I have spent more trying out note taking apps that I would like to admit. You could say I’m picky. Through all the trialing and testing, one app stands out for combining almost everything I want in a note taking app with a number of features I hadn’t even thought of. That app is Notebooks. The more I use it, the more I am convinced Notebooks is the best note taking app for study, research and academic work.
My enthusiasm for Notebooks is its own reward, so it’s a huge bonus to have that enthusiasm met with generosity. The developer of Notebooks, Alfons Schmid, is kindly offering readers of The Appademic the chance to pick up one of ten free copies of Notebooks for iOS.
Aside from being an excellent general purpose notebook, Notebooks has a host of features uniquely suited to academic work and study — or any kind of research for that matter. I recently highlighted the way I use Notebooks’ task management, and URL scheme features to collect material, and organise reading lists. I have a more detailed review on the way, which will include more worklows that make use of Notebooks' unique features. In the meantime, if you are unfamiliar with the app here are some of the highlights.
Deep URL scheme automation
Internal linking for wiki notes or zettelkasten
Support for almost any document type you can think of
Private Wifi syncing, WebDAV or Dropbox
Future proofed by plain text and html
Document processor, ebook compiler and PDF converter
Task Management, including GTD contexts
Integration with OmniFocus, Things 3, Todoist, 2Do and more
Customisable style sheets
PDF annotation and sketching
Win a Free Copy of Notebooks for iOS
Notebooks is a powerful tool with a clean, and slick interface. It is easily one of my favourite apps on the iPad. It is the best note taking app I have found for my own purposes. If you want a chance to pick up a copy, signup for the Appademic Mailing list below. If you are already a subscriber, you’re in the draw already. The draw will close on Friday 24th of August, and winners notified via email. There are 10 copies to be won.
If Notebooks isn’t best note taking app for iPad, it is definitely the most underrated. If you're looking for a markdown notes app, a writing app, or a document storage container with a few unique tricks, you won’t find many better. Part notebook, part storage locker, and part GTD task management system. That might sound like a janky combination, but not only does it work well, it looks pretty too. It has been around for a while, so in lieu of a comprehensive review, I want to highlight a particular feature I haven’t seen anywhere else. The ability to turn notes into tasks.
If you have a lot of reading to keep up with from a variety of sources, this is very handy. For planning and tracking big reading projects I still use TaskPaper on macOS, with its counterpart TaskMator on iOS. That system works well, with the outliner style lists making it easy to break up books, journals and so on with due dates. Using Notebooks has a distant advantage over that system, as it can collect the reading material itself. Web pages, notes, PDF documents, Word files, you can read them all directly in Notebooks. It will even let you index epub files to open in a third-party reader, like Marvin. Remember, at its core this is note taking app, while reading you can highlight text, make annotations, take clippings, and more. You can also take notes.
Notebooks Reading List Workflow
This is a simple idea that in practice will help keep track of reading lists, note revisions, or really anything text based. It’s true you can fashion a similar system by chaining apps like DEVONthink and Things 3 together. To my mind this is more elegant, or at least less confusing.
It works like this. As I collect reading material, I drop it into a Notebook that has been setup as a task list. When I’m on the clock I can setup due dates, reminders and so on. More importantly, I can tick items off as I go, meaning a quick visual guide is available to measure progress. It’s easy enough to use Notebooks’ share extension for this — or bookmarklets on the Mac — but there are two alternative methods I prefer. First, Notebooks has a very hand URL scheme which is clever about capturing all kinds of data, which makes setting up a custom action extension for Workflow trivial.
The Workflow action above is especially handy on the iPhone, but the iPad has another option that is easier still. Notebooks has excellent support for the drag and drop feature of iOS 11. So if you don’t fancy using Workflow, you can use multitasking to simply drag links and files directly into a reading list. Or, you can use something like the excellent shelf app Gladys to hold the material you collect before dropping it into Notebooks later. Gladys now has a Mac version too, which adds some continuity to the workflow.
Among the Best Note Taking Apps
If you follow this site, you probably know by now that all my data ends up in DEVONthink, one way, or another. Whatever passes through Notebooks still ends up there, but DEVONthink’s super power is search. It has passable editing and annotation tools, but I prefer doing the interactive work before it ends up in what is essentially a personal research database. For a lot of users Notebooks might even be enough. While the task management features were no doubt conceived for GTD nerds, they end up making Notebooks among the best note taking apps for college, or university users. The caveat being it's not a handwriting app. In fact if anything holds it back, that would be it. I would get around that by using Nebo as a capture tool myself, they complement each other well.
