I will need to present comparisons between some different software solutions. I'd like to produce something interactive, as in the way TheBrain exports to HTML.

TheBrain might be just what I need, but my long ago experiences with the old Java based Brain weren't entirely positive. I'm sure it's a far better product now.

In casting around, I found Standford's Protégé OWL editor, and I'm intrigued. It's probably too formal for my initial use, but I can see where it might make a nice planning tool for a complex project.

I have no experience with OWL, and my exposure to Protégé is no more than a quick glance.

It's free, TheBrain isn't, but that's not the only factor in the equation.

Any thoughts about Protégé and OWL for writing and research?

Protégé can be found here - https://protege.stanford.edu

Biggest ding on this project is that it's a Java Runtime app, meaning it's going to be relatively slow, and has intrinsic security concerns (I removed Java from my Mac and only use it when occasionally necessary inside Chrome, which embeds the latest version and sandboxes it for web use).

What OS do you intend to use it with? It looks serviceable but somewhat clunky

https://protege.stanford.edu/assets/img/screenshots/desktopprotege-screenshot-4.jpg

I do all my personal stuff on a Mac, with development mostly on Solaris and Linux. I keep my documentation on my Mac boxes at the moment, using Devonthink as an organizational and syncing tool.

Everybody in the department uses Onenote, so that may be my best way to produce an interactive, reader-driven report.

Quite a few of the information managers discussed here can export interactive HTML versions of their content, including expand/collapse, links, etc. From the cross-platform solutions I am aware of, Mindjet Mindmanager might be the most sophisticated, but it doesn't come cheap.

Aside the price, an additional advantage of Onenote might be annotating by peers, assuming this is something useful.

Amontillado wrote:

Everybody in the department uses Onenote, so that may be my best way to
produce an interactive, reader-driven report.

satis wrote:

Biggest ding on this project is that it's a Java Runtime app, meaning
it's going to be relatively slow, and has intrinsic security concerns (I
removed Java from my Mac and only use it when occasionally necessary
inside Chrome, which embeds the latest version and sandboxes it for web
use).

To mee, this sounds like story from the past. Modern JVM's speed is often close enough to native code (
eg. https://en.wikipedia.org/wiki/Criticism_of_Java#Performance

The security concerns date back to the time when Java applets were used in web applications and one would (unintentionally) execute foreign insecure code. With desktop apps this is not the case.

They are as safe/unsafe as code from any source.

I believe the last version of TheBrain that offered this HTML export feature was v8. The software is now on v10. TheBrain seems to have abandoned their pre-v9 export features entirely.

Amontillado wrote:

I will need to present comparisons between some different software
solutions. I'd like to produce something interactive, as in the way
TheBrain exports to HTML.

I think poo-pooing the continuing security issues of Java are a mistake. It was just in 2015 that Frohoff and Lawrence found a dangerous flaw in the the way data was deserialized in Apache Commons Collection, a very popular Java library - it ended up affecting well over 70 Java apps to deserialization flaws. As a result of that cock-up Oracle actually dropped serialization/deserialization because the problem was too thorny for them to fix!

https://www.bleepingcomputer.com/news/security/oracle-plans-to-drop-java-serialization-support-the-source-of-most-security-bugs/

This problem has not abated in any way. Even as Java becomes less used and marginalized, we continue to see security exploits. Just two weeks ago there was a major issue with Oracle's Java appserver:

https://arstechnica.com/information-technology/2019/06/oracle-issues-emergency-update-to-patch-actively-exploited-weblogic-flaw/

Relying on a Wikipedia article ignores real-world usage, be it vs C++ or Node or whatever.

https://www.reddit.com/r/androiddev/comments/bm0u7x/java_vs_c_app_speed_on_android/

https://www.tandemseven.com/blog/performance-java-vs-node/

Microsoft is abandoning Java for Minecraft, which says something.

To me, Java remains a dog, and a potentially dangerous one. If I can choose an app that uses it or doesn't there's no question in my mind which I'll choose.

Python has security issues with its pickle protocol, its version of serialization. Python's cure for that is to warn the developer that deserializing data from unknown sources is not a great career move.

But I hate to rush to Java's defense. It's a fussy language. Why is it wrong, for crying out loud, to put two public classes in a source file? What if I want to change the name of a public class - why do I have to rename the source file?

That's a shame TheBrain no longer does exports, but there may be other problems with it. User comments seem to reflect a product that is a bit too beta-ish. I left it when I lost nodes several times, I think in version 8.

Devonthink for me, then. Give me a clunky interface and rock solid reliability over glitz and graphics.