Automating Academic Workflows on a Mac – Part I

If ever I find myself in one of those tedious Mac versus Windows conversations I need only point to one thing that tips the balance toward the Apple machine, and that is automation. While it is true that automation software is not the exclusive domain of the Mac, Apple’s historical commitment to it has not only lowered the bar for entry to native automation, but has fostered a platform which has seen a slew of wonderful third-party tools that will allow anyone with a little time and determination to dip their toes in the automation waters. Honestly, it is embarrassing to admit the amount of time I might have saved had I have embraced some of these technologies early than I did. Admittedly, with services like IFTTT and Zapier, automation is becoming less and less platform dependant, but whether you want to go full nerd, or simply save yourself and your fingers from repetitive typing tasks, there is nothing like the Mac for getting started.

This will be another post in parts, there are far too many options for Mac automation to throw them all on a page and hope for that to be useful. The intention is to give you some ideas for getting started with this automation racket.

Text Expander

Perhaps the easiest area to begin is with text expansion. Limited support for text replacement is available natively in macOS, or you go further with apps like Typinator or aText. My favourite app for the job, and probably the most powerful of the lot, is Text Expander . Start with simple things, like commonly used email addresses, your own personal details, signatures or often repeated phrases.

Automating Academic Workflows Macos 4
One of its many tricks, Text Expander has built in macros for automatically formatting dates

Something I have found particularly useful is converting clumsy English spelling of non-English words and names. For example, my thesis contains a number of Māori words that have macrons for long vowels, Text Expander makes sure I neither forget nor mess up the spellings of those words. Likewise for accented European names like Zupancic to Zupančič. The more you use text expansion, the more you will start to notice commonly used text you can automate, and this is to barely scratch the surface of what a tool like Text Expander can do for you.

Smile’s Text Expander Blog is full of examples of how to use snippets in your workflow. One specifically research based use case is to setup snippets for common web searches. For more ideas on how to get started, Zapier have a nice write up on their blog you might like to check out.

Automator

Automator can seem a little daunting at first, and to be fair the user interface is not all that enticing. But, don’t let that stop you from messing around with it. Just as there are many text based tasks that you might not know you can automate, there are many more fiddly and tedious jobs littered throughout most people’s workflows. Academic workflows, in particular, are usually littered with tasks ripe for automation, and this is in no way limited to university work itself. If you are a blogger, an artist, or even a social-media junkie, chances are there is something you do regularly that you can reclaim significant time from. Having said that, like anything the problem is knowing where to start. There are a number of good Automator resources available, but you will never go wrong by starting with Sal Soghoian – the undisputed Jedi Master of Mac automation – at his Mac OS X Automation site.

In the meantime, here are a couple of basic examples to get you started. One of the most commonly cited examples of a basic Automator workflow combines selected PDF files into one document, like so:

Automating Academic Workflows Macos
Automator workflows can be setup as services to manage repetitive actions with a right-click

Another quick and dirty example of an Automator workflow is the one I use to resize images for blog posts. I have it setup as a service, so when I right click on an image and select the service, it simply scales the image, converts it, and renames the file. It looks like this:

Automating Academic Workflows Macos 2
Automator Workflows don't need to be complex, all this does is resize images, and rename the files. You can download a copy of this workflow below

You can even setup Automator do some of your research for you by setting up a feed with keywords and collecting the URLs for the articles it returns. This article has an example of one such workflow, along with a means for downloading images and video, and setting up a native, standalone web application for sites you have to keep open.

Hazel

Something all students and academics have to deal with a constant influx of digital documents. Whether they be absurdly arcane forms, journal articles, ebooks, expense claims, or whatever, they never stop piling up. Enter Hazel, put a little time into this thing and you can wipe your hands of repetitive file management and processing tasks. And, it’s not just the mundane and simple jobs either, Hazel can encode media, manage your photo library, add music to iTunes, use pattern matching to rename and file documents based upon their contents, run scripts, take care of your desktop, trash and downloads – in fact, like most good automation, it is more limited by a user’s ability to think of how to use it than by its own features. A little imagination and you can chain all kinds of services together, for example, there are party people who like to trigger their own welcome home soundtracks by using Hazel with Dropbox and IFTTT.

There is nothing overly difficult about setting up Hazel, start out simple and go from there. If you have ever setup a smart folder on iTunes, or in the Finder, then you will already have a sense of how to put an action together. If you haven’t, it looks like this:

Automating Academic Workflows Macos 3
Trigger Hazel actions by setting up conditions as you would in a Smart Folder

The Noodlesoft forum is among the most active developer forums I have come across, and the Hazel user base is full of helpful and proactive people willing to chip in if you get stuck. The forum is also full of inventive Hazel actions that other users willingly share with newbies. Finally, if you are getting stuck and you are the kind of person who likes a visual guide, you can either checkout the innumerable videos on Youtube or David Sparks has a detailed [3] Video Field Guide available.

