559: Research Apps

Yep. The visualization in TheBrain is vastly better than the silly graph views in Obsidian and Roam.

I’ve also been linking from notes in TheBrain to files in an Obsidian vault – and indexing those files in DEVONthink – so it’s excellent that a set of documents can operate across apps this way.

(Just don’t move the file in the filesystem!)


And it is a very thorough guide and review. Thank you for doing it.

1 Like

I would be willing to pay a lot for a mobile app.

Perhaps, if it’s free it can’t be good? :smile: Many years ago I sneaked a Mac mini into work just for documentation. Dumped everything on it and searched easily with Finder. At one point I tried DevonThink and thought it too clunky (apparently there has since been a refreshed interface) as well as unnecessary. Finder sure beat Windows built-in search as well as a couple of third party tools I tried with it.

1 Like

Fantastic and timely episode! I’ve been dabbling with Obsidian and interfacing it with my iA Writer library of markdown files and it seems very interesting. I still cannot see how useful the Zettelkasten method can be for my research (I am a researcher in a STEM field) but as suggested, I intend to try and keep my progress files in there and also try to thrown in notes of ideas based on the hope that “digital connections” can potentially help me in connecting lines of evidence.

Last year I started to run DT in a VM, because I was not sure I wanted to upgrade to DT3.

For a few weeks now I’ve been looking for a tool to help me manage DPA announcements, court verdicts and regulatory documents. Listening to this episode reminded me again why I had bought Devonthink. My use of it sort of migrated over the years, but it was first and foremost a way to link documents, make connections between items and being able to quickly search for them.

TL;DR: I upgraded my DT license yesterday.


One of my favorite uses of Devonthink was during some continuing education courses for theology. At the end of 6 weeks I would dump my reading notes, essays, lectures, etc. into devonthink and use it to write my final paper. It made it so much nicer to surface those connections. Then I could leave it in there or move it out.

I think that was nice because it was a project, and I could move stuff in and out as needed. Sometimes these research apps seem amazing, but also overwhelming. It’s kind of like when you learn to program and they say you’ll do much better if you already have a project, same with something like guitar.


Anybody else just want a @MacSparky podcast all about about the SparkyOS? I think it would be super interesting and helpful. Maybe on Focused.


Has anyone tried Craft?

I think I’ll stick with Drafts - and use various circumventions when it comes to graphics. (data: URIs featuring heavily in my experimentation).

I like the idea of complete control of my text processing.

1 Like

I enjoyed this talk (full disclosure: I am an academic especially interested in research apps), so many thanks for this!

And since @MacSparky talked about the emergence of the “Zettelkasten” approach, let me add a few facts and links (David, I hope you’ll find that interesting!).

The “Zettelkasten” is named after the enormous slip box (which is the literal translation) that Niklas Luhmann, a professor of sociology at the University of Bielefeld in Germany (not Austria!), built up over three decades of academic work. It encompassed some 90.000 (!) slips which were hand-written or typed up. Each has a designator (akin to a unique digital key), and there was a complex system of linking between slips.

Luhmann claimed that his slip box was able to communicate with him. Since he defined “communicating” as “being able to surprise”, this was certainly true – similar to David in MPU 559 talking about “organizing serendipity”.

Luhmann died in 1998, and the University of Bielefeld has tried to preserve the Zettelkasten. A long-running research project has recently managed to digitize it, and there are some webpages that those interested in “Zettelkasten” may find fascinating (only some of it is in English, but the pictures of the “Zettels” may still be interesting):

So, I hope you enjoy the links! Many thanks for this great episode of MPU!


I would disagree a bit on the Obsidian fitting into Gardener mindset primarily. I think it’s also got a lot of Librarian features with the ability to store lots of data and get to it easily. Although the structure does tend to grow more organically than in DEVONThink, unless you’re like me and sunscribe to the Usenet method of developing a filing system. :wink:

For years I’ve used (* comment *) in all my text writings (Showing my Pascal foundation) It’s also a rarely used sequence of characters so easy to search for and repalce with something else later.

