How to organize research notes

How to Organize Research Notes

[UPDATE: I’ve written a new and expanded post on digital note taking here.]

Your Problem: If you write a lot you most likely read a lot too. To inform your writing projects you gather information from all over the place: a cool blog, a journal article, a newspaper cutting, a PDF, a book chapter, a scrap of paper with an ISBN on it…

If your desk is anything like mine in recent times there are notes-to-self on bits of paper and Post-Its everywhere, and your computer desktop is littered with .txt files with little ideas that you intend to return to later (of course).

How to make sense of it? How do you organize all your research?


Now That’s Organized.

The Importance of Note Taking

We all know it’s good to read widely. Not least because,

Whatever problem you’re struggling with is probably addressed in some book somewhere written by someone a lot smarter than you. – Ryan Holiday

It’s good to have a thought journal to develop your understanding of the facts, ideas, and concepts that you come across and that strike you unexpectedly.

(You might be interested to know that Richard Branson wants you to make more notes.)

Here’s an interesting journal article on the importance of note taking to learning: Note Taking and Learning: A Summary of Research

Note taking, in particular by hand, is an incredibly powerful habit. When you commit your thoughts to paper you process them, distil them, and make more sense of them. Many studies report better recall and better comprehension when handwriting notes is compared to ‘born digital’ notes.

Quite simply, handwriting your notes is better than typing them.

(You can read about the dangers of Going Paperless in another post.)

The key point to consider is that digital note taking encourages shallower processing: it’s too easy.

Copying & Pasting notes, making highlights, and saving-for-later hundreds of PDFs does not count as processing information.

Do not seek shortcuts for your note taking! Do the work to get the rewards.

I’m a techie. I like my iPad. I want my stuff in the cloud. So my solution is a compromise: I work in hand but organize digitally.

This born-physical-stored-digital approach is my attempt to get the best of both worlds. It allows for the cognitive advantages of using a pen and paper and the ease of retrieval and tagging features of digital files.

Here’s my system to create and organise my handwritten notes in order to get the benefits of digitisation but avoid the cognitive costs.

[2017 update – I now use an iPad Pro and Apple Pencil to get the best of both the analogue and digital worlds. Blog post here.]

You need a good notebook:

Make sure you have a notebook that feels special to you. You should want to take it around with you and, most importantly, you should want to write in it.

A notebook with a hard back and a wired spine is my favourite. They don’t get battered in your bag and last as long as you need to fill up the pages. The hard back means there’s always a stable surface – so no wonky words.

A wired spine means you can always flip the page around and write on a smooth, flat page without needing to bend back the spine (which I find really annoying for some reason).

My notebook of choice is the Oxford Black n’ Red A4 Wirebound Hardback Notebook.

Its pages are also perforated, so you can cleanly rip out pages if you need to without ruining the rest of the notebook.

I know there’s a real fashion for Moleskine notebooks these days, and it’s certainly a great brand. But I don’t find their notebooks all that practical.

However, what I think doesn’t matter: it’s important that you have a notebook that you like and want to write in, so just make sure you love your notebook.

Get yourself a good pen:

What’s a good pen? The one you can find that’s a joy to write with.

A good pen might be a crazy-expensive Mont Blanc or a cheap Bic, just make sure it’s one that you like writing with. You want to have an incentive to get those thoughts on the page.

I was recommended the Uni-ball Jetstream recently and have been converted away from Bic Biros. The Jetstream offers a great balance between the ease of writing with a rollerball and the satisfaction of a ‘proper’ ink pen.

Make sure that you, your notebook, and your pen are inseparable:

A confession: I ‘temporarily misplace’ a lot of pens. This is not a good trait if you want to make note taking an easy activity. You can’t make notes without having those tools together at the same time, so why not get a fancy holder?!

Here’s a cool tool to make sure that your notebook and pen are best buddies.

I’ve tried a few ways to marry my note book and pen, from elastic band to a minimalist iPad cover for them both, but this is fairly inexpensive and does the job quite nicely.

Now go forth and take glorious notes! (Some tips here.)

How to digitize your paper notes:

Once you’ve made your notes and you’re ready to organize them and integrate them into your knowledge management system, it’s time to digitize.

