Academic use - workflow / hints, please?

I think it’s life changing but, yes, challenging. To your second comments: that’s why I don’t use MN for this. I gather info with MN, but synthesize in another program where I paraphrase what I’ve learned. :slight_smile:

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tbh I guess the ones who give me this idea are the users of macOS, though I cannot guarantee any of them works since I don’t need to use them. An alternative method comes to my mind is that you may write an Apple Script or download other apps for auto-sync between these two folders.

Thank you. But I think on reflection it’s no bad thing as I was over engineering it. I don’t really need references in my current studies and using a reference manager is a hangover from a previous course. As and when I need to use one, I’ll work out the best way and in the meantime focus on the study workflow. It’s been useful to think about it, so thanks for the input.

Hi Bart, I was wondering about your use of Tinderbox as a Zettelkasten tool. I’ve now got tinderbox but as you said, it’s quite a lot to take in and I was in danger of procrastinating through focusing too much on tools. So what I’m not clear on is whether using it for zettels requires a special set up and what that is - I watched a video by Beck Tench who mentioned a Zettel prototype but as I said I don’t know enough to know whether that’s a built in thing or something you have to create.

A prototype is a fairly basic concept within Tinderbox, once you get past simply writing notes. You can get away with simply typing notes as your zettels and doing nothing more. That’s already your Zettelkasten. A prototype is a way of creating a new note that has the properties of another note. So, for example, every Zettel I create is made from a prototype that has certain user attributes that I want it to have. You can think of attributes as custom tags on drugs. I mean a standard tag might be: WORK. But in Tinderbox, that tag, which is called an attribute, doesn’t just have a title. It can also have a value. So it could be WORK: Mondays. Tinderbox will display the field where you can type in the value of your attribute right at the top of your note. That way, you can have attributes for things like AUTHOR and DATE. (Those examples aren’t even custom attributes as Tinderbox has many build in ones, including those, that you can choose from a list.) So if I want every Zettel to have those attributes ready for me to fill in, the fastest way would be to create an empty note with those attributes selected, and then in the inspector tell Tinderbox to treat that note as a Prototype.

Ok, with that said, I’ve created some custom attributes that serve the purpose of inserting a title for me into new zettels. The title is basically a timestamp. The prototype note runs a little script that finds the attribute for the creation date and then inserts that text as the title of my zettel. You don’t have to do all that. It’s just that a zettelkasten is meant to have a numbering system, and I figure the best numbering system is a timestamp. Then, even if my notes get messy in Tinderbox (since it’s a graphical ‘desktop’ with your notes kind of like ‘icons,’ it’s easy to get messy. But Tinderbox has a powerful Attribute Browser. You can have it display every note (zettel), organized by title. Like magic, you have an outline view in order (true zettelkasten style) of all your notes.

I’m happy to walk you through setting all that up. But you may be happier, for now, just making notes and not worrying about all that. Even if you don’t add any numbering system, you can still use the Attribute Browser to view all your notes sorted by creation date, for example.

As you can see, Tinderbox is as simple or complex as you want it to be. The price tag for it is because you can do all that cool stuff if you want to, which you can’t do in any other program. I wish they had a competitor so that the price would go down. It’s grossly over priced in my opinion.

So anyhow, ask me for help if you like. I do suggest going through their tutorial and going through the help menu when you need help. It’s much better to understand what a prototype is, for example, if you make one yourself.

@bart That’s brilliant, thank you. I mentioned I’d put learning it to one side because I have things to work on ( and it would be all too easy to get distracted learning a tool that’s not really related to what you have to do) but knowing what you will learn about before you turn to the help / tutorials is hugely helpful. If that makes sense. Your description has really helped me understand what some of the usefulness might be.

I think you’re right that for now I’ll use it just as as basic note taker and work towards something greater in the future - what’s useful though is that using it as a basic note taker doesn’t provide a compelling reason in itself to migrate from my current note apps, but what you’ve described has made me excited about the future possibilities.

I think that this depends on how visual you are. The nice thing about having notes in a graphical map view that you can treat them as if they were index cards spread out on your desk. You can stack them much as you could on a desk to make groups. You can copy them, or better yet, make an alias so that you can have one note in many places…etc.

Have fun!

That’s a very good point - I’m a massive visual thinker. But I was also balancing it with the fact that currently 80% of my study time is iOS and at least some of that 80% is iOS by necessity as I’m in situations where I can’t practically take my MacBook (eg, studying during work lunchtimes or on my commute).

I experimented today with creating Zettels with a simple markdown / text editor on iOS and importing into Tinderbox and there’s a lot of promise in this, although it would be even more promising if I could somehow automatically replicate the links in Tinderbox. I’m wary of making things too involved too soon, though, so I’m just leaving that (the overall use of Tinderbox) as a possibility for the future.

