What are your long-form writing workflows?

Software
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I’m a PhD student and have been unhappy with my current writing workflow.

Right now, I’m using Essayist, which is a great looking app, has reference management built in, and handles all the formatting for me. On paper, it is perfect. A couple problems, though: (1) I prefer writing in Markdown, (2) it’s reference management is a little clunky, (3) I prefer writing in chunks, so I can focus on one section of a paper at a time, and (4) any modifications to the formatting for professor-specific needs is nigh-impossible. I still have to open in Word at the end and make changes before submitting papers.

I’ve tried iA Writer and Ulysses and can’t get either one of them to work how I need.

So here’s what I’m looking for in an editor:

  • Markdown
  • Regular files (no proprietary format)
  • Ability to write in sections and combine later. (Or collapse non-focused sections of one larger document.)
  • Robust footnote implementation (I can use Zotero for the reference management, I just need to be able to insert citations easily.)
  • Easy export to .docx for assignment submission (I have a tiny bit of experience with Pandoc, so if I can use that, it is probably an option.)

Ultimately, I think I might go with Obsidian, since I can get pretty much all of this with plugins. But then I’m using Obsidian, which I don’t love.

What are you all doing for this?

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I think if you search “writing workflow” in this forum, you’ll find a lot of prior advice and cautions.

Katie

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Hi there

Fellow academic writer here. Tell us more about your field! Sometimes, that will predetermine your needs. Talk to others in your field and ask them in what formats they need to deliver their writing. You seem to have thought this through already, and on top of your tech (‘pandoc’) – there may not be a perfect writing app for you.

I’ve answered versions of this question so if you will excuse me, I will refer you to another forum (I hope that doesnt’ break the MPU forum rules here). The entire threads are worth a read:

In short, what I recommend to my own PhD students and what works for me, is that they use best-in-class apps that specialise in one or two things (the one-stop-shop of Essayist would worry me a bit – but it does look very slick!). I’d always favour local file storage, interoperable formats, great backups, and no app lock-in. I use:

  • an archive for research materials (mine is DEVONThink)
  • a reference manager (mine is Zotero)
  • a linked note taking and idea development space (mine is Obsidian)
  • a long(er) form writing app (mine is Scrivener: I found that Obsidian just doesn’t scale to book length writing, but is brilliant for short interlinked notes)
  • a publication app (once you start writing for collaborators and publishers, you won’t escape the Microsoft world).

A well-build system like this will serve you a life time. Keep it really simple at the beginning, since it will grow with your needs.

 ... Obsidian, which I don’t love

I would say: love the writing, and like the app. I don’t love Obsidian, but it serves my needs fine. In the end, no amount of noodling with my plug-ins gets my articles written, so there, too, I look for an app that’s simple enough to get out of the way.

Good luck!

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Sorry @joshua612 I just saw from your description you are a theologian – very cool!

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Based on what you present, as already mentioned, look at what is offered in Scrivener for writing.

In addition to Zotero, consider Bookends for reference management.

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JJW

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I’ll second the Scrivener recommendation. The Literature and Latte forum (Scrivener’s developer) has a deep set of users discussing using Scrivener for academic writing.

@joshua612 mentioned they might go with Obsidian. As much as I enjoy Obsidian, I would never use it for creating formal documents. You’d spend as much time trying to manipulate the files into a presentable package as doing the writing itself.

Katie

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Thank you for your response! I have a feeling I’ll end up with a setup similar to yours.

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To hit all your bullet points with minimal friction I’d pick Obsidian.

Here’s where it shines: Markdown, regular files, sections can be combined later, export via Pandoc to a word file for final formatting if required.

Here’s where it’s difficult to set up but works well after weaking
footnote implementation (it can connect to Zotero but getting it working properly for your specific format can be tricky)

Scrivener is a good choice for long forms but the markdown and the fact that the files are not really standard until you export out of Scrivener makes it a less desirable choice IMO. I’m actually moving all my longer form documents out of Scrivener and into Obsidian because I can more easily link, edit and use them there.

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I’m curious, is there a reason you recommend Bookends over Zotero?

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I prefer Bookends to Zotero for the following reasons:

  • Multiple Libraries – I have been active in about a half dozen sub-fields in my studies. I greatly appreciate that I can create separate libraries for each sub-field.
  • Self-Contained (Archivable) Libraries – Continuing on the above, when I generate a publication, I collect references that may or may not be used as citations into a “Working” library. When the publication is submitted and/or complete, I extract out all references in that publication, store them in their own library and attachment folder. I can ZIP the entire set – LaTeX sources, BibTeX file, Bookends Library, and Bookends Attachment Sub-Folder – into a complete archive of the publication.
  • Direct Finder Views of Attachments – I strongly prefer how Bookends allows me to find a specific PDF attachment for a given reference directly in a designated Folder at the Finder level. I cannot deal with the approach in Zotero to store attachments within its own (randomly-generated) set of (hidden) folders. In short, when I want to open a PDF attachment for a reference to Topic A, I do not want to have to do so by first opening Zotero, finding the reference in a folder called Topic A, and doing an “open in …”. When I am working on studies belonging to Topic A, I know that I can find its Bookends library called Topic A (see above) and that I can find all PDFs associated with that library by going in the Finder directly to the ~/Documents/Bookends/Attachments/Topic A folder.
  • UI – I work better with the UI layouts in Bookends to view various aspects of a reference. For example, I specifically do not like to “dig” to find a PDF in Zotero versus seeing the PDF direction in a panel in Bookends.
  • iPad Workflow – I read and annotate PDFs on my iPad. I prefer the ability to work almost seamlessly with Bookends macOS and Bookends iPadOS.
  • Scripting – I appreciate that Bookends on macOS is highly scriptable to expand its utility.
  • Flexible – I appreciate that Bookends provides a (complex but tenable) approach to generate reports in various formats (e.g. here is an example of a workflow for Bookends → Obsidian)

