First, a big THANK YOU to all of you who at various times have answered questions related to this thread—your expertise and kindness helped me achieve what I genuinely believe will be my long-term research-writing workflow on the MBP and iPad Pro.
Because I do my research on the MBP but the majority of my writing on the iPad Pro, I was running into friction points in my workflow. That has now been resolved. I am now able to store and edit research in DT, create notes and graphs in Obsidian indexed in DT and add my citations on both platforms with everything syncing. I can do all of my writing and citing in Ulysses with access to everything I need. When finished, I can export the Ulysses document to Word or Pages and finalize the project and create the final bibliography.
For those of you who are true power users this may be simple but for one who considers himself only a “solid and persistent” user, this feels like a major milestone. What’s more, nothing is really locked down in a proprietary system. This is more or less “future proof.”
The image below is the test I setup to ensure everything works. It does.
A word of warning after hard learning about using Obsidian with Ulysses. If you are tempted to index folders from an Obslidan vault as External Folders, do NOT say yes when Ulysses asks if you want to use “Reference Links”. Ulysses will change all links in the document from inline to reference links, as shown in the image. There is no way to undo this except manually edit the files. Obsidian and DEVONthink can parse reference links, but many other applications can not. I screwed up a whole vault this way.
Man that would be frustrating! Thanks for the heads-up. I’m not using Ulysses to access Obsidian files–I’m only using Obsidian or DT to edit Obsidian files, which are indexed in DT. On the iPad I just use Obsidian for the notes. I’m only using Ulysses to do the writing and now, finally, to insert citations via Bookends. Seems to work great and I don’t anticipate problems.
Thanks again–you have been one of those who has been so helpful to me!
How does the referencing work with Ulysses? I’ve got some reports to write this year and was going to go back to LaTeX. However, I’ve been looking at writing in Ulysses and using Pandoc to convert. Are you using the Ulysses export? Is there an additional step?
However, the more I dig, the workarounds make it look like it’s easier just to use LaTeX again!
That’s been my conclusion again and again.
I’m working on an article and really wanted to write it in markdown, but it seems like lowering the river, rather than raising the bridge. So I write in LaTeX using Texpad.
I can’t speak to LaTeX and Texpad but I can say that the process is simple and fluid using Bookends with Ulysses and exporting to Pages or Word. Attached is a screenshot of a simple example in Pages that was exported from Ulysses. As I write, I pull the ref in from Bookends, insert, and done. When the article or book is done one simply exports from Ulysses to either Word or Pages. I’m admittedly early in using this workflow but thus far it has been friction free. I also get all of the advantages and features of Ulysses for writing.
Yes, that’s a good workflow. I need things like tables, equations, and images with captions, subfigures (1a, 1b, etc), ways to reference the figures (see Figure 1), ways to include graphic files from folders around my computer so I’m assured the most recent image is used, etc.
Perhaps all doable in markdown, but LaTeX is familiar to me and I know I can do anything with it. I also have a LaTeX class file for the journal I’m submitting to, which formats many aspects of the document the way they want. They also provide Word templates for non-LaTeX people, but I only Word under duress (like sending things to my PI for feedback).
My needs are simpler than yours. Ninety percent of what I write is text only. I add graphs, tables, etc., as needed in the final product in Pages or Word (which I too avoid whenever possible—though it has gotten better recently). In Ulysses I add an annotation ++add graph/table…++ to remind me where to add them in Pages or Word during the final editing stage.
I’m just happy that I have finally found a research writing workflow that works seamlessly across platforms and with my PKM system.
Does it pull across the Bookends references on export from Ulysses with no further processing? I know Zotero has RTF scan, which sounds similar to this Bookends references.
@drezha it extracts citations from Ulysses when exported to Word. Once in Word on the Mac, all you have to do is have Bookends process the citations and create the Bibliography. Here are screenshots in order of the process.
It is. I experimented with Zotero and like it, and the price is certainly right but I needed the feature set of Bookends. I imported nearly 800 reference articles from Papers 3 (now discontinued) into Bookends with no problem, even my categories in Papers were converted to Groups in Bookends.
Great update, @Bmosbacker. I’m having a bit of trouble between DevonThink and Obsidian for linking. What is your workflow for Obsidian Backlinks such that they also work in DevonThink?
@lsieverts Well, your post caused me to do some double checking and experimenting. You are right, it does not work properly between the platforms. It works well within DT or within Obsidian and because I’m INDEXING the Obsidian vault in DT, everything shows up but back linking does not work properly between the two apps. I’m hoping someone smarter than me in this forum knows a solution. If not, I’ll probably just use Obsidian on MBP and 1Writer linked to Obsidian in the iPad but keep the indexed vault in DT. Not ideal.
I’ll do some searching to see if there is any solution.
The other option is to not use Obsidian and just DT because all of the linking works.
My New Years Resolution is to do just that: I’m testing out using DevonThink for all the things I used to do in Obsidian. I learned a lot from Obsidian, and from Kourosh Dini’s DT book, and I think after a decade of using DevonThink half-heartedly, I’m finally ready to make a bigger commitment to it. Today is Day #1 and it’s going well.
I think the problem is not solved in that blog post.
I had started to add every link to Obsidian twice – once natively and once with Hook so DT could definitely use it. But I don’t need the stuff that is unique to Obsidian – I never use the graph, for example. I really liked the user interface in Obsidian, especially once I found my favorite CSS, but I can do some of that in DT. Life is simpler using one app rather than two.
I think I agree. I may just stick with DT. The linking process works great and I’ll have all of my notes, research, and linking in one place.
I like Obsidian’s graph too but it is not worth the hassle to juggle two apps to make something work. :-). I may write the Obsidian developers and ask about this issue. I’ve heard they are very responsive.
Ninety percent of what I write is text only. I add graphs, tables, etc., as needed in the final product in Pages or Word (which I too avoid whenever possible—though it has gotten better recently). In Ulysses I add an annotation ++add graph/table…++ to remind me where to add them in Pages or Word during the final editing stage.