If DEVONthink’s not your jam, or you’re looking to replace Evernote with something private and local, Notebooks is a handsome and feature rich app. It has relative feature parity across macOS, and iOS, and a lot of unexpected touches. GTD purists could configure tickler files, and contexts until their head is sufficiently empty of all that arduous, excess thought. 1. It can even run its own local WebDAV server for private local sync. It sounds strange, but it’s really not.
Presenting complex ideas in a clear, and simple way is as undervalued as it is difficult to master. It doesn’t help that established presentation software is mostly dated, awkward, and time-consuming. Just as we have with writing apps, we have painted ourselves into a corner with presentation tools. Keynote can standalone as an alternative to Powerpoint. And yet, if you pressed me for a list of cool presentation tools, you wouldn't find either of those. It would be a short list, but you would definitely find Deckset 2.0 there.
Deckset is a presentation making app with an entirely different user experience. Especially if you’ve only ever used Powerpoint or Keynote. It seems Focus has become common currency in creative software of late, but Deckset delivers it in an unexpected way. Taking all the fuss, and fiddle out of presentation design by creating slick presentations from text files. With Deckset you can get back to what you should be doing, focusing on ideas.
Presentation Software or Powerpoint by default
In 2013, Microsoft estimated there were 30 million Powerpoint presentations given per day. That figure is likely to have moved on considerably. Everywhere there are presentations, there is Powerpoint. Just as Word has become synonymous with writing, and other text-based productivity, Powerpoint is the de facto byword for slide deck presentations. At the same time, Powerpoint is time-consuming, confusing and frustrating. Despite efforts to trim the product, it carries the compound baggage of an ageing codebase, run through with compromise. Like most users of Word, I strongly suspect Powerpoint users are in the application by default.
Deckset has the pedigree to follow the recent success of writing apps like Ulysses, which continue to popularise a previously niche medium. A similar user base will find in Deckset an ideal alternative to Powerpoint, or Keynote. Even if you’re a wizard with one of those apps, I’d wager you could save yourself time, and get to the point quicker if honing the words, and not tweaking transition animations.
I expect Deckset users will be largely self-selecting. Then again, I’m confident that many potential users don’t yet realise they should be part of that group. If the point is communicating ideas, then eliminating friction in the design of a presentation is paramount.Deckset’s neat trick, is to build polished slide decks from the raw material of your content, the text itself. You create the presentations from Markdown files, in a text editor. The slide deck itself literally gets out of your way while you concentrate on the message.
Plain Text is Simply Plain, Text
Despite the growing popularity alluded to above, there still exists a curious irony around the uptake of plain text utilities. Many prospective users seem concerned that plain text software will be difficult to use. In reality, the program left behind is often more complicated. Applications built around Markdown are some of the most simple and effective apps you will find for any purpose.
I was latecomer to the joys of plain text. If only I could reclaim all the years flushed by grappling with rich text, word processors, and bloated slide-deck programs. A small amount of time learning to write in Markdown can save you hours upon hours. The obvious gains are from time spent dealing with constantly shifting design elements, configuring and adjusting styles over and again. But then, there are the more intangible gains from working with words in their raw form.
Everything written about the focus of writing in plain text applies to slide deck presentations with Deckset. This is what makes it such an ingenious app. Just the same, if you’re still unsure about creating in Markdown, nothing can make this point better than a quick demonstration. The beauty of learning Markdown is you only have to see it to know how it works. It’s not code, it’s a clever markup language that translates into code. With an app like Deckset, you can simply open up the template files, and you’re away. If you want a primer this is everything you need to know to get started using plain text productivity apps like iA Writer, Ulysses, or Deckset.
