness of the references — hell, no way. I rather continue to use a prior version.

But that’s no stable situation. The question in the back of my mind is whether Papers 3 is up to the task after a couple of updates and bug fixes. Because you cannot retain an existing version of any piece of software. You just cannot.

Give it five or ten years and your computer will need replacement and the old operating system will not run of the new hardware and the new operating system will not support the old software. In any software that is needed continuously, upwards compatibility is key. And while there are few pieces of software that you really need continuously, literature references is one of them.

But it seems that Papers 3 still has massive problems. I trust Aleh Cherp’s update (“Papers 3: still disappointing”) here.

Unfortunately, this reinforces my impression of the developers of Papers. They have brilliant ideas, but they lack the necessary skill to implement them on the required level. And — sorry — but when it comes to scientific literature, there is just the choice between “excellent” and “insanely excellent”, and it seems Papers 3 is neither of them. And I think they know it. The website states:

A Papers 3 license entitles you to use both Papers 2 for Mac, Papers 3 for Mac, and Papers 1.5 for Windows.

So, if you buy a Papers 3 license, you can use the previous version, too.

Seriously, if you have to offer the option to use Papers 2, Papers 3 is not ready to be released.

Meep. Yup, I really love Papers 2, but I am thinking about switching to Sente. Not sure whether it is better, and I am sure to miss the “cite while you write” feature. But that’s a minor annoyance if everything else works out.

And Papers?

Screw it.

Yup. Because literature management is not a game to me. Mistakes in citations kill a submission, and thus — over time — my career. Seriously, Papers, you are the Steve Wozniak of literature management for Mac. Great ideas, but terrible execution. Get a Steve Jobs into your company to get the quality issues under control.

You still have the chance to achieve something great.


  1. Sente is great. I don’t think you will miss “cite you as you write” so much. I switched from Zotero and had the similar concern. But then I found putting {Author Year} tag manually make your writing process even smooth–You don’t need to between applications, and you just do writing at the time. Scanning the file after you complete the writing is a breeze.

  2. Personally, I’m thinking of switching back to Bookends. It’s been bullet-proof for years, and the developer is VERY active and excellent at support. Bookends is fairly ugly (its looks haven’t changed for a very long time) but it is very powerful when it comes to tweaking the database entries, and adjusting citations and bibliography entries. It’s nowhere near as pretty as Sente, but it always works and has far better customer support. Moreover, it integrates well with Tinderbox, Devonthink, and Scrivener. It is worth looking at, though it will never win any beauty contests.

  3. Yes, you will miss the Magic Manuscript. that is heck a feature; magic, super magic.
    But, Sente also got some great features: specially the templates that you can write for your own bibliography style: the statuses for controlling your progress in reading your files: the mutlitude of database sources that you can fetch your reference data: the elegance of the ipad app..all in all combination, it has been very satisfying reference manager to me. I have been rambling all over Papers, Mendeley, Jabref, Zotero, Bibdesk; I never stick to any of them as I do with Sente (Jabref and Bibdesk are actually very cool for Bibtex, they are not just as such great for managing PDF files, specially if one is not into scripting business). You can have a look at how I am using Sente [here](

  4. As a Sente user, for you, I’d suggest Bookends. Sente is great as a Papers replacement. It does everything (except full text search across the database) that Papers does and more, only it does it properly. It is also extremely stable and has a great (free) ipad app. It is especially great for those who come across a lot of imagery and graphs, as it can take image annotations.
    Having said all of that, anyone who is a bit more tech-savy, will probably get more from Bookends. As great as Sente is, it is limited by design and slow to implement user requests. They have been hindered by prioritising development in the last couple of years on their syncing technology (first sync1, now sync2). I am hopeful that now that is done, they will get back to working on the app itself.
    It has great features, all mentioned elsewhere (like Bookends, it supports Mellel’s Live Bibliography feature).
    Limitations of Sente:
    – Does not allow you to sync specific collections or folders to your ipad. It is all or nothing. That means you need to have enough space on your ipad to accommodate your entire library (not always feasible). Otherwise, you are left with the option to download each pdf upon request (not the best alternative).
    – Still no full text search across the database (only per individual pdf). It does allow you to search using spotlight, but not within the app (defeats the point).
    – Not prepared for full database commands (i.e. search and replace across the entire database, etc…). This does mean however, that it is quite fool proof. It is hard to break the database.
    – No easy way to organise the database according to authors, etc (it will not merge authors, etc…). It expects everything to be done through tags.

