Academic use - workflow / hints, please?

Hi, would anyone using MN for academic purposes care to share HOW they use it - I keep getting drawn to it but then stumble at making it actually work for me.

I’m studying humanities with a focus on philosophy, so understanding concepts and linking ideas is more important than building a hierarchy of hard facts that can be excerpted straight from the document, which I think is where I fall down a bit.

I also like to use handwriting as much as possible since it improves retention and understanding.

Thanks in advance.


This sounds like you could be interested in the Zettelkasten approach that I‘ve linked to here. MN is pretty great for this already.

1 Like


I’m a masters student, studying applied linguistics. I’m writing my dissertation at the moment. I’ve been using MarginNote for a few years. My current academic workflow, which is changing, shifting and developing all the time, might not be what you want to know. I’m not sure if you’re asking about specific ways to use MN or about academic workflows in general. This is about the ladder.

Margin note is what I use for reading. I highlight and make, well, margin notes. I don’t put too much thoughts into my notes and highlight indiscriminately. That’s the first step. I consider it something like rapid logging in a bullet journal. The point is not to loose focus on what I’m reading, while not forgetting thoughts that arise while reading.

The second step is to synthesise and assimilate the highlights and my rapid notes into a summary and proper notes. This involves possibly using the mindmapping tools within MN or external mindmapping tools, usually MindNode, if I need to understand systems that were explained. No matter how I play with my notes and new ideas, I create completely new notes in Tinderbox, adhering to the Zettelkasten approach, as @Nils mentioned above. One nice aspect of Zettelkasten is that the tool of choice doesn’t matter so much. You could very well stay within MarginNote. But Tinderbox is a note taking, idea synthesizing playground that is hard to explain, intimidating to start using (just cause it has so many advanced features–but they’re hidden so there’s no need to be scared) but that is on a whole different level.

I create Zettels in a zettle container. Each zettle is then linked to, at a bare minimum, two different places. The first is a container of citations, and the second a container named people. People contains notes with pics of authors, and snippets of info on them (usually taken from a wiki). Attributes are added to these notes about people about dates they’ve been active in their fields. Each Zettle is one single idea, and I brainstorm any questions that I have, weaknesses in the arguemnts that I’m noting about, etc. The Zettels are not organized in any way. Instead, aliases are made of them so that they can appear in other places within my note taking structure (map/outline). They are also linked (kind of like on a mindmap) to other notes and aliases elsewhere on the map (kind of like in Mind Node).

The purpose of all this is that I’m forced then to asimilate/synthesise the new information. Anything I didn’t understand fully, I re-read (easy to do thanks to MN). Any references made that are worth following up, I add to a To Read container in Tinberbox. Any questions that come up are also added to a Questioins container. Gaps in research, especially ones that I could exploit in my study, are added to a Gaps container. Things are moved around on the map and grouped unofficially. Do some of my questions follow some pattern, as to be deemed important? Finally, I decide what my next steps will be. Will I read something referenced before to get more info? Will I follow up on questions I have?

The actionable items I have just come up with go into my GTD app, currently Todoist. At this point, I deem my MarginNotes and/or highlights, mind maps, or anything else created in the above process as complete. I will likely never look at this information again. It’s likely I’ll only return to find quotes and so the highlights could potentially serve a purpose again. That said, my zettels already have citation information linked to them, and plenty of copy pasted quotes if I figure they were important. A page number is included as an attribute. I can therefore, generally speaking, remove texts from MN. More importantly, the texts always get put into Devonthink. I don’t export my notes because as mentioned, I’m basically done with them. Zettels from Tinderbox get exported to Devonthink, however. Devonthink is my safe place for stuff, but also the place I do powerful searches that span all my texts and notes at the same time.

I don’t sit through many lectures nowadays, but do many conferences. My workflow is similar except that, obviously, MarginNote wouldn’t be too helpful. I still like bullet journaling style note taking for such events. I’m really enjoying Notion for that, at the moment. I’m also experimenting with Noted where I can record long form audio and type notes at the same time. The notes get timestamped. During my assimilation stage, I can click on any note and the audio will start playing from that spot. Both these apps are just so awesome. But there’d be nothing stopping me from using Tinderbox for this other than, as I mentioned, having to synthesise and rewrite forces me to revisit ideas after the fact. I’d be tempted to just leave notes where I jottet them down without revisiting them if I didn’t have the second step.