# Big Heading
## Slightly Smaller Heading
### And so on...
Use two asterisks on either side of words, or either side of a sentence to emphasise words in bold, like so:
Likewise, place an underscore on either side of a word, or sentence to emphasise in italics, like so: 2
Unordered, and ordered lists are intuitive. Each line starts with a hyphen, or numeral + period, like this:
- And, something else
- Make up an unordered list
1. First item
2. Second item
3. Item number three
If you want to turn a word into a clickable link, place it in square brackets, followed by the link itself in parentheses:
Explaining how to format a footnote is more complicated than making one, so it looks like this:
[^1]: This is a footnote
Or, you can do the same with a name
[^Bentley-Payne, 2018]: Something Completely Different
With this, you have everything you need to get started with Markdown. There is more you can do with it, of course. There also exists a few variations on the original syntax, with flavours that support additional elements. The differences are always minimal, but the foundations always remain the same.
User Experience, and Careful Decisions
Enthusiasts and geeks like to talk about responsive developers. By all accounts the builders of Deckset, Unsigned Integer, have taken a user-centric approach to developing their app. There is nothing more responsive than improving an app with user feedback. Much requested customisation features in the new release allow users to create and share themes, or tweak existing one to suit their needs. And, it’s not just about the nerds.
For a seemingly geeky app, Deckset is welcome respite, either as a Powerpoint and Keynote alternative, or as a first slide deck app. The user experience scales from simple automated layout based workflows to more bespoke, and sophisticated presentations — and all without sacrificing itself to complexity. One gets the impression that behind every feature lies a careful decision.
The considered approach is evident beyond the interface itself, with clarity a feature of the product on the whole. For instance, clearly Unsigned Interger recognise the relevance of Deckset to education. Among the documentation there is a deck outlining features inherently important for teaching presentations. Tabular information, equation formatting, captioned images and videos, it’s all there. As is rehearsal mode, speaker notes, and a PDF export function for class handouts. Taking the decision to leave the Mac App Store, means more flexibility in pricing. Deckset 2.0 is now available to education users for a discount.
Goldilocks and the Slide Presentation Tool
Having run Deckset 2.0 through its paces, I almost wish I had more presentations to give. It would easily make my lists of current favourite macOS apps. The revelation that slideshow software had become a sinkhole into which ideas themselves could easily fall persuaded me to all but give up on slide decks. Powerpoint is especially guilty. Although I find Keynote still has its uses, they’re mostly off-label, and fewer all the time. For the past couple conferences, I’ve gone analogue, delivering from a piece of paper to the room. Deckset has turned my head back the other way, by finally providing a happy medium.
If you want to take a look, Deckset offers a free trial. A single license is available for a one-time cost of USD $29. Or, if you’re an education user, you can request a generous 50% discount.
I’ve never enjoyed preparing slides for presentation. Even allowing for the improvements of Keynote over PowerPoint isn’t enough to make me enthusiastic. Deckset, however, is an all together different proposition. If you write in Markdown, and want to simplify your presentation workflow, trust me this is for you.
With the new release, Deckset has also gone sans App Store, which means it now has an education discount. 1
The main reason for us to leave the App Store is greater flexibility in pricing. For example, we are now able to offer a 50% discount to students, teachers and other members of educational institutions. That is something we simply couldn’t do before, and we feel it’s essential to reflect the realities of how and why people use Deckset.
Time willing, a full review is in the works.
Incidentally, as if the 30% tax isn’t obscene enough, it is absurd that Apple doesn’t facilitate this. ↩
I have tried to stay away from Black Friday and Cyber Monday deals as much as possible. However, I want to mention the discount on Brett Terpstra’s wonderful Marked 2 app. Given the only other deal I mentioned was DEVONthink — for its relevance to the overarching concerns of this site — that should give you some idea of the esteem I hold Marked in. I'm confident Marked will be relevant to a number of readers of this site. It is one of those apps that you don’t necessarily know you need until you have it, then you wonder how you ever worked without it.
If you don’t know about Marked, it is an essential tool for writers working with Markdown, but it is so much more than that. Marked comes loaded with a stack of advanced tools for formatting, proofing, checking, and analysing your work. Highlighting keywords, checking for repetition, and analysing readability; Marked will give you a Fog Index and Flesch-Kincaid scores. It is essentially a powerful Swiss army knife for text, I honestly don’t know what I used to do without it. That’s not true, actually, I either didn’t have access to tools for improving my writing, or I had to go here, there and everywhere to use a fragmented and forgettable system that gave me a headache.