You’ll need an Evernote account and the Scannable app from the iTunes Store on your phone / iPad. (If you’re on Android there are alternatives: i.e. GeniusScan)

Scannable is an app from Evernote. It’s great at detecting the edges of documents and then adjusting the lighting to enhance your writing on the page. Here’s an example of a Scannable capture vs. a normal photo using the camera app:


The pdf created by Scannable is on the left, the camera app picture is on the right.

I think the Scannable version is better, don’t you? It’s far easier to read the text, and that’s exactly what we want.

Save the scan and give it an appropriate title, then upload the file to Evernote.

You could stop here: your handwritten notes will now be digitized and available in Evernote. If you’re an Evernote devotee, then you’re good to go!

But I’m a Devonthink person, so there’s one more step to get my handwritten notes into my database software. (You can read more about how I use Devonthink in this post here.)


Importing Evernote notes into Devonthink is straightforward. Make sure you have both Devonthink and Evernote installed on your computer. Then open your database, click [File – Import – Notes from Evernote] and you’re done. Easy.


Now that your written notes are in Devonthink you can tag them, store different notes in different folders within your file structure, or just dump them in an archive folder for reference.

I like this system because the hand-written notes are still available, and the digitised version is in addition to the physical version. Because you can tag and date your digitized notes, the digital copy is easier to retrieve and access, but you’ve also benefited from having made the notes by hand in the first place.

You’ve had your cake and eaten it too.

[UPDATE: I’ve written a new and expanded post on digital note taking here.]


  • Always makes notes in your notebook; buy cool tools that make writing a pleasure
  • Once a week, scan and import; use Evernote and Scannable, import via Devonthink (if you use it)
  • Be awesome – your notes will have a digital home, and still, you’ll benefit from handwriting them

Final Thoughts on Organizing Research notes:

You should always question whether it’s worth adding another task to your workflow (such as digitising your notes). Avoid workflow complexity like the plague, as it creates a disincentive to do creative work.

If you don’t defend simplicity you’ll end up doing loads of busy-work that has no real purpose other than amassing a collection of impressive technology and clever software integrations.

That said: I scared myself with the research I did for my recent post on Going Paperless.

Born-Digital notes are not a shortcut – pen and paper should be what you reach for when doing thinking-work. But the benefits of going digital are real.

The workflow described in this post is my attempt to get the best of both worlds, and the additional effort to use Scannable and import to my research database is worth it.

[UPDATE: I’ve written a new and expanded post on digital note taking here.]

Any thoughts on this? There’s a comment section below ↓

The Benefits of No-Tech Note Taking –

4 Benefits of Writing by Hand –

A Learning Secret: Don’t Take Notes with a Laptop –

The Pen Is Mightier Than the Keyboard: Advantages of Longhand Over Laptop Note Taking –

Marginalia, the Anti-Library, and Other Ways to Master the Lost Art of Reading –

Why Reading On Paper, Scientifically, Makes Us Happier People. –

Going paperless is not the answer

going-paperless-is-not-the-answerThe paperless promise:

To someone who grew up in the 90s it sounds like a futuristic tech fantasy: All your books and notes on one device, instantly accessible, and with perfect recall. It will be as if technology has made your brain obsolete.

Your main task will be merely to add more information to the pile.

Tom Cruise demonstrates the paperless dream in Minority Report.

Tom Cruise demonstrates the paperless dream in Minority Report.

But don’t worry, you’ll barely need to read it, let alone understand it. All this information will be automatically organized, classified, and optimized.

Scarily, this vision is here already.

Do a tinsy bit of googling and you’re certain to find all manner of inventive and clever workflows that automate this, produce that, and encourage you to sign up to the latest hot web tool. You can now achieve the paperless dream.

But is this exciting paperless technology really all that it’s cracked up to be?

I think we should be a little more critical of the technology that’s constantly thrown our way. I’m more guilty than most in buying into the paperless dream, but as I bring one large project to completion and start on the next, I’ve given some close thought to my paperless aspirations.

Here are some thoughts on what paperless is trying to do, the costs of going all-digital, and some of the ways I’ve tried to take the benefits without making the sacrifices.

Your goal:

CC Image courtesy of mrsdkrebs on Flickr

CC Image courtesy of mrsdkrebs on Flickr

Let’s start with a question: besides looking like Tom Cruise in Minority Report, what benefit does committing to going paperless give you?

For you, personally, right now, what’s the attraction of the paperless dream?

Are you looking to make a particular task easier? Or are are hoping something new and shiny will overcome your problems with motivation and procrastination?

