Tinderbox Forum

Just starting to study .... after a long, long break! Looking at setting up my workflow


I am just about to start a degree and I am setting up my learning and studying workflow. I haven’t done any studying as such since I left college 30 years ago!!

In reading a lot of the posts and watching some of the really helpful video tutorials I have decided on the following work flow.

all docs and files and pdf’s and web clips will be stored in DevonThink.

All my ebooks will be stored in calibre and indexed to DT.

I will read the above in Marginnotes and annotate /highlight/make notes there.

Question - how do I get the notes/highlights/annotations from there into Tinderbox as separate notes ?

Thank you

I think that’s a great process you’ve laid out. If you use MarginNote on the desktop you can export your notes (including images, etc.) as RTF/RTFD documents. Import or index in DEVONthink, then watch the DEVONthink group(s) in Tinderbox. Or drag the exported notes directly into Tinderbox.


Unfortunately, MN on iOS doesn’t offer the RTF/RTFD option, so working with MN and DEVONthink to Go is a bit more complicated.

There are several relevant MarginNote + DEVONthink + Tinderbox threads on the DEVONthink forum and here.

You might also export OPML from MarginNote (through iThoughts), which will import directly into Tinderbox nicely if you don’t want to go through DevonThink.

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I’ve been assisting a fellow user (in a private message thread) with trying to get data out of MarginNote (MN) notes and into Tinderbox attributes. For all it does well, MN’s export is poorly thought out in terms of exporting a note’s structured data (text, tags, etc.) rather than as a single long-form text.

We tried the OPML route via iThoughts and had to give up. One reason is OPML is quite a thin format mainly envisaged for passing an item’s date and title - most other things are ad-hoc enhancements to the format and thus prone to odd effects and unexpected edge cases. So, my take on OPML is try it: if it works, fine but if not don’t try to fix the edge cases and move on.

Currently, the data is formatted - in terms of order and unique markers - in MN, then exported to RTF. The RTF is given some light cleaning in TextSoap to deal with some inadequacies in MN export before being saved as plain text. The plain text is then added to Tinderbox and processed using action code.

Since Tinderbox v8 I’d probably use AppleScript to route around all the hassle, but MN doesn’t support external scripting.

From 14+ years of community support for Tinderbox users the biggest pain is the hoops jumped though to overcome the inadequacies of apps used for initial note-taking/data-collection that totally overlook the fact that the information created likely needs using outside that app and yet having sub-par export methods. It’s something to bear in mind when deciding to use otherwise well-lauded utilities - can you get your data out?


I must try MN - I hadn’t noticed that there was a macOS client, and I’m always pleased to see software from Chinese developers moving into the forefront.

( For some reason I tend to feel a visceral and probably quite irrational claustrophobia if I can’t immediately spot the data exit door - but I would probably do well to take deep breaths, think more creatively, and rely less heavily on scripting :slight_smile: )

I fear you quite misunderstand my point (though I’m sure not from ill-intent - so please don’t strike your comment above).

I’m not disparaging MN as an annotation tool, but simply pointing out some limitations from, IMO, poorly thought out export. MN->DT->TB is OK, assuming you have and want DT. I know you’re a long-term and expert DT user. Again, this isn’t to disparage DT, but in this it’s another purchase ‘just’ to get at MN notes; and like Tinderbo, DT is a deep app that repays investment of time in understanding it, though that’s moot if it’s simply a pass-through medium.

To be open handed, a reason to ‘flatten’ RTF is that RTF-based links can’t (yet!) be accessed as TB links. MN exports a back-ref to the item, by name of the PDF, with the MN pseudo-url as the embedded URL. Does that matter, why not just click the link in the imported TB $Text? Well, ‘No’, not if you wish to store the MN back-ref in a TB attribute.

Yes, there are ways around this. Indeed, I guess I could use Applescript in TB to locate the MN RTF url, place the actual URL in the TB attribute and then delete the otherwise unwanted $Text. But, the user has a difficulty (not through laziness) understanding /reading code and Applescript was a step I was trying to avoid (and has only become an option in v8).