If you want to see the full list of features, check out the documentation . The details on the deal are these:
For today and tomorrow only, you can get 40% off the direct version of Marked 2. That’s the non-sandboxed version that allows more full-fledged running of your own custom scripts and processors, but is otherwise the same as the Mac App Store version. Use the coupon MARKEDMONDAY at checkout and get Marked for $8.39, 40% off the usual price of $13.99.
The easiest way to grab the deal is to follow the link through Brettterpstra.com. That way the discount will be applied auto-magically. Otherwise, you can head there directly and apply the coupon yourself.
You can also get Marked as part of the Setapp suite.
The Appademic has a year's Subscription for Setapp to Give-away, you can find the details here..
This site is still in its infancy. While it was created in March, I only started posting in earnest in May, and have steadily increased the frequency of content over the past couple of months. I’m managing a couple a week, along with relevant link posts. It is still early days, but the traffic is increasing, and interest is growing.
The site is currently built and hosted with Squarespace, which is a fine platform for any number of use cases. The advantages of using Squarespace are obvious, it is quick and easy to build a site, the templates are visually appealing, and you don’t need to concern yourself with scaling hosting for spikes in traffic. I have been reasonably happy with Squarespace, for starting out. Something that comes with the territory, however, is learning certain things about your preferred workflow. As you start to develop your blogging style, you are more likely to pick up on shortcomings in the tools at your disposal. As I get further into this, there are some examples for the way that I work – or rather the way that I wish to work – that are starting to get in the way.
The first, and probably the biggest annoyance, is I write in Markdown. While it is possible to use Markdown with Squarespace, the service only supports a very basic implementation, which means adding nice touches like fancy looking footnotes  requires both implementing awkward hacks, and converting your posts to HTML before adding them to the site. Both of which undermine one of the platforms major selling point – i.e., ease of use. Further awkwardness is encountered when working with images in your posts.
Squarespace has its own content delivery network (CDN), which for the most part is great, but in some cases it is another double edged sword. The CDN takes care of compression, and makes the media assets of your site load easily, regardless of where your audience is. However, working with Markdown or HTML on Squarespace you lose some of the benefits of those formats when working with images. Essentially, you have to leave the images out of your composition and load them separately, and the file management is by far the poorest feature of the platform. If you want to use the Squarespace editor and work with images in the manner that the platform is designed form, then it is great. Unfortunately, that doesn’t suit my workflow at all. What I am left with is a fiddly process of uploading images after the text, and dragging them into place. This might not sound too bad, but the reality is a degree of trial and error that can be frustrating. Dropping the images into the post splits up the text  in seperate blocks, which don’t always line up the way you want them to. Often I have to adjust the wording of the post to make the image sit right. Or I can use another workaround by inserting what Squarespace calls a spacer, but that results in excessive white space through the post. There is more, the Squarespace interface shifts your whole site top the right to accomodate its sidebar as you edit design elements. This may well be a by-product of the template that I use, but something to be aware of, you can get things looking the way you want them, only to have them move out of place again when you leave the style editor.
Delivering mixed content blog posts is one thing, and to date I have been willing to persevere with it, but the most vexing side-effect of that is the way it pushes me to do so much of my work for this site on my Mac. Don’t get me wron, I love working on the Mac, but these days I am doing more and more serious work on the iPad Pro, and I want to be able to manage the site on the go. Sure enough, Squarespace has an app for creating and managing your posts on an iPad, but it has some bothersome problems. First, the images problem is made worse by the fact that the app considers those mixed content posts to have complex layouts. If you edit posts that have images placed alongside or wrapped by text, it will collapse their layout so the images are at best inserted between paragraphs – the images are then increased in size to fit the margins. The app will warn you before doing this, but if it happens you have little choice but to return to the Mac. You can of course access the web editor on the iPad, but it is designed for precision use with a mouse, so you are asking for trouble trying to use it with a touch interface.
Unlike WordPress, there is no longer a posting API for Squarespace, meaning the only way you can use a third-party editor for composing your blog posts is cut and paste. This applies to working on macOS just as much as it does to iOS, but it provides nothing like the same degree of difficulty. Crafting a Workflow, or a similar process in Editorial or 1Writer on the iPad will allow you to manage the Markdown to HTML problem, but the app’s integration with the iOS share sheet is poor, so you are still left with cut and paste at the end of it – and that is before you get to the images. It is true that you can just simplify things, and working with simple layouts in the app does work well enough.