I have worked with Zotero for collaborations with colleagues who are on Windows. I appreciate its allure and I can tolerate using it. Compared to Bookends, Zotero is simply not a good fit for how I want and need to handle bibliography references.

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JJW

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Thank you for that detailed response. Super helpful!

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I’m a full-time journalist dabbling into fiction writing, so my writing is broken up across a few separate apps.

Drafts: my go-to app for dumping all my ideas. I use it for story pitches, newsletter ideas, and any general thought I’m not sure where to store yet.

Obsidian: all of my highlights and notes from my readings, as well as drafts of articles for work and for my newsletter. I have a few plugins, but basically just to make it look and feel more like Bear. I’m not a fan of all the fiddly stuff you can do with Obsidian — glad it’s there though — so I’m running a strictly text-based system.

Scrivener: I’ve been experimenting with screenwriting just for fun, and I’ve been really impressed with this app. It’s made organizing my outlines, ideas, and scenes a breeze. I wish the iOS app were a bit cleaner, but it still works like a charm.

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It’s proprietary but worth mentioning. I use Tinderbox

It has a step learning curve, but can do a lot of sorting of your notes automatically and has good export. It gives you different views of your notes. It’s probably one of the few single environments I know for studying a topic that I use. It would tick all your boxes apart from regular files.

Their forum is supportive and the company responsive. Many academic use this software. I know a lot of folks on here use it and @beck has done videos on using it.

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I should add one further note about Bookends versus Zotero. Zotero stores annotations outside of the PDF. You have to take an extra step in processing to bring the annotations inside the PDF to work in other applications (e.g. Preview). Bookends follows conventions to keep the annotations within the PDF.

So, if you need to work with annotated PDFs in applications besides Zotero, you face extra steps to a) bundle the annotations back into the PDF itself and b) export the PDF from and import it back into Zotero (rather than working at the Finder level directly).

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JJW

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Writing workflows - a favorite subject of mine. I think I’d be ahead in the game if I put actual writing on a higher priority. In the meantime, it’s fun messing with writing software.

I generally write with both my document and my outline open. As I discover things that ought to be in my MS, I add them in a logical place in the outline.

If that’s where I’m currently at in the document, cool, I add the new ideas right away.

If the best place for a new idea is somewhere else, then I add it appropriately in the outline. That scratches the itch to blurt something new without getting hyper about new ideas.

In rewrite, I’ll find the stuff I added to the outline and fix the right places.

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I like it! What do you use for outlining?

I work somewhat similarly and have been using Bike for outlines. I only wish there was an iOS app.

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I’ve heard good things about Tinderbox but never really looked into it. I’ll have to do that once I finish up the semester. Thanks for the recommendation!

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I’ve used a tree of notes in Devonthink as an outline, and I’m pretty happy with OmniOutliner.

I recently discovered an interesting thing about the word processor Mellel. If you use a style set with a feature called Auto-Indent enabled, virtually the same stream of keystrokes that would create an outline in Bike (a fine outliner) will create an equivalent outline in a Mellel document.

Word processors aren’t generally my choice for outlining, but there are some advantages.

I can put related commentary in text box sidebars. Mellel is so well matched to Bookends they feel almost like a single application when used in tandem. I can add citations to my outline from the same citation database I’ll use in my manuscript.

Chapters, scenes, or different levels of an outline in Mellel aren’t done with heading styles, at least not by themselves. The headings in a document are inserted as what Mellel calls Auto-Titles that can be promoted and demoted, automatically adjusting their format and indentation.

Chapters/scenes/outline headings can be rearranged with drag and drop in the navigation pane, moving child items automatically.

It’s also intriguing to link notes to chapters or scenes. Something in chapter 20 might need to be foreshadowed in chapter 3. Linking a note to the thing from both places is a good way to remain aware in rewrite of chapter 3 that groundwork is being laid for chapter 20.

One way to do that is have two top level outline topics, Outline and Notes. The outline is written as subtopics of Outline and research goes under Notes.

A cross reference in Mellel or a row link in OmniOutliner can tie them together as needed.

All fun to muse about. There are probably many ways to leverage features in Obsidian, Notion, or any of the popular note taking tools out there, too.

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Thanks for this information, which I should have known, but didn’t. It’s got me thinking about transitioning to Bookends, because sometimes I do want to use an annotated PDF elsewhere.