The more I learn about inter-app data triage, the more I hold onto the fact that I’ve acquired niche skills not obvious to a wider audience; obvious/simple is very much a subjective judgment. MN is a really interesting app - were it earlier in my studies I’d probably try and use it even if I’d still face the export issue if I wanted to use the notes in TB. I get that the MN devs may not see (easy) use of data outside their app as a valuable feature. All small devs have less engineering effort than their users can supply with new desired features - and that’s without the make-work of supporting ongoing OS-level changes over time. My earlier point, if obliquely made, is that perhaps they are wrong in assuming a rich export (and in some case also import) mechanism isn’t a key feature to unlocking the value of the app.

I played around with MarginNote and abandoned it fairly quickly. This is completely personal, of course, but I couldn’t really find a use for it. For me, it worked much better to make annotations of PDFs in something like PDF Expert or Highlights, export those to text or Markdown, and use that material in DEVONthink or Tinderbox. I didn’t really find all the linking and mapping in MarginNote was useful to me. I’d rather do it in another program – like Tinderbox, for example. But we all have our own methods.

Edit: for those who are not familiar with Highlights: https://highlightsapp.net Not a bad little app.

At a slight tangent, re PDF annotation tools but the free/open-source Skim offers a lightweight PDF annotation tool. I’ve not used the export feature though I note there is a wiki that offers some export customisation and that there is AppleScript support. Most usefully, I now use it for reading academic PDFs as it allows twin-pane viewing allowing text in one pane and references in the other. I do this with PDFExport but even with no docs open the latter is unfortunately a real resource/memory hog if otherwise a good app.

I used Skim a lot, but I haven’t used it recently. One nice thing about Highlights is that you can have your Markdown of the annotations in a side panel as you are reading. It is worth checking out the app. It will not be for everyone, but I find it handy for exporting annotations.


For all its downsides, MarginNote appears to be the only (mobile) app for serious review of ePub files. There are many fine options for PDF. But if anyone has found anything similarly robust for ePub annotation, I’d love to hear about it!

Highlights is nice, but doesn’t seem to work with exporting notes to DEVONthink 3 on macOS.

Thankyou for your reply - you have hit the nail on the head! When I was waling though my workflow testing all the paths with a demo book it became obvious too me that the sticking point was exactly that. How, once I have done all that writing in MN was I going to extract it and use it in TB. Did I jettison TB or did I jettison MN and find an alternative note taking app. One of the things that I like about MN is the ability to record the lectures as while as annotate the pdf’s. Do you know of another piece of software that plays nicely with TB and will still fulfil that function?

You could have a look at Notability. But I would question whether recording is really useful. Perhaps it is, but it is very time-consuming to listen to recordings of lectures. And such recordings take up a huge amount of disk space. I would say try it, but be prepared to abandon the idea in favour of other uses of time.

I have just spent the last nine months tutoring an adult learner at degree level, and the main problem was probably “drowning in material”. My own view is that searching for stuff and not being able to find it is a huge drain on time and mental energy. It might be worth having a look at the discussions at https://zettelkasten.de. It gets pretty deep and philosophical, but they have looked at a lot of the problems of “knowledge work” and you might find the discussions helpful. I think it is worth asking oneself the question “What am I going to need to find, and how am I going to find it?” Though it may take a while for the answers to emerge as you study.

Edit: I suppose what I am trying to say is that it is worth considering what the end product of the study is going to be, and working backwards from that to see how the workflow could result in that. It is easy to get caught up with organising the initial stages of the workflow and then find that you have all sorts of things that don’t actually contribute to the product you need (essay, thesis, dissertation, report or whatever it is). You then have to wade through all the stuff you have that isn’t useful to find the stuff that you actually need. You may not suffer from this problem, but I know I have, and I have seen other people get caught up in it, too.

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Thank you … I have been reading about Zettelkasten and watching the video posts. I think this is a really good way to consolidate my knowledge - and not get drowned in it! Do you use “the Archive” in conjunction with Tinderbox?

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No, I don’t. I tested the beta, but I didn’t think it would be useful to me. If I want to capture notes very quickly, I use nvALT (which is pretty much the basis on which The Archive was built). And on that score, it is worth noting that Brett Terpstra, the developer of nvALT is working on the app that will replace it (in co-operation with Fletcher Penney, if I remember right). So I will be interested to see what comes out of that. But in any case, I think Tinderbox is a better Zettelkasten app than The Archive can be. Or perhaps I should say that you can use it as a Zettelkasten, but its capabilities go well beyond that, so that you can start simple and extend as required. I need visual things like mapping, and The Archive is really text only, which doesn’t suit me. Visualising multiple connections, or networks of relationships, can be very useful (if not essential) in some cases. The Archive can’t do that. Moreover, Tinderbox gives so much more in handling meta data.