So I think my workflow at the moment is something like:

  • store documents in DEVONthink.
  • initial read in DEVONthink to get a feel for the relevance and usefulness of the paper / chapter.
  • (where necessary) share to MarginNote for detailed analytical reading, identifying concepts and creating proper notes rather than just highlights.
  • (Still a lot of work to do on refining my reading technique - so lots of opportunity for improvement here)
  • (maybe) exporting highlights and notes to pdf to file alongside document.
  • Updating or adding new zettels in markdown / text app (possibly The Archive on Mac, 1Writer on iPad), creating links to existing ones (still learning about this)
  • (possibly) using Tinderbox to ‘map’ imported zettels into visual representations of the specific question in seeming to answer.

I’ve still got a huge amount of thinking to do on the method, so this will change, I’m sure.

But I’m happy to report that my day in the library today was one of my most productive for a long time, even though I was grappling with a topic that’s new and confusing.


What do you mean? Each note in Tinderbox has it’s own address, much the way Devonthink does. I’ve automated my process to the point that with two clicks in TBx, all my new Zettels are imported into Devonthink, with links between notes and titles maintained. It doesn’t work the other way round, though it’s likely possible, especially with the new versions of both apps.

At the moment, I’m creating new zettels as txt files in 1Writer,and linking them via their unique titles (very early days for me, both in terms of naming and linking. Naming is the unique numeric code generated from yyyymmddhhmmss plus relevant text description. Linking is via internal markdown (?) links, so [[yyyyymmddhhmmss Relevant description]]

When imported to tinderbox these are currently plain text, not links. I was mindlessly wondering whether there’s a way of doing something with those links on import. But as I say, probably too much thinking - better to focus on creating good zettels, linking in a useful way, etc.

Hello JKF ! I’m trying to make a short animation about my understanding of note organization and knowledge production from the perspective of academic research.

I have some simple thinking in this respect. I think mind-map can only help us to establish an understanding of the internal information structure of materials in the process of academic research, but it can not really help us to preserve our own perspective of problems and produce our own knowledge.

In the aspect of knowledge production, based on my own experience, I find that using the link function of marginote to create a local concept-map instead of mind-map can help us to simulate the flow process of thinking to the greatest extent, so as to discover knowledge through a unique perspective, rather than being limited to the category of notes arrangement.

I also got excited about this, but you just cannot do it on iOS. If there were some support for autocloud sync in both directions though, you could have Marginnote update pdfs in a Zotero-watched folder, and so you would add all your documents through MarginNote and they would be imported automatically to Zotero as the export synced. is this a reasonable #FeatureRequests ?

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Adding icons that corresponds with Ur hastags might be useful

This allows you locate easily you important notes

#mostimpotant = lightbulb icon
#commoninmales = male icon

Please let us choose on what icon we want to put

Interesting. This is indeed what I need - a conceit map not a mindmap. I’ve used the link function but not really understood its potential. I’ll take another look, thank you

PhD Philosophy here.

I’ve only just started using MN intensively (e.g., for my work) recently. So there might be future improvements, but as of now I use:

  1. Papers3 for paper collection / reference management and skimming through papers;
  2. Ulysses for writing;
  3. MN for studying texts - instead of having mindmap side-by-side, I just delve into the text (2-page view), and have my highlights automatically added to the mindmap. Then, to review, I sort out the mindmap.

Hope this helps!

Hi Edward

The issue I’m finding with this is that linking the notes duplicates the text in each note. This is visually overwhelming.

So true! It completely destroys the point of making links between notes when the text or title is duplicated. At least for visual learners. I so much wish MarginNote could focus more on the link feature, making it equal to or more prominent than the child/branch system. Please allow free form linking and customization of links.


I just stumbeld upon the a quite interesting Note-Taking Tool, but which is still in development:

“A note-taking tool for networked thought.
As easy to use as a document. As powerful as a graph database. Roam helps you organize your research…”

I think the Idea to implement a Web of thoughts in Zettelkastenstyle is well considered here. An Idea with big potential?!


I played with Roam for a while and I loved it. I’ve not moved to it though because they will start (quite rightly) charging at some point and there’s been some speculation that this might not be cheap, and if it is more than £10 a month, say, it’s out of my budget. So I don’t want to get locked into it until I know the cost.

Thanks for such a splendid description of your workflow. It overlaps with mine more than 90%, and I still learned a few tricks from this and your other posts. I wonder if you could answer a quick question to help me avoid running down a rabbit hole. From your description, it seems that you read one document at a time in MN. Is that the case? If so, does that reduce the learning curve? Do you ever read multiple documents at the same time? If so, how does that work for you?

MN caught my eye because my current project involves about a dozen pdfs (around 30 pages each). There is considerable redundancy among them, and I’d like to be able to compare them to track the overlaps as well as to track the specific contribution of each document. I’ve thought about doing this in Tinderbox, but it’s possible that MN might work better for the task. My concern is the multiple warnings that MN could be quite a challenge to pick up, and there’s plenty of that already in the apps that we have in common.