There are design elements on Squarespace that are dependant on the site template, but even when available might not work very well. The nature of The Appademic, as a site for bringing together tech and education, lends itself to link posts. I have separated them out from the main blog, as I’m not a big fan of sites dominated by link rolls . Unfortunately, the template that I use doesn’t render block in a sensible way – there is no indentation, for example. This leaves me with another awkward workaround, among the bad options for this I have landed on adding a rich text block, but this adds yet more layout complexity – and to posts that should be the simplest of all.
I want to be clear, this is not a post bagging Squarespace. There is so much to like about the platform – both for functionality, and the company’s support of content creators more generally. For a lot of people, it is an obvious choice given how easy it is to use if you are happy to work as the platform wants you to. The visual design aspect is pleasing, one thing I have been very happy with is the way the site looks. It took no time at all to get everything setup. For photography sites, the CDN, and template the gallery designs make for one of the best experiences going around. This site, however, is not a photography blog. Neither is it a store front, another area that Squarespace excels in. Squarespace also gets a hard time about search engine optimisation, which I would urge you to take with a grain of salt due to the army of affiliate marketers working on WordPress selling would be bloggers on themes, plugins, and all manner of other snake oil to ‘make it rain’. The free source and extensible architecture of WordPress is its biggest strength, but it also opens it up to the current zeitgeist of internet sharks.
Having said that, I do have a genuine problem on Squarespace in that my use of Markdown and HTML seems to create errors in the data that Google and other search engines index . If you are going to use the platform in the way it was designed – composing and posting with rich text, using a simple structure, and so on – you will not encounter the same problems. If you are an edge case for the way you work, like it appears I am with this site, it is worth considering how this might affect your discoverability . The other side of that equation is that you are more likely to have readers stick around if they land on a slick looking site than if they find a dog’s breakfast on the end of those search results. Squarespace is not going to let you down in that regard. But more than that, Squarespace is in some sense a set and forget situation, you don’t have to concern yourself with more moving parts — there is hosting to manage, so you don’t have to deal a server. You don’t even have to go outside the platform for your domain management, everything is self contained within Squarespace. These are compelling selling points for the service. Again, be wary of affiliate marketers when choosing between WordPress and Squarespace, while WordPress is not difficult to use or to learn, it still takes time to master, and to my mind not only will Squarespace will get you up and running a lot quicker, but nobody is getting a cut to tell you that .
Why post any of this? Well, the workaround I mention above have created enough friction for me that I have made the decision to migrate to a self-hosted WordPress installation before the site gets too big to contemplate that. The main reason is the workflow, I need the flexibility that WordPress can offer for working with Markdown, and on iOS. If you have made it this far through this post, you can probably tell it hasn’t been an easy decision – even now I have my doubts. This site is paid in full for another six months on Squarespace, which is another reason to not take this decision lightly. As I have gone back and forth, reading innumerable frustrating and vapid articles, sifting through the noise of resellers, affiliates, hosting companies and self-appointed gurus, I have continually come back to the one thing that matters to me most in this, my ability to work in the way that I want to. Ultimately, The Appademic is a site about doing your best work – whether as an academic, a student, or any kind of creative nerd – and I feel it is bordering on disingenuous to be writing about that via a means that contradicts the message. I looked seriously at static engines, particularly Jekyll, which is not only a brilliant solution, but is perfectly adaptable for mobile use. Inevitably I settled on WordPress for the flexibility and better ability to eventually open out the site to other writers.
The Appademic will still operate as usual for the moment, as I clone it and test it elsewhere. However, any content going up in the next few days will be basic by necessity. There are bound to be mistakes, although I am working hard to mitigate them. If you happen to find any, please contact me to let me know. I will post an update on the other side to report on how it all went, but it should be obvious when the site design changes that the switch has been made.
