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 
)
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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.
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Here’s one 
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.
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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.
Thank you for your great input and interesting thoughts! @JohnAtl: Excellent points! My main problem is that Scrivener and DT did work for me but I never loved it (with the exception of DT for Mac). In the past I tolerated all the little things bothering me but it piles up over time. DT to go for example received its last update six months ago and is still not able to open docs in place. There are many more little issues like that which made me wonder if there could be a better possibility.
Furthermore, I try to solve more of my work with first party software. Recently, I moved from OF to the new Reminders app. Just as a test for now but I don’t miss a lot from OF. Another example is my increased use of the Notes app. So that’s some background why an app like DT might not fit anymore.
I guess, I’ll put some more thoughts into what it is that I require and what a feasible solution could be.
Thank you all so far!
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I agree it is very frustrating that it is not possible to edit PDFs in place reliably in DTTG. But it is a bit unfair to suggest the developers have lost interest when they have been in the process of releasing DT v3. The edit in place problem, however, does mean my use of DT has dropped off substantially.
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Absolutely, I totally agree. DT 3 is a huge undertaking and they are a pretty small team. I had the opportunity to talk to one of them and I can see why they focus on the desktop. However, as someone who works all the time on his iPad Pro when not at home, it is a deal-breaker for me and no progress in more than six months is just disappointing. Again, I get why it is what it is but I still don’t like it. 
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Is the Notes app to simple as a substitute for DevonThink? I’m also hesitating on upgrading to the latest version.
For Writing, I particularly don’t like the idea of moving to a paid-subscription format like Ulysses or Bear, but those two seem the most popular options that have compatibility with Markdown. I double on the suggestion of Manuscrits (which is now open-source), or AI writer.
This blog might also help (?) https://appademic.tech/
Another factor, Devon Technologies customer support sucks leaves a lot to be desired.
- This behavior is unexpected.
- That’s the way we made it.
- This thing is hard to do.
- That’s the way we made it.
- When I press ⌘/ in MATLAB, my computer hangs while DEVONthink launches.
- That’s the way we made it.
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I’m going to revive this thread by asking the question (the elephant in the thread) - what about teaching? What do you use for planning and writing with regards to the courses you teach?
I try to use Obsidian for this (before I did it in DevonThink), but I’m thinking about using something little lighter like Apple Notes. What are your thoughts?
Notion seems popular for this as well, but I am very skeptical about web servers holding onto my notes. I guess another alternative could be Craft.
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My greatest success was using Evernote with a template. I could have my objectives, linked materials, and a table that held my outline. It was very easy to keep in an a large overview for planning.
This last year I used google drive a lot. A weekly breakdown with lessons built in docs and presentations in slides. Each day got a folder if needed and it held my materials (music).
This actually worked pretty well and probably with one more year of refi event would be better.
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Bookends > Highlights > Obsidian > Pages > export to MS Word/PDF
I’m also in arts and humanities, so it’s a separate vault for each conference paper/article/chapter. I’m 25 years in academia and can’t get a page metaphor out of my writing practice, so I always end up finishing everything in Pages. But I wish I could learn to drop the double space after a full stop (period), inculcated by the MLA Guide back in the 1990s, from my writing!
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I have to admit that I do my notes on just a notebook and then transfer ideas into a private repository in github. I use just-the-docs as a template to structure and divide my ideas. Whenever I am ready I put it open and online and share it with the students
I would also like to ask something that, I presume, has been discussed a lot in the past: annotation/reading workflow. I am searching for an app/container that allow me to better keep track of things.
I generally using my ipad for reading/annotating, and highlights is a great tool for it, plus it sync with the mac and Devonthink, so it is really a fantastic solution. I have two problems: I cannot annotate epub, and I cannot have free hand annotations.
Is there a solution out there? I even checked if some new e-ink device, like remarkable, just to have a one box solution where I can drop everything into the device and be happy, but exporting/sharing annotations seems to be chaotic. At this point, I do not want a workflow with 4/5 steps, because I know I will not follow it if I am in a hurry, I just want a container where I can drop things to read, annotate (sharing the annotations) and organise them.
Any help?
With teaching, I find I like to attend to different levels of the planning process in different apps. When setting out to plan an entire semester from 50,000 feet, I think apps like OmniPlan or a good calendar app (I like Fantastical) that can give you quarterly perspective are helpful to sketch out the big themes, goals or units over an entire semester. Then, to drill down a bit, for the past year or so I’ve use MindNode to have a mind map with each node corresponding to a week and then classes within that week. I have found this really to get at the right level of planning for me: more detail than the big picture, but not the more granular information I might put into a lesson plan and very easy to quickly edit, tag, link, etc. within a mind map.
I prefer to put a lesson plan into a notes application. You mentioned Obsidian and Craft, which I have used and could see as useful for this. For a while, I relied on Drafts—so quick and easy to work with lesson plan templates and accessible on whatever device I had around. This past semester I tried using Agenda—I like the interface of the app and how it formats Markdown, and being able to link a lesson plan to that lesson on my calendar was really helpful: I could open up the ‘Today’ view in the morning and there were my lesson plans. The back end supporting most of this is DEVONthink, where I store/house teaching materials.
For perspective, I needed all of this to work nicely on both iOS and OS X, as I usually do the planning and prep on a Mac, and then work with an iPad in the classroom.
I worked with Notion a few years back. It seems to require more up front work creating databases, etc. before you can ‘use’ it. That may be a plus if you’re into stuff like that, which I suspect many of on this forum are, but it’s worth considering. And—a big issue for me—Notion (at least a couple years back) didn’t play nice with URL links to other apps. So if I added a link to a DEVONthink item or whatever else, Notion couldn’t open it. This is a big issue for me, as to make all the apps mentioned above work in harmony, I need their content to be linkable with other apps.
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For the past two semesters or so, I have experimented with building out my teaching materials in Obsidian. Each course gets its own vault, and the vault lives in a public GitHub repo. I have a folder for literature, where I put pdf’s with the course readings, and a folder for slides. For the readings, I use Highlights to mark them up, and Highlights creates a separate markdown file with the highlighted text in it. For the slides, I create one .md file per presentation, write the slides in markdown, then run a shell script that converts all the presentation .md files to html, using pandas with revealjs. The syllabus is also written in markdown in Obsidian, and converted to html with pandoc. Because the html files with the slides and syllabus are on a public GitHub repo, I can then give the students a link, and they can open the materials in their browser. In the unlikely event that I need to update one of my slides because I made a mistake (!), I just fix it in Obsidian, run the shell script, and everything gets automatically updated at the students’ end as well.
I really like this method, and I’m going to stick with it for a while, and see how far I can go with it. Potential downsides are that the slides are going to be much more simple than you can make with e.g. Powerpoint or Keynote, and there is a danger of spending too long fiddling around with css and javascript to make revealjs mimic things that would be really easy in actual presentation software, but once you get going, making slides in markdown can go very fast. Upsides are: it’s great for the students that everything is online, and I like having everything in Obsidian, instead of spread out over Word docs, powerpoint files, etc. etc. And most important, it keeps me entertained!
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