The other reason why I don’t use The Archive is that I use DEVONthink, and the combination of DEVONthink, Tinderbox, Scrivener, Bookends and some scripts or utilities is very powerful. The UUID item links you get with DEVONthink are a good way of keeping track of documents, and of course Tinderbox, DEVONthink, Bookends and Scrivener all co-operate very well. Which perhaps is another reason why I couldn’t really find a use for MarginNote – I didn’t have much room left in my workflow.

  • It is helpful to read Niklas Luhmann’s essays on note taking (translated by Manfred Kuehn here, since he is often cited as the “originator” of zettlekasten. (Not really, but that’s an esoteric area of debate.) Luhmann’s own zettlekasten is online here, to get a feeling for what he did in practice.
  • I use MarginNote extensively, so I’m very biased – perhaps therefore my thoughts are untrustworthy. The best use of MarginNote is to do all the notetaking internally in that app alone, and to link notes and documents within MN. It is not primarily a PDF annotation app – it use is far broader than that. Originally, it was intended to assist development of flashcards for study – and still does that. Over the years, Sun Min added export features. The limitations with RTF/D notes are, in my view, Tinderbox’s limitations with handling RTF/D imports.
  • Years ago I used the then-current version of the Livescribe “smart pen” to take notes and record lecture snippets simultaneously. I never recorded whole lectures (useless practice IMO). The Livescribe tech allowed me to tap a note and hear the related audio portion that I recorded earlier. I suppose modern versions of Livescribe can still do that, but haven’t used it for 10 years or so.
  • From reading and participating in threads like this over the last few decades, my own take is that linking together numerous softwares (e.g., MN + DEVONthink + Tinderbox) can lead to confusion and frustration more often than being helpful. I agree with @MartinBoycott-Brown’s core advice: figure out what are you looking to accomplish, then work backward from there to decide how to do it. I add to that: settle on an approach, test it for a while, then stick to it. At that point stop reading forums to avoid falling prey to CRIMPing :smile:
  • Watch @beck’s videos.
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I’m a martyr to CRIMPing! :grinning: It’s a displacement activity.


At that point stop ready forums to avoid falling prey to CRIMPing

Damn! I didn’t know a word existed that defined my debilitating mental problem… I must add this too my TinderBox, Evernote, Omnioutliner, DEVONthink, Things, Omnifocus and Journal!

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^^^ This

If you aren’t already committed to particular tools/workflow, it repays you to consider your end-to-end ‘toolchain’ from before generating lots of material. I’ll admit I didn’t do this early in my study and wasted time as a result getting things to play nice and swapping out tools. For instance, I’d planned to write my thesis in Scrivener and export to LaTeX, but the process—whilst possible—was so poorly documented for a non-coder that I gave up and write directly in LaTeX as it was actually less effort but still cycling through several LaTeX tools to find one I was happy with (with concomitant wasting of time).

For academic work, also check your chosen reference manager* plays nice with your writing environment or that too becomes a time sump. Note: reference managers do not check/clean your references, especially ones pasted in from online sources, so garbage-in-garbage-out (a fact many of my erstwhile colleagues overlooked until in a deadline crunch).

* I use Bookends but various other reference management are available (free or pay-for)—pick one you find comfortable to use.

Unless you are fairly tech-savvy, and like text wrangling, I’d choose whether you want to work entirely in a rich-text WSIWYG environment or not. Mixing the two may afford more yet more unexpected and un-planned effort.

Lastly, bear in mind the duration of your study. If multi-year, you OS, and tools will likely all change slightly and so you can’t just verify your workflow at start and consider it ‘job done’.

Now back to thesis writing…

Thankyou this information is really helpful. I am in the process of trying to decide which ref manger is going to work for me and how I actually store my ebooks. At the moment I store them in a Calibre Library, but I don’t think that is going to work for me long time,. So I have converted all my ebook formats to pdf and I am just about to import them into DevonThink and OCR them. Am I correct in thinking , from what I have learnt so far, apart I think from Zotero, the ref manager is a very sophisticated database - but it doesn’t actually store a copy of the book
? Hence the need to store it on DT.