Downloads

Scale Images Automator Service

Combine PDF Images Automator Workflow

Working with Drafts for iOS

Gabe Weatherhead oover at Macdrifter.com has a nice post on how to setup the excellent iOS note-taking and automation app, Drafts. If you haven't ever come across Drafts, there really is nothing quite like it when it comes to capturing and processing text on iOS. The JavaScript engine that drives it allows for endless automationpossibiliies, from the mundane, to the borderline riduclous.

Review of the New iPads Pro

John Gruber has a nice, concise review of the new iPad pro. Ordinarily I would put this on the links page, but I have been looking for something succinct that might be helpful for anyone weighing up a purchase after last week’s WWDC. For a long time the iPad has been a decent ancillary device for academic work, but my sense is the new form factor and the forthcoming evolution in functionality with iOS 11 will start to make this a serious option as a primary work machine. There is still a way to go with certain apps [1] , but the iPad has already become an outstanding writing tool, and with this latest iteration it can be considered a serious alternative to a laptop for focused work.


  1. most notably in the area of citation management  ↩

Starting with Text Expansion

This little gem from Brett Terpstra illustrates just one of the ways text expansion can be used. One of my as yet unstated goals with this blog is to hopefully lower the barrier for entry to some of the wonderful, simple automation tools available on the Mac. For anyone dipping their toes in the automation water for the first time, I will often suggest text-expansion as an ideal place to start. There are numerous utilities available for this, from apps like QuickKey, TypeIt4Me and Typinator to what is considered the gold standard in TextExpander.


Learn Anything Mind Map

Where to start with this. In the developer's own words: ‘The main goal of this project is to expose human knowledge in a visual and structured way to accelerate learning'. The result is a kind of meta-mind map of research pathways across the internet. If it hardly scratches the surface of some areas, it offers a start at least, and where the internet is concerned that is always more than it seems. Moreover, this is an open source, living project with different implementations. The title link will take you to the version hosted by Mindnode, but the Github project is well worth exploring.

Note-taking Part II: Handwritten Notes

There is still a lot to say for keeping it old school with note-taking.  Handwriting after all is a key tool for comprehension and retention. Although, judging by the wall of glowing Apples one sees in lecture halls these days, that does not appear particularly persuasive with regard to note-taking. Still, this intersection between technological trend and learning technique is, I believe, just one among many things that make the iPad such an excellent device for study. While you can get pretty serious about handwriting on glass with an iPad pro and Apple Pencil, even with the standard model you can benefit from some of the great handwriting apps on iOS.

It is true that there are clear advantages to maintaining typewritten notes. Combining lecture notes, PDF annotations and other general research materials into a searchable database is hugely advantageous for both writing and revision. Luckily, none of this necessarily means handwriting should be excluded from a note-taking workflow. The only question is how integrated you want it to be. As ever, there are options.

Goodnotes

Goodnotes iOS
Goodnotes is considered the go-to app for handwriting recognition

 

For a lot of people, Goodnotes is the standout app for handwriting on the iPad, and with good reason. Although, it still holds to somewhat dated skeuomorphic design elements, that is a bit of a double-edged sword, as much of the app’s appeal lies with the convincing replication of an analogue writing workflow. Its real killer feature though, is handwriting recognition and text conversion. This means you have the choice between searchable handwritten notes, or converting your handwritten notes to text for use in the app itself, or for export if you keep your notes elsewhere. Possibly the most underrated aspect of Goodnotes is its PDF annotation, which I find to be smoother and more intuitive than any of the myriad specialty PDF apps I have owned and used. If handwritten notes and document markup are the extent of your workflow, then Goodnotes may even be all you need; especially now that it has a solid macOS companion app.

Notability

Notability’s audio capture feature makes it an ideal choice for lecture notes
Notability’s audio capture feature makes it an ideal choice for lecture notes

Notability is another sound writing app, although one that comes as something of a tradeoff. Notability does not have handwriting recognition, so handwritten notes can neither be searched, nor converted to text. Nonetheless, it does have its own marque feature with its ability to capture audio. The appealing simplicity of recording a lecture and taking notes in the same app can account for much of Notability’s popularity among students. Furthermore, Notability is a nicely designed software, and many will find its interface to be much more appealing than other similar apps. Moreover, its palm rejection is frankly much better than Goodnotes, the PDF markup tools are again very good, and its own macOS app is more fully featured and polished. The lack of handwriting recognition is a little disappointing, but you don’t have to go far to find people, students especially, who see audio recording as a more significant feature. Again, there is enough in this app that it may even be the one to rule them all for you.

