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!