“Things would be so much easier if [insert paperless tool here] was part of my workflow…” – Me.

Searching for productivity ‘hacks’ has become a procrastination fetish for many of us. It’s something that I’ve caught myself doing and have aggressively cut down on. There are infinite articles that speak to our anxiety of not being productive enough – we’ve all been down that internet wormhole. [Someone should do a study on the economic cost of our constant search for productivity tips.]

Are the promises that the advice and tools leading us towards the paperless promised-land realistic?

‘You could be so much more productive if only you signed up to our tool.’ – ACME corp.

It’s so easy to buy into that message. Paperless seems to be the way forward, so you ask yourself why you haven’t done these things already. You’re promised that when you get there you’ll be a productivity God/Goddess, so of course you sign up to that new tool.

Before long you’re taking your laptop everywhere, only read on a kindle, and refuse to use a pen. If it’s not digital, it doesn’t matter. (A slightly exaggerated me.)

This might seem like an unrealistic situation and something that you’d never do, but, unchecked, it’s the direction we’re heading in.

The costs of going paperless:


The all-digital, paperless utopia has a darker side.

I don’t want to suggest that everything is awful – there are very obviously useful tools that can massively improve the way you work – but it’s not all milk and cookies.

There are an increasing number of studies that suggest your brain might not like it so much. In fact, much of this research is suggesting that you should go paperless only with extreme caution.

If you’re going to make a commitment to go paperless, you should be sure to understand the sacrifice you’re making by ditching your pen for a stylus and notebook for an iPad.

Here are a few things to consider if, like me, you spend most of your time in front of one screen or another:

  • Taking notes on your computer has been shown to lead to worse comprehension.

The suggestion here is that using pen and paper trumps typing digital notes when remembering conceptual information in the longer term. When you’re typing information up there’s a tendency to transcribe rather than to process and synthesise information in your own way.

Not thinking about your notes before you write them prevents your brain from more fully comprehending the information that you’re attempting to capture.

people should be more aware of how they are choosing to take notes, both in terms of the medium and the strategy‘ – Pam Mueller

(The underlying study is available here)

  • Reading digital text has been shown to affect the ability to recall.

A number of studies have suggested that paper reading boosts recall ability. Paper is a physical object, which means that as you read it your brain can relate to it in different ways. This extra-dimension allows for additional memory capacity. Given that it’s important to recall details to truly ‘know’ a topic, this is certainly something to consider.

‘There is physicality in reading, maybe even more than we want to think about as we lurch into digital reading—as we move forward perhaps with too little reflection. I would like to preserve the absolute best of older forms, but know when to use the new.’ – Maryanne Wolf

ergonomic dimensions, the tactile feedback of holding paper, might actually matter‘ – Anne Mangen

people on paper started to ‘know’ the material more quickly over the passage of time‘ – Kate Garland

  • Using technology increases the tendency to multitask (and procrastinate).

Rather than another cognitive study, in this article Clay Shirky writes about his classroom experience of banning technology in his lectures. His observation is that it’s undeniably harder to focus on an intellectual pursuit when using a computer. Our monkey brains will switch to the cheap rewards of Facebook notifications before too long. This is probably why Freedom App and RescueTime get so much coverage in writing circles.

‘Our visual and emotional systems are faster and more powerful than our intellect; we are given to automatic responses when either system receives stimulus, much less both. Asking a student to stay focused while she has alerts on is like asking a chess player to concentrate while rapping their knuckles with a ruler at unpredictable intervals.’ – Clay Shirky

A suggestion: Don’t choose between paper and paperless:


These studies give pause for thought. We need to think more carefully about what we are doing to ourselves by going paperless.

Clearly, utilising additional paperless tools does not necessarily mean a better, happier, more productive you.

There are clear costs to removing paper from your life and you do need to think carefully about when you should keep a pen in your hand.

But going paperless isn’t an either/or proposition.

It’s important to realise that there is no obligation to go all-in. Rather than committing to paperless, fudge the issue and do what works for you in certain situations. i.e. It’s ok to buy paperbacks and ebooks.

Don’t beat yourself up for not having a totalised, unified, and seamless paperless system – just make sure you can keep track of your notes wherever you put them. Taking notes on paper is going to work best in certain situations; i.e. when you are hoping to recall data in the longer term. It’s more important to have a reliable collection system than for all your writing to be born digital.