I write in Scrivener. It can’t be beat. It can be replaced my Mellel for academics, likely, though I prefer Scrivener. I don’t want to think about formatting when I write. I want to think about writing when I write. There’s a robust metadata system build into it, too. Mellel now has a decent outliner with drag and drop functionality of sections. I don’t want to spend the time setting that up as I write. I export to Mellel when finishd with a first draft, format, create tables of contents and appendicies, and export to PDF. Mellel allows me to have a live biblieography and it’s just the most powerful word processor for academic work (but not to write; I make distinction between writing and formatting and editing). I manage all my citations with Bookends, which integrates with both Scrivener and Mellel nicely. It’s cheaper than most citation managers, doesn’t hog resources like the others do, and it powerful. I don’t use any of the features other than saving citations in it and using it to cite as I write in the other apps. I also save PDF’s in it just so as to have un-annotated, original versions somewhere safe.

I use a pomodoro timer to stay focused. I like using BeFocused for that. There’s plenty of other thinks I use everyday that aren’t as limited to an academic workflow, but help it: Fantastical, Fastmail, Arq, Dropbox, TimeMachine, Vue Scan, Launch Bar, Cinch, Bartender, 1Password, Bean…

Woops, this is really long. I hope it interests someone. Have a great day!


Awesome! Thanks both - much appreciated

All of this seems to be a fine approach. Yet I’m curious how your approach fare w/o the ability to archive MarginNote-created export files while being able to use MarginNote links, once they’re offline / out of iCloud.


My notes are only temporary within MarginNote, but it would be nice to link to quotes within my permenant notes outside of MarginNote. Or sure, link back to everything just in case. But in my workflow it’s not really necessary.

Understood. It seems some users, like me, work on larger files, and so we have to cycle them in and out out MarginNote; we cannot use MarginNote - iCloud as a central storage repository for files that we annotate, and need to keep referring back to them after our annotations.

As a result, several other users are asking how we can accomplish this within MarginNote, if @marginnote / @Support-Team can accomplish this – or if it’s time to find another app solution.

Thank you for your input.

Is it note exports you’re looking for? We can’t link to notes within MarginNote, as far as I know. But that’s true for any PDF annotation app that I know of. You can export notes and you can keep them organized somewhere such as DevonThink. Then each note, or any item in the database for that matter, can have a permenant link that is accessabile Mac system wide. In fact, that link will work on other computers where you are using Devonthink and have that database open. But linking to annotations on a PDF is not something I’ve seen anywhere yet, though is a great idea.

MarginNote is very powerful, and in my opinion the best, app for highlighting and taking notes on PDFs. The functionality comes at a price, which is that the notes are stored as a seperate file to the PDF. This means that the PDF doesn’t have your annotations in the proper Adobe format, and that’s why we can’t just take that same PDF and open it with another program to see the annotations. That is, for me, the only drawback of using MarginNote. It’s worth the trade off for me because of the functionality. No other program lets me highlight text, and hand write a note in the margin of a PDF with such ease. It does much more, but again, I don’t use the mind mapping tools at the moment. Even so, it’s worth it.

Hmm, as I’m writing, I just thought of a way you could accomplish this. Put a code at the beginning or end of your notes. It could be a a timestamp, for example. Then you can export your notes and use them where and how you want. When you want to find the original note inside MarginNote, copy that timestamp from the note outside of MarginNote and paste into the search box in MarginNote. You’ll quickly find the original note.

Here’s an example:

20190915132700 Possible Title of Note
Hi, I’m a note with a timestamp in my title. You can find me again easily by searching for the timestamp.

There’s likely a some automation you could do to create the timestamps quickly without having to type them out. I can’t think of that at the moment. A program like TextExpander could do that for you, though it would be overkill to purchase it just for that. Word processors like MS Word will insert a date with a keyboard shortcut. You can use that as an intermediate place to generate the timestamp. This website does it as well. Just refresh the page and click on copy:



I wouldn’t reiterate the “basic” read, study, and review mode since you can figure them out by yourself early or lately or just search youtube or forums. And the usage is quite different depending on your major.

But there is a trick of combining MarginNote with other academic tools such as Endnote, Mendeley, and Zotero. That is, you can set the storage folder of MarginNote as the storage folder of these tools as well. Therefore, you can collect the academic references from those databases and get access to them within MarginNote directly and automatically.

I didn’t test this method by myself since I don’t need to write a paper now, but afaik it works. Hope it help you.


Wow that helps immensely, you have saved me from so much headache. Thanks for this

1 Like

@Nils @bart, I wanted to return to this to say thank you for the pointer towards Zettelkasten. When I first read your posts, I thought it probably way too complex for me, but having reflected on it and read some more, I can see a great deal of value in it.

Thanks again

1 Like

I got quite excited by this idea (pointing both MN and reference app to same folder) but I’m not sure it’s going to work with my largely iOS set up since there seems to be less flexibility on setting folders. Eg I use bookends which for iOS sync has to use its own iCloud folder and I can’t currently see that I can change iOS MarginNote folder to this. I’ll keep thinking about my workflow though. Thank you

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:

1 Like

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!