Handwriting Hacks

If you're an EverNote  user, then Penultimate is a free app that will integrate your written notes with the rest of your Evernote database, including search-ability. I’m not a big fan of the app, but it works as advertised, so if you are deep in the Evernote ecosystem then you will no doubt get at least some of the requisite mileage from Penultimate. There was a time I was all in with Evernote. A combination of becoming wise to the problematic nature of proprietary databases, and my increasing discomfort with their privacy policy fumbles has driven me away. In saying all that, I’m not churlish enough for absolute dismissal of its utility. Ease of use, and impressive integration with practically everything remain its strengths. One example of its enduring usefulness is a hybrid workflow using Carbo for digitising paper notes. And, while we are on this track, both Evernote and One Note allow you to scan handwritten notes directly into the app for searchable text with OCR.

MyScript Handwriting Keyboard
The MyScript Handwriting Keyboard makes long-form note-taking an option in almost any text editor

The MyScript Handwriting Keyboard makes long-form note-taking an option in almost any text editor

Finally, if you want the cognitive benefits of deliberate long form note-taking, but you don’t care for the end result, there is something of a hack you might like to try. The MyScript Stylus Handwriting Keyboard allows direct, handwritten input into any app that you can use with a third-party keyboard. It hasn’t had any updates for a little while now, but it still works well. In fact, the handwriting recognition is impressive. You can use it as an input device with any text-editor or notes app that allows a third-party keyboard.

Honourable Mentions

  • Notes Plus is very similar to Goodnotes, with even more features. It even has audio recording. I find the interface to be a little too cluttered for my liking, and the user experience can be awkward at times. I suspect these relatively small quirks are what keeps it lagging a little behind Goodnotes in the popularity stakes, as the handwriting recognition engine is excellent.

  • Nebo is renown for handwriting recognition excellence. Underwritten by the my MyScript Ink engine, it has been winning awards and slowly gaining acclaim. The only problem is it requires an Apple Pencil to work, unless you are working on a Surface device that is, then your active pen will do fine.

Handwriting Without Apple Pencil

The 2018 iPad is a big deal for bringing Apple Pencil support to the cheaper model. There remain a lot of reasons to upgrade to one of the iPad Pro models, but Apple Pencil support is no longer one of them. However, if you're still rocking an iPad Air, or iPad Mini, you don't have to give up on handwriting altogether. A good old dumb, capacitive stylus can still work better than you might expect.

In my experience, the results from a capacitive stylus are just as good as any of the so-called Apple Pencil alternatives. When I was using the iPad Mini 4 as my main capture device for notes, I would come across all manner of claims around magic smart, bluetooth styli that make them Apple Pencil competitors. The truth is, they pretty much never work as advertised. None that I have tried work any better than a plain, dumb capacitive stylus. Why? Well, the Apple Pencil is not a third-party hardware device, it is an integrated input interface designed as part of the iPad itself. It is part of a system that works together. That said, there is good news, all modern iPads are fast enough now that, where handwriting is concerned, a capacitive stylus will give you a convincing writing experience. I have two that I particularly like, both from Adonit

For writing, the Adonit Jot Pro

 

And for marking up PDFs, or drawing the Adonit Mark.

If you only want one, get the Jot Pro

 

 

Note-taking Part I: Typewritten Notes

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 [1]. 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 [2], 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.

Notes Apps

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.

Notebooks

macOS Plain Text Notes App

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.

Uylsses

Ulysses Macos Plain Text Notes App
Note-taking is just one of many use cases for Ulysses

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.

Honourable Mentions

  • 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.
  • 1Writer is an iOS only app, but as if to prove a point, being plain text based you can use DropBox to sync it with any text editor you should choose on macOS. In fact, it is the preferred iOS companion app for old-schoolers still rolling with Brett Terpstra’s nvALT, which is still a useful app in itself. [3] What makes 1Writer truly unique is its Javascript automation engine . If you have a look through the Action Directory on the app’s website, you will see already includes some researched focused workflows. If you have a little scripting ability, then you can just about fill your boots.

 


  1. Not to mention, it will give you something to talk about with other nerds  ↩

  2. Yes, it’s called syntax  ↩

  3. Brett Terpstra is promising a commercial replacement to nvALT, with an app called BitWriter that is close to beta release  ↩