Reading and writing technologies have always evolved – and coexisted:


Changing Our Textual Minds: Towards a Digital Order of Knowledge is a great book that charts the history of reading technologies. It prompted me to think about all the technologies I use when I read and write.

One of my big takeaways was that these technologies have always existed side-by-side, and with varying degrees of tension between them. But that’s okay.

We’re lucky to have these technologies to choose from in different situations.

To deal with some of the issues that recent studies have highlights, I’d like to see the bundling of reading technologies. Amazon has a feature where you can get the audio version of an ebook with a discount. I’d love to get a free digital version when I buy the paper version. The physical copy would be to read, the digital copy would be to have on file for recall and analysis.

In the past, I’ve digitised books after reading them in physical form and I definitely remember them better than the books I first read digital. I’d like to do more of that.

My solution to the paperless problem:


The evidence seems fairly clear that thinking on paper is better. Better in terms of recall and understanding.

But digital storage makes search and retrieval so much easier.

What to do?!

My own solution is to use my Black n’ Red spiral notebook for most of my jotting. I can scribble, doodle, and then tear out pages to digitise if necessary. (I use Scannable for this.)

In practice, I digitise meeting notes and semi-structured brain-dumps, but not to-do lists or rambling free writing.

I’ll make the effort to transcribe my handwritten book notes for larger, multi-year projects that benefit from text search. This includes my PhD, which I organize with Devonthink.

I mark-up PDF’s with Goodreader, using a stylus to write on the PDF. I make the digital file my own with highlights, notes, and doodles. Marginalia is more satisfying and memorable than appending typed-text notes.

[Side Note: Marginalia, a lost art]

When I want to take in a book – its information and its arguments – in a lot of detail, I will buy the hard copy. Intuitively, I know that I remember the content better, and the science seems to suggest that is indeed the case.

There is nothing like taking a red pen to a new book and making it yours. (Tim Parks thinks we should all read with a pen in our hand.)

My kindle is now mostly for fun books. The highlight feature is far too easy, there’s no real brain processing, and I rarely remember what I chose to highlight. When I do read ‘important’ books on the kindle, I make handwritten notes to slow the process down and aid comprehension.

It’s a difficult balance to make the most of the incredible tech tools we have available, but not to take so many shortcuts that the brain suffers.

I now try to read just as many articles on the effects of e-reading and handwriting than productivity-porn articles. That gives me some way to work out which paperless tools will add convenience, and which will adversely affect my recall and understanding.


Open-book-at-a-beach-001Will grabbing the new shiny paperless technology really advance your personal and professional goals?

This isn’t about restraint or frugality, it’s about making sure that you’re doing your brain a favour. If you’ve made the effort to foster the admirable habits of regular reading and writing, don’t sell yourself short.

There’s a balance to be had, and it’s different for everyone. I still find using Devonthink to organize information for my writing projects is incredibly useful, but I’m no longer deliberately restricting my paper production just to get digital notes into my database. The science is indicating that using pen and paper and reading physical books have too many benefits to ignore.

I’m trying to think more carefully about when I should use my paperless tools, and when it’s better to switch back to the old-fashioned way. Paperless is not always the answer and I strongly doubt paper will disappear anytime soon, at least from my desk.


The Problem With the Web and E-Books Is That There’s No Space for Them

Exploiting the Neuroscience of Internet Addiction

Take Notes by Hand for Better Long-Term Comprehension

A Weapon for Readers

A Kindle Designer’s Touching Online Memorial to the Marginalia Scribbled in Books

Do E-Books Make It Harder to Remember What You Just Read?

The Reading Brain in the Digital Age: The Science of Paper versus Screens

Reading Literature on Screen: A Price for Convenience?

Why I Just Asked My Students To Put Their Laptops Away

How To Read On A Computer Screen


I try to read on-screen as much as possible. Why? Because notes typed on-screen can be searched for later, marking/highlighting can be saved, and it makes keeping track of what I’ve read and then retrieving it again later much, much easier. (UPDATE: I’ve changed my thinking on this.)

You can even take your entire library with you for that moment on the beach when you just *have* to flick through that book you read 3 and a half years old…

But the switch to paperless reading isn’t effortless. Initially it’s not as easy or comfortable as reading on paper. Paper is ‘real,’ you can mark it anyway you like, there’s no computer related eye-strain, all you need to do is pick up a book and you’re ready to go. I don’t need to explain how books work :-)

Setting up your computer for heavy duty on-screen reading is not quite as simple as picking a weighty tome from the shelf:

  • What software should I use?
  • How do I manage pdf documents for reading?
  • How can I reduce eye strain?