I tend to agree with you. But I am finding that I am slowly gettign used to it with my Obsidian use case.

Finder is great when you know exactly what you are looking for but IMO falls flat on its face when trying to create links across structures or need to find small things you kinda remember but yoru memory is faults. Indexed folders in DEVONThink tends to solve most of those problems.

I’m finding the Kettelkasten method very helpful in documenting and tracking the use of SNPs vs Microsattelites vs mitochondrial DNA as a way to determin genetic variability in domestic farm animals. Very much a STEM research project and I’m making more progress since implementing even basic Zettelkasten methods in the stuff I’ve collected and where I want to take the research.


If one owns Tinderbox, would one gain much from TheBrain v12?

Good question @JakeBernsteinWA. Historically, they both grew out of early hyptertext theory. The implementation diverged.

It’s certainly possible to create a Tinderbox document that mimics the linkages between atomic notes which are possible with TheBrain. With TheBrain a link is a parent, or a child, or a “jump” relationship between two nodes. Tinderbox has a different notion of links.

TheBrain is more of a “permanent” database that can easily be cultivated and expanded. With Tinderbox links are not required. But when links are used, everything is always built-up bottom-up in a very manual process. Whereas TheBrain, IMO, makes the linking process simpler.

Another difference is metadata. A “note” in Tinderbox can have a potentially limitless set of standard and custom metadata (“attributes”) associated with it, thus augmenting the meaning of the note in a very plastic manner. TheBrain’s notes (“thoughts”) have only a small handful of metadata elements associate with them – and does not support custom metadata at all.

I use both, of course, and pickup Tinderbox when I want to focus on a project, and when I’m done I forget about that particular document. OTOH, I turn to TheBrain when I want to build up and maintain over the long term a base of related notes. My databases in TheBrain have been cultivated over a long horizon.


I think of TheBrain’s Types and Tags as metadata. True though that they aren’t parameters or variables that can take on values as in Tinderbox.

That’s why I said “only a small handful” and “does not support custom metadata”

Tags and Types in TheBrain are actually a special category of “thoughts” (nodes) – adding a tag, e.g., makes the selected “thought” a child of the tag “thought”. Is that metadata? Perhaps if liberally defined it is.

1 Like

I downloaded and tried The Brain. While the Mac app had some good features, the iOS app was a deal killer for me. Hope they continue to develop the platform.

So…would you view TheBrain more as competition with Roam/Obsidian and other “Zettelkasten” apps (The Archive, Zettlr, etc.)?

It’s interesting to me that both TheBrain and Tinderbox are quite old apps (if I’m not mistaken, over a decade for each, easily?) but have taken such different approaches. It’s clear to me that TBX is still meant to be a document-based app, though I know there are people who just have one TBX file to rule them all.

I’d be curious to read more about the differences between TheBrain and Obsidian/Roam, particularly as I’m one of those people that remains skeptical of the value of “the graph” when it comes to text notes. It looks cool, sure, but to what end? I’ll have to fiddle around with TheBrain a little more to see if the Pro cost is worth it to me.

Given that none of Obsidian, Tinderbox, or Roam really have iOS apps at all (though Roam is at least a web app usable in Safari…sort of), this isn’t a huge deal for me at the moment.

I have difficulty making judgments about pairwise comparisons of applications. It all depends on the feature set and what the end user is capable of and wants to accomplish.

I don’t like zettlekasten wannabes, never liked The Archive, haven’t tried Zettlr, and wouldn’t get involved in that school of note taking. It’s a fad and will disappear in time.

(Though I am fascinated by the psycho-cultural implications of zettlekasten’s popularity. Something I intend to study a bit more in depth. When I read the Obsidian forums I feel I’m in the middle of the geek apocalypse.)

TheBrain was first published around 1998-2000, IIRC, and Tinderbox about 2002. Their intellectual roots go back to post-war research on textual systems and technology. The technology available to commercialize the theoretical framework often lagged the theory, as it did 20 years ago. I think this has changed over the past few years, and favored the publication of Roam and other offerings.