    All in all, it is an excellent app, and my recommendation for beginners and people who just want to get stuff done. Don’t expect to work around its limitations though. Its a bit of a fortress in that sense. Anyone who wants to use it along with other programs (i.e. with Latex, and to a certain extent, scrivener with mmd) would better look at bookends, and get past its unfriendly UI and steep learning curve. It really depends on what you want to achieve.

  5. @ Trisha: Hmm, manual insertion is a way to go, but the nice thing about Papers was/is that you can select the insertion based on what you have written in the notes field. You did not really leave the application as you have a small window to search for/select the reference. Given that I use content outlines and have the author_year scheme (sometimes with a, b, c) as keywords in my content outlines, I found this a quick and easy way to select the correct citation. But using {Author Year} might also work in most cases.

  6. @ Martin: Thank you for the tip, I’ll have a look at it. I’ll probably write another posting about this topic soon, as Sente’s syncing really bugs me. An alternative would be nice.

  7. @Dellu: Looks like an interesting workflow, merci, I’ll have a look. And yup, after trying to write a sample text with Sente and comparing it to Papers … hell, Papers’ Magic Citations is just something … but it’s a bit like having a sports-car that looks really nice and is very fast, yet occasionally let’s you crash into a wall.

  8. @Joao: Another recommendation for Bookends, merci 🙂 Hmm, I’ll have to try out the full version. Looks like the iPad Lite version only allows for a couple of references, but still, it looks fast. At least by switching my Literature to Sente (even if I continue to use Papers for a while or go with Bookends), I have the peace of mind that it really is possible to switch the reference manager. Never seriously tested the export and import functions so far. And with all of the Magic Citations, iPad sync, etc. pp. — that is for me the top priority. If you cannot easily move to another app, don’t use it.

    Regarding Sente, my main issue at the moment is the extremely slow sync. Work literature is about 1.3 GB (a couple of full book scans and the like) and while the premium account can accommodate up to 20 GB, it takes ages to sync (and I do have an extremely fast Internet connection here). Not only because I do not want to openly “share” the literature, I think I prefer a more direct syncing option. Papers 2 and Bookends provide it (via WiFi, which I can control).

  9. Seconding Joao’s Bookends recommendation, to add a few points:
    – Bookends is easy to use for basic ref management, and you get full regex/sql functionality if you need that too.
    – Syncing between machines is covered: there is built-in support for master/client, local/remote library syncing, though for years I’ve been using the (not-officially-supported) database + attachments folder in a synced folder (via dropbox and now bittorrent sync) — it’s solid if you remember to close the app.
    – Although no match for Magic Citations, ⌘-Y grabs citations and switches you over to your specified editor ready for pasting, with little fuss. It works with every text editor I’ve tried.
    – The main attraction for me other than stability is how easy it is to manage citation attachments: you can match citations with both local and remote pdfs, remove orphaned attachment links, all coupled with fine-grained settings for duplicate removal. Since the database and the attachments can be in completely different folders, you retain file naming schemes and access to your favourite pdf reader, devonthink/hazel/etc. In other words, little to no lock-in.
    Its iOS companion `Bookends on tap` syncs attachments fast (over wifi), and does a good job as a basic citation manager and pdf annotation tool. So, it’s not going to win any beauty contests just yet (though bog improvements have been made in the latest major upgrade), but Bookends beats every other competitor on features and stability.

  10. Nthing Bookends. I used Papers 2 for a long time, and it was great, but occasionally the database would chew something up. Bookends has always been solid, and the developer is awesome at support. Personal response to email questions within a day, constant upgrades over many many years, and great integration with devonthink and tinderbox. That’s worth the price in my opinion.

  11. If you use your app for processing pdf (comments, quotations), then Sente might be superior to Bookends. Sente has a far superior, sleeker, pdf annotation & comment capability. Yet, neither allows you to tag the comments, sort and collect with smart collection (???). Devonthink Pro comment template is also quite useless in that respect — but you can at least create notes with tag and link to the page of the pdf. The process is ok but not seamless. You have to look at qualitative analysis apps (nVivo, etc.) for apps that allow you to tag comments. This is highly unfortunate.

    Sente would be excellent with a small incremental improvement of its comment function (tagging, search and smart collection). The best, but certainly not cheap, alternative might be to keep reference in Sente and use a QDA app for comments, tagging, etc.

  12. I’ve found PDF Stacks at a much better tool than the new Papers 3 version. I made a mistake upgrading. Papers 1 was the best but things are heading in the wrong direction and now do everything with PDF Stacks.

  13. I had a quick look at the video and it seems like a good program to simply store all literature PDFs. How well does using it for citation work, e.g., can you quickly cite an article when you are writing a text, how well does it create the reference section in different formats, and how easily can you change the references to a different format?

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