Academic Workflows

I tried to support Papers since they sponsored The PhD Movie, but it just didn’t work for me.

Bookends is pretty good, better than EndNote, etc. for me, though the UI needs a refresh, and some of the more esoteric things can be challenging.

Zotero is also excellent, the API is especially handy. I have been messing around with both Zoero, and Bookends and the way I would pit them against each other is fairly simple in the end.

If you want an excellent native reference manager for macOS, and you would like a GUI for scanning your citations, then download a trial of Bookends and have a look. I used to have similar feelings about the UI, but spending some time with the app disabused me of that notion. It’s true that it can be complicated, but take that as a positive. The app has been rock solid, and it is built by a responsive indie developer. Case in point, he turned around a feature request in a month (a month!) to help folks writing with Scrivener etc

On the other hand, if you want to get nerdy with Pandoc, use your references on the web, or do any kind of automation then Zotero is the way to go. For example, I was able to build a bunch of shortcuts for writing on iOS. However, if you don’t like the Bookends GUI, the Zotero will give you sea legs.

If anyone is wondering how I could get away with using both, the answer is a common BibTeX. However, I don’t recommend it. I’m doing it for Blog Science. :wink:


This article on using Zotero on iPad is tremendously helpful thank you. This is a nut I’ve been trying to crack.

Where do you store your PDFs?


I find I"m having to switch to Zotero. When ReadCube got ahold of Papers they pretty much ruined it. I finally got a response back from them but haven’t had time to really pursue it yet.

The vast majority of my work is medical with some education thrown in.

Browzine and QXRead to bring me articles
Into Papers 3
I use a mix of Drafts and Ulysses for mobile work which is becoming more and more my workflow.
Word and Powerpoint unfortunately
Keynote for my personal presentations

I’m also playing with Bookends right now as a Papers 3 replacement.

In that case, you might be interested in these posts I came across a while back. I believe the writer is/was a regular on the forum:

And a more general comparison:

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Thanks. For some reason, I hadn’t stumbled across him.

Thank you so much, I have been looking for academic workflows for Mac and iOS! just added to my RSS feed!

Just wanted to say, thanks for this reference to the book, How To Take Smart notes is like “Getting Things Done” for academic workflows. Paradigm shifting for me. Thanks!!


Interested to hear about your adventures as you get into the system!

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I read the book, and now am trying to figure out the details and the best way to implement it electronically. It would be ideal if it crossed over from iPad to Mac leaving some programs out, and allows easy linking between notes.

Evernote seems like it would work well, but I worry that company won’t be around much longer given the mass exodus. I’ve not used DevonTHINK yet and don’t have the time to learn it.

I’m not an Evernote fan. Tried it, but it became a dumping ground that I rarely revisited except to dump more stuff.

I’m wondering if Apple Notes might even work. Since @ChrisUpchurch enlightened me on how to create links, that might be an option.

Ulysses is a thought, Agenda, NotePlan, Drafts even? Something I’d like to look into more myself, unless you do the leg work for me :slight_smile:

I’ll happily do the legwork! I watched these video casts by these two German fellows on a channel called Zettelkasten. They seemed to feel that programs like Ulysses that keep everything together in a big chain didn’t work well for them. I’m not sure of that, but I do like my text files to be stored in a non-proprietary format that I can get into should I stop subscribing their program.

After giving up on Papers (admittedly I haven’t looked into Bookends yet), I’m just relying on my 90’s workflow of nested folders in Dropbox. It’s not perfect, but I’m keeping the numbers of folders small and naming files YYYY Author <2 word topic>.pdf (e.g., 2018 Edlow Managing LBP). Then I’m storing the “permanent notes” as text files in DropBox via Byword. I can use URL callbacks for links, but it’s not as nice. I’ll look at Ulysses more. I downloaded Agenda and Bear to take a look. Haven’t heard of NotePlan.

Apple Notes has all my garbage things I can’t forget (codes to things, books to read, etc).

I’ve been using Ulysses as a note repository for the last 18 months or so, before and after reading the book. Its main weakness is in linking sheets easily but I’ve written a couple of solutions which work great for me. One advantage is you can use whatever title you want for your sheets and links rather than having long date stamps that clutter things up without adding meaning. Links are cross-platform and when hooked up with OmniFocus or Filemaker (Go) make for a pretty seamless experience across devices.


This stuff always sounds so simple until I have github and terminal open and can’t figure out how to do anything.

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Hey there, is there something you’re doing to make the links clickable when pasted into Ulysses? They’re formatting as proper markdown links, but not as functional markdownXL (?) links.

shift-command-V I believe it is brings up a pasting context menu where you can select to paste as Markdown.

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Bookends is my choice for storing PDFs and doing references. They recently added a quick key for cite as you write. The proprietor is amazing with updates and responses. From it you can go to any PDF editor, though there is a native one in the iOS version.

BTW I’d love it if David S. featured it (and other academic workflows) on the MPU podcast. MPU did feature academic workflows a couple years ago, but not much since.


Ulysses works. So does Byword or any series of text files. Linking is not as convenient with text files, but you can use the Luhmann system of namin/numbering (1a4d12 etc) to refer to a note by it’s number.

Drafts is where I write the initial notes, but then have been moving them to Dropbox/Byword.

I’m a little wary of putting things in iCloud or a proprietary system (Ulysses or Agenda). Should I ever leave the Apple ecosystem (and with it, iCloud) then everything is stuck in Apple-land.

UPDATE: Actually Ulysses is working wonderfully. By linking it to DropBox, each text file appears like a sheet, each folder like a group. A nested folder is a nested group. The file is named by the first line in the sheet proceeded by a @:, i.e. @: Luhmann 2018. And I get to use the organization and writing features of Ulysses which is a bonus.


How well does bookends handle shared groups?

FYI in a new article on Chrome productivity extensions Cite This For Me: Web Citer is noted; on any web page it can generate a correctly formatted citation in your choice of APA, MLA, Chicago, or Harvard referencing styles.