Academic Workflows

Inspired by one of my favorite MPU episodes 221: Academic Workflows with Aleh Cherp

I would love to know and geek out about academic workflows on Mac

My research & writing process includes:

  • Zotero - Reference Manager
  • PDF Expert
  • Devonthink Pro and The Archive for my Zettelkasten
  • Scrivener 2

Some complements:

  • TextExpander
  • Evernote for web clipping on an Android Phone
  • Xmind for Mindmaps
  • Grammarly

If you’re (open to) using LaTeX, MacTeX includes BibDesk, which I use to manage documentation (citations and references) information and act as a PDF repository (BibDesk doesn’t actually hold the files, but it automatically renames and files PDFs of articles; I use a file in Dropbox for that). That greatly simplifies the writing and documentation workflow for me.


Thanks for this. I’ve dabbled with the idea of working in and with LaTeX in the past, but have yet to be convinced. I’m working in the arts and humanities (so don’t need equation power) but I’m interested to hear about getting started with LaTeX – resources, etc. Thoughts?

Just to add, this is a slightly old blog post (ie some things have changed) that covers my academic writing workflow. Perhaps of interest?

Cheers, Simon

You can try to get started without any downloads and use it as a sandbox. I’ve found the very helpful. Start off with the fewest, most basic (required) options, compile it, and see what you like and don’t like about the finished product. Don’t like the font? Search “LaTeX fonts.” Don’t like the margins? Search “LaTeX margins.” Need a table or figure? Include it, see what you don’t like, then figure out how to improve it. It’s tedious at first, and even ten-year LaTeX pros still find new packages to add or deprecated ones to replace. Over time you’ll build your own style (LaTeX lets you summarize all your packages and choices into a single, separate style sheet).

Another benefit of LaTeX is that it can handle article- or book-length projects and even presentations (using Beamer). That means the same tables, figures, citations, or whatever in your text can be brought into your presentation very quickly and easily.

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Cool! Can you talk about using DTPO and the Archive for your Zettelkasten? I am interested in doing something similar. Problem is I’m not sure if/how IOS can fit with that system.

I’ve been interested in Latex, but then realized its completely unnecessary for my field (psychology). I only had to use it once when submitting to a computer science education conference. Luckily I had a collaborator who knew Latex. I’m trying to avoid learning skills that don’t improve my work and are not necessary for my work (Latex and Markdown for example), but then again, I’m constantly downloading and learning new apps.

I guess I’m trying to be more like Katie. Find something. And stick to it when it works.

I use the following:

  • DEVONThink for research (DEVONagent) and document storage
  • Papers for references and citations, some research
  • MindNode for outlining research, papers, projects, and lectures
  • Ulysses or Scrivener for long-form writing, I’m using Ulysses more and Scrivener less
  • Keynote for slides
  • PDF Expert for PDF annotation

I don’t think LaTeX is necessary for any field. Yes, some fields benefit more from its use, but anyone who produces typesetting output of any kind—and that includes any academic field—can benefit from it. Yes, it does well at typesetting mathematical equations, but it does so much more, too. As I said before, LaTeX’s handling of documentation, flexibility with formatting tables and figures, and other things (ever tried to reformat all the section headers in a paper, change all the citations from Chicago to APA, or make an index for a book after it’s written? Yeah, LaTeX can do each of those with a single line of code) make it worth learning the relatively simple language to me (feel free to disagree).

This is an unfortunately common short-term thinking approach toward learning plain text language. Sure, crank out a paper in Word as quickly as you can, for it gets the job done. I get that. On the other hand, a long-term vision would highlight the importance of version control, integration with relevant programs (documentation and statistics), and ability to reformat or add entire sections with single lines of code.

Use whatever workflows and programs work for you, but if you want some control over your writing output, I recommend reading The Plain Person’s Guide to Plain Text Social Science by Kieran Healy (a sociologist, so from another field that doesn’t need LaTeX :wink:).


For research, I use DEVONthink. When writing, Ulysses for most texts (blog posts and online articles), and Scrivener for conference papers and long publications. Drafts for ideas (especially dictated from my watch). I also use Grammarly, Keyboard Maestro and TextExpander all the time. I use Endnote as a reference manager, mainly because I’m used to it and have used it for almost 20 years.

The OmniGroup tools are handy. I plan my working life with OmniFocus, and I prepare all my courses on OmniOutliner (as well as plan my marking). I then produce class plans (showing when assessments and exams will be) in OmniPlan - my supervisors like the results from this a lot because I teach Information Systems and most of the professors are ex-project managers. I even use OmniGraffle to do the diagrams in my slides, mainly when doing ER diagrams and Data Flow Diagrams.

I still use PowerPoint for slides because I have to collaborate with Windows users every day.

On iOS, I use iDoceo to do my grading and attendance and GradeScanner to automate exam marking.


I use Texpad extensively. The new live typesetting is crazy. it doesn’t re-typeset the whole document. Somehow it renders the changes in place.

Texpad may be the future of using LaTeX on a Mac if tighter security is ever required. They re-wrote the TeX engine. At one point they are updating the iOS engine to live render the same way.

Not affiliated just a very happy user.

Same as everyone for DevonThink.

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Devonthink users - do you find the supposed AI actually works? I have tried the program several times with corpora of 7000 pdfs of secondary lit. and 2500 or so of primary lit. & search never seemed better than what I can do with file system-based tools. I’m sure it’s great for filing invoices and utility bills but it never seemed to be able to handle more complex content.

@dfay Are you referring to the magic-hat/see-also functionality, or the actual (advanced) search function?

Magic hat / see also

I am currently transitioning back to academia after a 13 year stint in industry. Used Medeley to organize my publications/references on my Mac. Papers were prepared and published working with a medical writer, so little use for many of the tools mentioned in this thread - docs would come in Word format for review and comment. Any suggestions on what I should consider using as I ramp up? I expect the first year or so to be focused on research and preparing grant proposals. Thanks!

Hi, Kevin!
Well, I’m in a beginner stage on the Zettel. Before the launch of The Archive, I use to have a Data Base called Zettelkasten in DT and notes in plain text named by a unique identifier with the help of TextExpander.

But now, I’m writing my notes on The Archive an app made by the authors of a blog about all things related to Zettelkasten and the plan is to indexing those notes on DT to use the AI features.

All this workflow have been inspired and recommended by Nicholas Cifuentes in the slack channel Research Hacking.

I don’t use IOS, but maybe you can find some help on these forums.



I’m following this thread with interest :slight_smile:

I used to follow the Macademic blog until it went silent since mid-2016. Some really nice ideas/reviews there!

I love Texpad for LaTeX but recently switched to VS Code + Latex Workshop. I was especially tempted by Texpad because it had/has a nice iOS app, but I found myself doing most my typing on the Mac anyway.

I use Noteshelf a lot for handwritten notes and Mindnode for high-level mindmapping. Airtable, Notion and Things for tracking projects and ideas. Using Documents on iOS and Dropbox to sync books and papers and exploring Bookends as a more specialized reference manager.

Still trying to figure out Devonthink and also a follower of the Zettelkasten material!

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How do you find using Things for academic projects? I’ve been using it for everything else, but I am worried it might get bogged with planning for papers and related projects.

I wish he kept that blog up, super interesting to read.

What is Zettelkasten? Also I’ve heard mixed things lately about Papers, I’ve heard some people who actually store PDF’s and academic articles in DevonThink and use another citation manager.

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That’s me! I store the reference itself in Zotero, the PDF of the reference (i.e. article, journal, web page) in DevonThink, and then notes which I’m using go in AirTable :slight_smile: