A question for Post Grads and Academics

I am about to embark on a Masters. For context when I did my Bachelors degree there were no computers outside of mainframes. I wrote every note and every essay long hand. My dissertation was written on a Wang word processor so it could be handed in as a typed document.

I am looking for advice as to what might be the best software to help me in my new endeavour.

In terms of note taking, note keeping, reflective journal I was thinking Obsidian. I am relatively familiar with it. However, I have just started playing with Logseq - which I really like, but it does feel like an either or with Obsidian. I have also started to look at Notion (having resisted the call of the you tubers for a a long time.) I am impressed, but I wonder if it is better for organisation and filing, rather than active note taking and study.

I am doing the masters part-time while I work. That means I wont have a huge amount of time to fiddle-faddle trying out lots of different software (and believe me I would) I need to get a system and make it work.

I would be great to hear your thoughts and experience.


EDIT: Happy to be told that my current software thinking is way off

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Well, my best advice (but full disclosure: my grad work a while back), is if you like Obsidian, use Obsidian. Focus on your learnings/courses/thesis and use what makes sense for your needs as they develop.


Honestly, if I were you, I’d take lecture notes by hand, and transfer them to the computer or use a tablet. Your brain is used to that, you can concentrate on hearing and putting things in your own words (which helps recall/retention).

But Obsidian is fine. Anything you know how to use and don’t have to constantly tweak is fine.

You will want a good .pdf reader and annotater, which can be preview on the Mac.

Your specific grad program may have specific software and hardware requirements, and educational pricing. It may use an LMS, like Blackboard or Moodle or Canvas, which you may find doesn’t like Firefox or Safari, and assumes Chrome is The Only Web Browser.



I like @Medievalist advice on taking notes by hand or using a tablet. I did this for my coursework. One thing I find, though, is that it’s unsatisfying and sometimes quite difficult to find digital notes, especially when written by hand. I can quickly find things in notebooks years later that I am at a complete loss to find after only a couple of weeks in digital format.

More info might be helpful (or maybe I’m just curious!). What do you like about Obsidian and Logseq? What’s the discipline you’re working within?


There’s a lot to like about Notion, but I’d offer one caution about it — there’s no proper offline access. So if you’re ever stuck without internet or Notion’s service is down, you’re stuck until that situation is resolved.

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The note taking systems I’ve used over the decades:

  • pen & paper spiral notebooks (rarely look at again, but that information served its usefulness)
  • Moleskin notebooks (what student can afford these)
  • Evernote (data nearly locked in, but otherwise great)
  • Notability (results in very big, hard to search files)
  • PDF Expert annotation on PDFs (hard to search)
  • Bunch of text files and Byword (no images or diagrams, Markdown tables are not helpful)

Ultimately my ideal system would:

  1. avoid proprietary systems where I don’t control my data
  2. easily searchable
  3. easily editable
  4. accessible on all devices
  5. support images and tables and maybe basic formatting
  6. linkable to one another

When Obsidian came out with Live Preview, it mostly met all of these criteria.

The oft cited study by Mueller & Oppenheimer noted students who took handwritten notes fared better than those who typed (see @Medievalist’s comment above), hypothesizing that slow writers have to process what they hear to make choices about what to write down versus fast typists transcribing everything the professor said without thought.

That said, when using Obsidian/Drafts, I structure it while taking notes (and then again a short time afterward) to make sure I’ve processed the material.


Essays in long hand, ahhhh…. Sigh of nostalgia.

Have you considered a tablet with pen? I purchased a reMarkable 2 last year and can almost recommend it over my trusty notebooks; the only downside being it’s A4, which is probably fine for lecture or lab notes, but a sometimes a little too large for my uses. Other than that it’s excellent, you can have as many notebooks as you like, can organise them in folders and use a cloud service for handwriting recognition. You can also use it as a ebook reader, but I still prefer my Kindle.

Speaking of Kindle, I heard that Amazon has released a new one with similar capabilities, but I’ve not encountered one yet.

As another alternative, has any one tried an iPad mini with scribble (or whatever the iOS hand writing software is called)?

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[edit this showed as responding to @oldblueday but I meant to reply to the OP directly, sorry!]

Some really good advice on this thread in terms of tech and apps. For what it’s worth, I’d also suggest sticking with something that reliably works offline. @Medievalist 's point about the pen-and-paper link to cognition and processing seems to have been established but your mileage may vary. Like @beck I agree, it would be useful to hear more about your field.

