I am a professor who also does research heavily weighted to documents. I have come to love Ulysses but also have a huge database of PDFs I manage with Bookends – which also does my referencing. I also have ebooks on Kindle and Logos Bible Software. I work mainly on MacOS but sometimes use iPadOS.
I am considering adding Devonthink because of its ability to index and make connections.
Question: Does DT play well with Ulysses and Bookends?
This thread has me interested! I use Ulysses, Logos, Kindle and DEVONthink a lot. But, I use Endnote rather than Bookends (mainly to avoid a subscription). May I ask how you want DT to play well with Ulysses and Bookends? You can copy links to a DT article and paste into Ulysses and I assume also into Bookends. You can copy a Ulysses link to paste to an DT article and I assume to Bookends as well. The Beta version of Ulysses now has internal linking.
Right now I have about 7,500 references in Bookends including 4,000 PDFs. Of these perhaps 1,000 have highting or annotations on the PDF – but most of that was done before Bookends. I have about 800 note-taking files. Most of these have been imported into Ulysses, which is also where I do my planning (using the Project category in Ulysses) and writing. Keywords are all over the place. I have on several occasions tried to implement a keyword or tagging system in both Ulysses and Bookends, but there is no consistency. Some references are tagged. Most are not. Some PDFs are tagged. Most are not. Some note-taking files are tagged. Most are not. Add to that the highlighting and annotations in Kindle and Logos, and another 500 or so PDFs I’m currently scanning as I’m clearing out old files.
You get the idea.
The dream is to have One Manager To Manage Them All.
One more thing: all this started 30 years ago while doing my PhD with Notabene and Ibidem for DOS (yes, DOS).
My preference has been to keep my research documents and my references separate. I get nervous having everything being in one application. I may be wrong about this, but at some point, I fear that when a database gets extremely large overall performance is affected. I also worry that if something happened to that particular application or the database, I could lose everything, even though I am rigorous about my backups. My concerns may not be valid, but I feel better not putting all of my eggs in one basket.
I found they worked well together. In fact I used the same three as you do for a fair time. Ulysses, Bookends and DEVONthink 3. I really use bookends for formatting to be honest though and to keep a kind of ‘list’ I can look at sometimes. I store all PDF’s in DEVONthink 3 and all my work revolves around it to some degree. All finished work, notes, Papers, anything in fact, ends up there, usually pretty quickly.
I now use Typora and find it as good and works as well as Ulysses did if not better. I have a workflow that after I make a note, I use a Keyboard Maestro snippet (s) for dating and starting the title. When I finish writing it I save to the DEVONthink 3 Inbox, a smartrule moves it from there to the current database I am using.
Ulysses was, ironically adding too many bells and whistles for me. I also use the native markdown in DEVONthink 3 for writing and also Mellel. I used to have LaTeX but hardly used it and stopped updating it this year. I do like it and might start using it again if I have need for specialized symbols and so on.
I would consider Typora but they don’t have an iOS app, that is a show stopper for me as I use my iPad for a lot of my writing.
I would agree and the one thing about Ulysses that bothers me is the fact it doesn’t make access to particular documents easy. I much prefer a common folder of markdown docs that various apps can access on a “level” basis. I know that Ulysses allows you to set up an external folder, but I never figure out a way to make that operate smoothly.
My question about DT: does it do the same thing? Can I edit PDFs in the DT folder with other apps (such as PDF expert or Goodnotes, which I use for my grading and lecture prep)?
aahh, I didn’t realize that. Useful to know. Maybe I should say more often that I don’t actually use iOS for any kind of writing or note taking or reading really. Really it is an important element of what people here do but not for me personally. I did use DEVONthink 3 a bit on iPhone and I have to day, had no problems with it. I didn’t realize that was one of Ulysses’ selling points though.
I listen to podcasts, mail and text on my iPhone a lot though. My wife sends me links and stuff on iPhone texts, I read them there mostly on the iPhone though. She does everything on iPhone, including a lot of business stuff, outside some proprietry software and highly ring fenced, and once ran two enterprises, if you include a HOA, from the iPhone, Three if you count our personal business which she does everything regarding. I tried to work out how but I couldn’t.
I would love to use a standard markdown editor for this reason, but I have yet to find one with Ulysses’ feature set, especially outlining and built-in grammar checking that goes beyond that available in the OS. What I do is export for archiving my Ulysses material to an iCloud folder AND to DT for keeping and access with other apps as needed.
You can on the Mac, and changes you make in PDF Expert show up in DT. However, I cannot figure out how to do this in DTTG. Keep in mind that DT has its annotation tools. They are good but not as good as PDF Expert.
I can barely do long text messages on the phone. I can’t imagine conducting business on it! 
So, keep using that iOS writing app to make your markdown files and when at desktop use whatever, maybe even Typora (which is very nice). Never ever are the apps with same name but on iOS and macOS the same anyway.
Thanks for the reminder. I tend to think in terms of using the same app on all of my devices. But you are correct, even when I do, they seldom have complete feature parity.
There have been a lot of incompatibilities between PDF Expert and DTTG on iOS/iPad if you want to edit PDFs in-place in DTTG.
With a disclaimer that I’ve not been using it much lately, in-place PDF editing should technically work if you start from PDF Expert and open the file from there (Files > DEVONthink). Changes made should sync to DTTG (DTTG should detect them) when you close the document in PDF Expert. The issue was that these edits and annotations were previously always entirely lost when going back to DTTG.
So, there has been a history of issues with that, and some users are still reporting them, so I’m not sure whether this has indeed been fixed and whether you should rely on it. We’ve been trying to get DEVONtechnologies and Readdle in touch back then (see the linked thread below, I’ve sent several support tickets to Readdle, as have others), but Readdle was slow to respond at first and were not responding to DT’s contact requests, and then more pressing matters happened for people in Ukraine.
It seems this required fixes at both ends but mostly at PDF Expert’s if I recall correctly. At some point it looked like this was fixed, and was reported as fixed, but it apparently still isn’t working reliably for some, judging by the latest post in the thread below.
Other PDF editors on iOS worked more reliably with DTTG when I last tested that, e.g. Foxit. There’s a thread somewhere on DT forums where we’ve compiled a list of PDF editors supporting in-place editing with DTTG.
It’s just plain text. You don’t need to use the same brand of text editor on Mac and iPad. That’s why plain text is so powerful.
Indeed. I have a bad habit of thinking in terms of using the same app on all of my devices for the same purpose. I’m still getting used to the flexibility of plain text. Besides my finance course that used punch cards, my computer experience has consisted of using propriety software for everything. This has made me think I need “x app” to do “x thing.” Most apps follow this same formula. I must remind myself that I can use any editor with plain text.
Habits can be hard to break!
That’s a major advantage of markdown apps like Obsidian and NotePlan that store documents as .md text files in system folders over those like Bear and Joplin that store them in databases. Your files are always ready to use with any text editor you want, whenever you want.
I wish Ulysses did that. Alas…
It’s strange it doesn’t, because it would be a perfect app for that. I suppose you could submit it as a feature request.