There are notable exceptions, and they are not without their place ↩
You can address some of this by switching on Developer Mode to gain full access to the code, or using code injection hacks, but neither is an ideal solution ↩
Note, this is a contentious point too, there are plenty of people likely to say it won’t make a difference ↩
To be clear, this site uses affiliate links, in fact the only source of revenue – a very loosely applied term, as trust me this site runs at a loss by a long shot – is by way of links. However, not only is that is far from its reason to exist, but nothing is linked without personal experience and more often than not, considerable personal expense. I would hope the difference is pretty obvious. You can learn more on the disclaimer page ↩
Zapier has posted a handy introduction to Markdown. There are a lot of these guides around, but they look to have done a good job here. If you are still mystified by how to use Markdown syntax, this might help. I am working on a bit of Markdown for academic work content, in the meantime, if this guide whets your appetite I also posted some links very early on to a YouTube series on using Markdown for academic writing
This is an ongoing battle, but for some there is a strange kind of jouissance in fiddling with one’s note-taking system. To state the obvious, note-taking is one of the more crucial academic skills. So it would seem there is a certain amount of justification in trying out different solutions to see what might stick. Whether this is new territory or not, there is always the question of where to begin. To drastically oversimplify the matter, the essence of note-taking is twofold: capture and retrieval. Naturally, there is a lot more to doing it well, but if you are just looking to get started then having these two things in mind can only help.
Typewritten Notes and Markdown
If you prefer to type your notes, then there is one simple piece of advice I would happily give anyone. If you don’t already know how, spend the brief amount of time needed to learn how to write in Markdown. Markdown will allow you to embrace plain text, which will not only future proof your work but it will make it as portable as possible and give you a uniquely focused medium for all your writing . In turn you will be free to try different solutions while keeping your work intact, and this barely scratches the surface of Markdown’s usefulness.
I am yet to find a satisfactory source that makes a clear and concise account of the benefits in using Markdown for academic work. That is not to say there is nothing written, rather there is nothing I have found that doesn’t either run full geek into the weeds to soon, or treat the reader like an idiot. So here I will be brief. In fact, this is it. If you are willing to take 5–10 minutes and learn how to use a couple of basic tricks , you can free yourself from the clutches of bloated, archaic word processors and proprietary systems – and who knows, you might even start to enjoy writing. If that sounds appealing, have a look at this short tutorial.
Armed with Markdown, you can make an informed decision about your note-taking, and even how you approach writing in general.
Yes, there are well-known names in this category. But, there is more than enough written about the likes of Evernote, OneNote, and even Apple Notes. Each of them are useful in their own right, but to my mind there are more interesting apps available.
One of my favourite apps at the moment is Notebooks. I’m not always a big fan of software that tries to be more than one thing, and to be fair I only use Notebooks in a very specific way for one particular thing, but if I were a smarter, more efficient user I could just cut the tape here. Notebooks is an onion of an app, there are layers upon layers of functionality across macOS and iOS – it is a media rich repository for collecting, organising, searching and syncing any kind of research material you can throw at it. The markdown support is excellent and it even has task management support, which if setup properly for research and document review is kind of ingenious. The iOS version has PDF annotation tools, audio recording and handwriting/sketch support. Give it some thought and you will realise that Notebooks could handle a great many of your study and research needs, no matter what level your are working at. While it is certainly not perfect it is definitely going to be enough for a lot of people. If you are looking for a well-deigned, self-contained solution for note-taking and organising your research, or if you are looking to replace that gaudy green elephant, Notebooks is worth more than a cursory look.
It is hard to go past Ulysses as a writing app. Whether you want to use it for note taking, essays, long-form writing, or really any kind of writing you can think of. It is another app that benefits from going all in, the more you add, the more you start to realise its potential. Where Ulysses shines is its ability to organise text, for my own purposes that makes it particularly useful for longer form writing. While I am using Scrivener to write my thesis, Ulysses would be more than up to the job for a text based thesis, such as my own. But, in keeping with the note-taking theme here, Ulysses is an excellent candidate. Admittedly, it doesn’t quite have the feature-set of Notebooks, but its careful and intuitive design on both iOS and macOS will appeal to purists. Ulysses also has hooks in automation, particularly with regards to its Workflow integration on iOS, which opens up all kinds of possibilities for note-taking on iOS.
Bear is an intriguing markdown based, notes app. Attractively designed, with a unique tagging system and cross-note linking for database referencing, and feature parity on macOS. It still lacks features ideal for academic use, but it is still new, and in very active development. It has gained a loyal user base quickly, so worth keeping an eye on at least.
Not to mention, it will give you something to talk about with other nerds ↩