A joint up note-taking environment could also really help you making connections across your units/subjects/assessments and so on. Rather than starting a new paper notebook per unit, I think Obsidian will suit you very well thinking about your learning in the round, and applying your learning as you go forward (students - though no you, I am sure! - can consider different units and topics in a very ‘siloed’ manner, and that’s rarely helping them).

I’d consider other issues here too about effective note-taking in classrooms. If your teaching staff make lecture slides available before the event (many do these days in the UK), download these and annotate as you go, saving you lots of time. You don’t then have to outline a structure and you can focus on what matters to you.

There are also different kinds of teaching situations calling for different kinds of note-taking. I’ve been in seminars that look like typing pools, Admittedly I am biased here – I teach in the Humanities at a UK university perhaps not too far away from you! – but workshop / seminar / tutorial type settings can be killed dead by students more intent on trying to take down the entire meeting. Some students operate more as stenographers than as seminar participants. I often recommend to my students they focus on participating; listening; sharing ideas; practice argumentation on the hoof, and so on. And then they schedule 30 mins after a class to write up their notes. In case of any questions, follow up with your tutor in their office hours (they’ll love you for it – honest!).

Have a great time on your Masters programme!


I’ve been using an iPad Mini with an Apple Pencil and GoodNotes for live lectures (well, not so live; audio sessions or video streams). It’s not terrible, but I’m going to continue with paper and pen.

It still requires a little too much effort to write; I’m paying a little more attention to the process than the lecture. Going back to pen and paper, transcribing them or a summary and location (notebook and page) for the computer.

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I’m a huge fan of writing by hand, it’s slower, so one needs to kind of summarize as you go when making lecture notes. I think it helps thoughts marinate as you’re writing too.

Lots of good advice above.

Whether you’re doing STEM or humanities can influence your tools.

Overall my recommendation is to put the work into your masters, not into your note taking system.


Will the lecture notes be posted in advance in a downloadable format (e.g. PDF)? If so, I recommend an iPad at least at 11in size with an app that allows you to annotate over the PDF using an Apple Pencil. If not, I still recommend an iPad at least at 11in size with an app that you are comfortable either typing notes or hand-writing notes, again with the Apple Pencil. A Windows tablet could suffice too. I’d not do hard copy directly as opposed to printing out the final notebook for archival purposes later if desired.

At the review step, rather than transcribing notes verbatim to digital format, I recommend completing a template from each lecture session. Here is where Obsidian or equivalent can be of use.

Course _____ Lesson Summary

Lesson # ____ Date ______

  • Calendar Events (e.g. assignment due dates …)

    • (example) Homework 2 due Monday
  • Topic Title – ________ (repeat for each topic at lesson)

    • new concepts or principles
    • new formulations
    • new approaches
    • key take-away messages
    • questions for next lesson??



Yes. Listening should be more important than transcribing. A specific reference, to a date, a page, a term, a citation, absolutely should be written down. But listen, and integrate what you are hearing with what you know.

Reading notes too should include YOUR thoughts, about what you heard in class, what you know, what other texts or lectures say. Ultimately, an M.A. is determined by a proof of concept final work, whether it’s a paper or an exam or both. Everything is meant to be fodder for YOUR work.


I’ve just started a part-time Masters here in the UK (September 2022)

For research papers, any word-processor will do, although check with your institution. Mine want everything submitted as a PDF. Having said that, there are a couple of things I’d mention.

Citation Manager
I chose to use a citation manager (you don’t need to, but it makes life easier). I’m using Bookends and bought the Bookends/Mellel combo. Mellel is a word processor. The reason for this is that most word processors only convert the citations in one direction. Once the conversion is done, you can’t reverse (you can in the immediate, but not after the document has been saved). Mellel integrates with Bookends allowing full integration and more importantly converting Bookends reference to full citation references and back again. Plus Bookends will also create a bibliography from your citations.

We all know that there is really only rewriting. I’m using Scrivener to do this. Simply because I can re-arrange things in the draft. It is very flexible. It will also output something I can open in Mellel.

My course requires Turabian citations which come from the book, “A Manual for Writers”. This book is excellent and guides you though writing research papers, dissertations, how to cite, and how to take notes. I highly recommend reading it as it will give you great tips and allow you to workout where you want your notes. There is a spiral bound version that is excellent.