However, with a little setup and downloading mostly freeware or open-source software, it’s quite easy to go paperless and reap the rewards of on-screen reading.

Here are some tips and techniques I’ve found to be useful:

Pocket / Instapaper / Readability:

Reading webpages without all the banner ads and other distractions makes it a lot easier to get through web text. A number of read-it-later service can do this for you. They strip out the fluff and leave only the core text.

You could use an ad blocking service for this (i.e Adblock: But you’re still left with website layout design of varying quality. Isn’t it annoying when you have to click ‘next page’ every few paragraphs?!

I use Pocket, which syncs across the web, my Mac, and my mobile phone. I try not to procrastinate (too much) with long-form reading throughout the day, so these services are also a good way to ‘save up’ reading for later.

In fact, this has become my Golden Rule, which I seldom break:

“I am only permitted to read stuff online through a read it later service”

– The Golden Rule

This way you can read clean text and also avoid the internet rabbit hole.

You can start using Pocket here:

Start using Instapaper here:

Start using Feedly here:

Use Skim to read PDF Files:

A large chunk of academic reading is of pdf journal articles. I use the open-source software ‘Skim’ to make sense of them.

Skim lets you highlight and make notes directly within the pdf file, which means you make the article your own and don’t lose track of your notes or markings. I find that it’s much more useful to have that one easily retrievable annotated pdf file on the computer. The article and my notes are all saved in just one place.

Skim is available for free here:

PDF Xchange Viewer is Windows compatible and is available for free here:

I’ve also started using an iPad for reading and annotating. If you have an iPad (or other tablet) you might this post on ‘Annotating PDFs on an iPad‘ useful.

Avoid Scrolling:

I previously used a tool that automatically scrolls down the page at a slow speed. (Info available here.) Auto-scroll seemed fantastic: ‘No more page turns,’ I thought, ‘I can read forever!’.

The reality: I could only read for half an hour before my eyes began to burn.

Following the text as it edges down the screen is a terrible eye strain. You’re asking your eyes to focus on a back lit screen, comprehend a digital font, WHILE IT’S MOVING. Please don’t do it.

Rather than continuously scrolling, use the page down key; it means your eyes don’t have to continuously readjust to the moving text. It should be right there on your keyboard and if it isn’t, learn the short cut. (It’s fn+down on my Mac.)

Pocket has a feature called ‘flipping’ if you use it on your mobile device. Once enabled it stops scrolling articles and instead formats them as pages. If you use Pocket I would strongly recommend learning how to use this feature!

Automatically Adjust Screen Settings with Flux:

Flux is a bit of freeware that alters the screen lighting on your computer, shifting the colour based on the time of day. It’s brighter when the sun is out and automatically changes when it gets darker. I find it helps reduce the eye strain from screen glare that sometimes comes with reading in the dark.

Flux is available for free here:

Zoom In and Use the Biggest Font You Can:

Reading a big font is more comfortable than reading a small font. Obvious, right? There’s no reason to be squinting to read web text on your screen. It is very easy in most browsers to change text size, usually with an easy shortcut. I use Chrome and the shortcut “Command & +/-” to increase and decrease font size as needed.

When reading a pdf, zoom in. If you’re using a small laptop with little screen space, consider getting a second monitor. I have a cheap second monitor I use alongside my laptop that’s extremely useful and worth every penny.

Resize the Window:

As well as zooming in and out to adjust text size, you should adjust the actual window size as well. This way you aren’t scanning across the whole width of the screen, which invites eye strain. It’s easier on your eyes to make the window narrow and allows your eyes less lateral movement.

I use the Kindle app on the computer fairly often and it lets me manipulate the window size very easily. I like a narrow, single column format on a sepia background.

Any Others?

I’ve listed just a few simple things to do / tools to use that make reading on the screen that much easier. I’d love to hear your own tools and tips in the comments:

Think of your eyes:

Nothing in this post is very imaginative, most of the suggestions are to reduce the workload on your eyes. Be kind to them and on screen reading will be much easier.

Some Links:

How to Make Reading on Your Computer a Better Experience

Computer Eye Strain: 10 Steps for Relief