Academic use - workflow / hints, please?

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?!

about: Roam Research – A note taking tool for networked thought.

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.


Here is a mind-map (work in progress) of my various workflows, they require more explanation but happy to provide some if required.


Hi there, I am an academician too and I use MN3+Zotero+MsWord+icloud on Mac-iPad mini to build a Zettelkasten :card_file_box:. I took rough notes on MN than I export them to Zotero where I keep all my bibliography and notes, which can be created independently and related to each other or to a book.
I preferred MN over Liquidtext since one can start creating notebooks even without a source document and also documents can be used in different notebooks over and over again so does not took up too many storage.

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Wow, thanks for sharing, looks like your workflow is organized for every situation, cool!

@clarkie1977 This is great — thanks!

This is fantastic, thank you.

I note that you do pdf annotation in PDF Expert and synthesis in either MN or Liquidtext. Could you say a bit more about that, please? I can never decide when to stop using the annotation tool (I also use PDF Expert) and move to MN / LT - my ‘perfectionist’ brain doesn’t enjoy starting in one and moving to the other, but equally MN / LT get too cluttered with less relevant docs if I use them too early in the process.

Thanks for sharing this. Would it be possible for you to share any kind of pics that represent your work process? Thanks!

Hi, thank you for your detailed explanation.

I wonder if there were two same documents created in your storage system from your step 1-3.

I am confused how to organize my folders that all my documents put in, I hope all those documents could be linked to the library belongs to the MN3, other than I duplicated the document into MN3 each time. Is there any advice?

Hi, I worried about this a lot at the start too, but then I was persuaded by another person on this (or maybe the Devonthink) forum to not look for a perfect system and not worry about duplicated documents. That person’s method, if I remember correctly, was too duplicate it marginnote, annotate it, make the relevant notes / derive the required information, then they had no further use for the annotated document, so they deleted it. I’m not sure I will take quite that route, but it made me more own to allowing duplication.

I think (but I’m not sure) it’s possible to index the marginnote folder into devonthink, but I decided against investigating that in the end.

I’m also a user of Devonthink Pro, I has indexed one folder belongs to the library of MN3( iCloud Drive/MarginNote 3 ).

For the present situation, I have to endure some documents occupied in two locations

  1. ~/Documents
  2. iCloud Drive/MarginNote 3

this seems to waste my storage.

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Can you please explain how to use links to create a concept map? I feel very constrained by the mind-map - really it is just sequenced excerpts, and it is very difficult and time-consuming to rebuild those excerpts into something more useful. But the “concept-map” you mentioned sounds more like how I would like to use MN. Can you please elaborate on how to do/create this using links as you mentioned?

Hi Irc. Just wanted to comment about reading several documents: I could integrate the notes of 7 documents into one mind map - MarginNote has a feature for that. Hope its helpful

Do you have an example how to achieve the zettelkadten method you could share to help us in the good direction ?

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Two things would help with better academic workflow with others apps

  1. Allowing for linking files and annotating them in other apps (So pdf would sit in another folder and would be only linked to margin note library
  • Mindmaps would be accessible only from marginnote note, but annotation like highlighter should be intercheable with other apps, making annotation in other app and oppening it in marginnote would create an excerpt that use could put to mindmap
  1. Allow MN to work with Hook for single excepts and notes

I’m still looking for an app to do the annotations on my iPad. My workflow is very similar to the one described by @bart (DevonThink, Tinderbox, Scrivener, Bookends).
I like the way MN3 works a lot. But because there is no working export of the PDFs including my annotations I will stay with Highlights on the iPad. The PDF export is not usable at all. No annotations were exported and also the character set of the PDF is not usable. If I annotate in a PDF exported by MN3 in DevonThink I only see garbage and no text for the annotated text part. The export of separate rtfs for DevonThink is no option for me.
To see AppleScript support for MN3 is a nice new feature. If the PDF export follows the Adobe standard format for annotations MN3 would become a great companion for my work.



In the future, Marginnote may provide a non-flattened PDF export function.

Kind Regards,
Support Team