I did too much thinking before the course started. The induction week was excellent and gave me everything I needed to know.

The only frustrating thing for me is that I prefer books to ebooks. Sadly, colleges and universities have most of their stuff in online libraries, journals and databases. I find this makes making notes harder, but you need to work out your workflow. The other frustrating thing is that the online libraries want you to make notes in their web browser application and copying and pasting quotes outside of this is often disabled, although they do allow you to export your notes and you can pull a citation from pages you are reading (very handy).

I’m making notes by hand and then typing them up in Scrivener to process.

Finally, it is worth investing in an audio recorder to record lectures for the times you do need to be in lectures. You do need to ask for permission from the lecturers, but all of mine have been happy with me recording their lectures. This has been a great help to re-listen to the teaching, especially when they detail the research paper questions you need to complete.

Hope that helps!


Wow, thank you everybody for some excellent advice. My Masters is an MSc in Systems Thinking In Practice.

What I know is that my typing is not fast enough, as such I will be handwriting my notes, and then transferring them into a digital format (using a sample of one I find that I remember handwritten notes over typed notes, so I am inclined to agree with paper linked by @oldblueday) I lost 20 years of notebooks books recently - a story that involved heavy rain, bad packing and a leaky shed roof - so I want to get everything digitalised. I think it will end up being a bit of a hybrid system

I have an iPad pro (11 inch) and an apple pencil - I will use that to annotate and highlight PDFs. I am using Noteshelf and Goodnotes now, but I will need to fix on one. Probably Good notes as the folder usage is much better, although the writing is better on Noteshelf. and the Mac companion app is better. I will use pen and paper to write (real) book notes and lecture/tutorial notes. From what i am hearing Obsidian would be a good place for everything finish up in. I am not sure I will be able to keep track of the number of periodicals/ journals and papers I will be to read using paper alone.

I agree with those that said Notion is great but with limited offline (and a significant learning curve) I might put that to one side for now. However, it is an impressive piece of software.

Thank you @DrJJWMac for the template advice. I was reading more about some of the templates the university recommends as well today.

@SvSmailus, firstly good luck and second, thanks for the book tip. I had not yet settled of a citation manager. I was looking at Zotero, but I notice Bookends have a free trial so I will give it a go. I haven’t used the online library in anger yet, so I am not sure of the rules. I did join the SCONUL library scheme, so hopefully I will get permission to visit other university libraries.

@beck, Obsidian just clicked with me, I have no idea why. I am not a super heavy user of it (yet) but I find it a pleasure to use. I like the fact that the files are local and in a format that open and transferable and I love the integration that can be achieved through the plugins. However, it really is not that rational, I just feel very at home in it! Logseq is new to me. I did try Roam Research early on, but the pricing and cult put me off - but I did like outlining the nature of the software. Logseq feels similar. I like outlining software - in fact I probably have more types of outlining software and mind mapping software than any other (love me some opml!


Search here in MPU for posts on Zotero and Bookends. They are both excellent citation databases. You will be able in your reading here to find strong advocates for one or the other. You may find caveats to help you support your reasoning to prefer one over the other. You may also find the UI approach in one or the other clicks, but do not neglect to review in advance the back end “heavy lifting” you will have to do when it comes time to annotate on citations and build them as references into your publications.

Figure out the method you will use to search for literature based on having one resource that gives you the most up-to-date information and one resources that gives you the broadest coverage of information related to your discipline. The two may not be the same.

Otherwise, it sounds as though you are off to a good start (as we might guess for someone heading into “systems thinking”).


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Might the Rocket books be of help?

I think Scrivener would be of help but, admittedly, it has been a while.

I’ve been an academic for 34 years and can tell you that while technology is useful for so many things, every once of data I have seen suggests that taking notes by hand is the way to go. If you would like to use technology then consider and iPad and Apple Pencil along with a good note taking app (there are many)

Like you when I was an undergraduate back in the 1970’s pen/pencil and paper was the only option. The college’s mainframe computer was an HP3000 that they proudly displayed through a glass wall. My current iPhone 14 Pro Max likely would dance rings around that thing now. Today my university’s computers sit in a small closet.


Check out the options for exporting with both of them.

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Rocketbooks pale in comparison to an iPad.

A subject near and dear to my heart. I have yet to finish Donella Meadows’ book (and the half-dozen others I have on the subject).
Best of luck, and would love to hear some updates as you progress!

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