Academic Workflows

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.

I’m looking for apps that work well together in split screen. I.e. Bookmarks and Ulysses. I’m trying to find a PubMed app that will split screen with other apps. The one I”m currently using floats, but won’t split screen.

Hello everybody,

I currently work on my PhD (political science) and don’t really like my workflow. I used to rely on Devonthink and Scrivener. However, I am not that satisfied anymore. When not at home I work on my iPad Pro (iMac at home) and especially for Devonthink it feels like it is only an afterthought to the developers, i.e. no open-in-place functionality. Additionally, I often have syncing issues. Scrivener on the other hand feels clunky and not well-suited for iOS.

Therefore, I look for a workflow which better fits my needs. A workflow I would like has to tick the following boxes:

  • everything should be synced via iCloud
  • I need a writing app which is capable of large-scale projects but doesn’t overcomplicates everything, I want to focus on the writing process
  • I would like to write in Markdown
  • the project has to be seperatable into smaller pieces
  • it would be great if I could insert reference links for research material
  • somehow it all has to work with my literature management (Mendeley at the moment)

I use Ulysses for blogging, do you think that it could be an option for my PhD as well? Or does it miss anything, one definitely needs for academic writing? And do you have any idea how to link to reference material in iCloud folders?

Thank you very much for any suggestions! :blush:

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Brett Terpstra’s Marked 2 app includes working with multiple markdown files (as chapters:

I have 1.1 million words of reading notes etc. in Ulysses but I can’t imagine writing a dissertation in Ulysses (having written three in WordPerfect 5.1 to 8…which wasn’t ideal but which I’d probably use in favor of Ulysses still if those were my only options…). I don’t think its organizational features come close to what’s possible with Scrivener (which I’ve used for nearly everything I’ve published, since switching to the Mac on my 1st postdoc). I use Markdown for the first draft of probably 90% of what I write these days but once you get to second and third revisions, responding to reader comments, etc., I’d expect you’re going to want the additional organizational and markup features that Scrivener makes available. By all means write in Ulysses if it lets you get everything on the page - its export is good and easy, too - but don’t expect to keep everything there.

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I don’t know of any app that’s available for academic writing that is excellent on both iPad and Mac. If you’re intent on writing in Markdown then of course you don’t need to use one single app, although niceties from a dedicated Mac app may not be accessible.

If I were writing a dissertation that utilized references from something like Zotero/EndNote/Mendeley I’d consider a specialized Mac app like Manuscripts, whose workflow is similar to Scrivener on the Mac but is designed for academic writing. (Note: I have not used this app.) The main downside to it is that it is not cross-platform, and I’m not sure it works with iCloud.

Ulysses could be an alternative given your listed requirements, depending on how you’d intend to insert reference links. In this Reddit thread, the top-poster describes using Ulysses (along with LaTex, TexPad and Citations) for his/her thesis:

I had high hopes for Manuscripts, even bought it to encourage them. It is now open sores, and still not reliable enough for me to play with it without crashing or other problems. I cut my losses.


Ah well. I did the same thing, paying 1.5 years ago for Gingko, but it’s still not in the kind of shape where I’d trust it with extensive writing.

Rather than jettisoning a system that has been working for you, maybe you can determine why you aren’t satisfied. You have tools you are familiar with, and they have been working for you. What problems are they not solving for you now? Is it because your dissertation is difficult, rather than the tools?

Also keep in mind you don’t have to work on the whole document at once. You could work on a particular chapter (or paragraphs) on your iPad, insert references to be fixed when you get back to your iMac, etc.

Finally, if jettisoning Scrivener is the correct solution, I would recommend looking at thesisdown and its derivatives for various universities. There’s also Tyson Barrett’s workflow using RMarkdown and LaTeX class files for formatting and layout.

I’m evaluating both for my dissertation writing. (Did I just write that :grin:)


Same. My Gingko is withering in my Applications folder. It’s such a novel and interesting paradigm too.


If you can identify one person who’s completed a dissertation (tenure is too high a bar…) purely in Markdown I will be astounded.


Here’s one :slight_smile:

I wrote my PhD thesis using Word and folders on a hard disk and it was not a pleasant workflow at all, but back in 2003 there were not many options. Now for longer publications like journal articles I use Scrivener and DEVONthink on the Mac and the combination is a joy. I always feel in control of the writing and confident I can access my research materials easily. Honestly, I couldn’t imagine better tools.

On the iPad they are nowhere near as good, but I think you’ll be hard pressed to find better.

For short publications I use Ulysses but it’s not suitable for writing a thesis. Keep It is another option, but this is not as full featured as DEVONthink.


There’s also Texpad, which is amazing.
Copy/paste isnt working for me on iOS beta, but search here on the forum for more details.