Academic Workflows

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.

A couple of Zotero integrations

Google docs:


I am surprised there is not more discussion about The Archive text editor. Maybe all the zettelkasten stuff confuses people.

It’s a pretty good app - a kind off nvalt upgrade.

It’s been discussed quite a bit actually -

IMHO the reliance on long date-time stamps for linking clutters it up too much. I’d much rather use the title of a sheet in Ulysses and have the id hidden, as discussed above in this thread.

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Interesting workflow: Scrivener, Endnote and Nvivo:

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I like the deliberateness of writing annotations on everything one reads. Not so sure about committing to NVivo though at $700 or so for a license once the PhD is done. I’d want to know how it does its PDF annotations.

I am currently suffering buyer’s remorse ($800+ but fortunately all grant and institutional funding) with MaxQDA as it uses Foxit PDF instead of the native PDFKit on the Mac, with the result that text selection and copy/paste don’t follow Mac standards and import/export of annotations into Preview etc. is impossible.

NVivo doesn’t “annotate” PDFs in the way we typically talk about. So you can code (or “add nodes” to use the parlance) to a PDF, and export that PDF in such a way that it will behave like a PDF annotated in Preview or PDF Expert or PDFPenPro. In other words, the marking-up you do in NVivo doesn’t translate well outside NVivo. Of course you can use NVivo to export your nodes and other excerpts, which is useful in its own way. But if you want to have portable highlighted PDFs, NVivo is not your tool.

Almost identical on my end. Great set of tools.