## DEVONthink Markdown Annotations with Highlights and CSS Stylesheets

Here are a couple of quick tips for DEVONthink markdown annotations using the Highlights PDF app, and CSS Stylesheets.

### Annotations with Highlights App for macOS and iOS

The new version of Highlights is by no means a complete app. The search functionality is basic, it cannot access a document outline and one of the best features from the previous version is gone 1. It’s also a comparatively pricey app. For all that, it has a few neat tricks that other PDF apps don’t have. One, it still writes annotations out into a neatly formatted markdown file with neat page links, however now it also automatically grabs metadata for journal articles to head up the annotations. It also does some impressive things with the OCR layer of a PDF, allowing smart copying of citations and extraction of tables — although to be honest this makes the lack of search functionality all the more surprising.

However, the next trick is where Highlights makes itself almost indispensable. With a single click it will export your annotations to your archive of choice, with a few pre-linked apps like Bear, Keep it, Quiver and so on, or direct to file for any other app. With all those apps the page numbers will appear as Highlights callback links, so when you click on the page number, as long as the original pdf is still available it will magically open on the right page.

For DEVONthink users the export is even better. Highlights comes with a DEVONthink script that will replace the page links with DEVONthink-links. If you keep your documents in DEVONthink, your exported annotations will be magically linked to the document in your database.

### Styling Annotations in DEVONthink with CSS

One of DEVONthink’s hidden features is the ability to add style sheets for markdown documents. If you know a bit of CSS you can create your own, as per the DEVONthink blog , or find more detail on the DEVONthink forum

If you’d rather grift a pre-made stylesheet, there is no better place than Brett’s Marked 2 Style Gallery. Or you can use his very handy StyleStealer Bookmarklet to grab the CSS from any site you like the look of. Incidentally, if you really want to dig into previewing markdown documents, Marked is the best tool bar none — it even works as a Pandoc processor. Marked 2 also comes with Setapp.

Once you have the stylesheet you want to use, link it via the DEVONthink settings and enjoy the new pretty look of your exported annotations and other markdown documents. The file path is hidden under the Media settings tab in DEVONthink preferences. Once you drop tyhe file in, all of your markdown documents will pick up the styling. This is how my markdown documents look in DEVONthink now:

### Smart Group for Annotations

This is a basic rule to collected all documents with annotations into a smart group. It has two parameters:

1. Kind is PDF/PS
2. Where PDF Annotations is not 0

This gatheres your annotated PFDs into a single group. From there I can simply open the document in Highlights and export the markdown document back into DEVONthink. The next step is to automate the process of updating the files when new annotations have been added. DEVONthink is designed to handle multiple copies of documents, so this requores some lateral thinking, stay tuned for an update on that.

1. In the original app you could edit the annotations markdown file like it was a note

## DEVONthink 3.0: New Tricks for Reading and Research

DEVONthink is one of the only software suites I remain unequivocal about. I’m a keen user of DEVONthink to Go for iOS, and I was happy to recommend previous version of DEVONthink Pro for macOS, even as it aged considerably. However, the recently released DEVONthink 3.0 has modernised and enhanced already excellent software. It is integral to the way I manage my research.

### DEVONthink 3.0 Can Feel like Cheating

DEVONthink 3 is a remarkable piece of software. The Devon Technologies crew don’t do small, you’ll be peeling this onion for a while. If you come from the previous version of DEVONthink, the user interface is immediately familiar, yet modernised in all the right ways.  If you were one of those people who liked the idea of DEVONthink, but couldn’t stomach the way it looked, the new interface has taken care of that. I spend most of my day in and out of DEVONthink at the moment as I finish writing my thesis. Not only do I rely on it, I actually enjoy using it —and this at a time when the likes of Apple continue to suck the joy from computing.  The advanced search functionality alone has always made DEVONthink worth it, and even that has improved, but it can do a whole lot more.

### Smart Rules

DEVONthink has always had serious automation tools. However, it has traditionally relied on deep AppleScript hooks and actions donated to the native macOS Automator app. Then there is the AI engine that can help automate the classification of documents, along with its core heuristic data analysis. Beyond that, the global inbox means a little forward thinking can always bring third-party tools like Hazel into play before the DEVONthink sorter takes over.

Most of this functionality is now built into the app itself. With DEVONthink 3.0, we now have granular, dynamic user automation built into the software itself. The automator actions are gone, but in their place are user definable automation tools for building the kind of smart rules, and smart groups that Mac users will be used to. From the liner notes,

Last but not least, we have massively extended DEVONthink’s automation options for version 3. Smart rules perform actions based on events and search queries, where events can be anything from a scheduled time to the arrival of a newly imported document. You can also attach one-time or repeating reminders to any document. They support several alarm options including running scripts. Insert dynamic data in templates, imprints, or smart rules without requiring any programming skills.

If you’ve ever built an advanced search in Finder, or made a smart playlist in iTunes (er..Music app), the logic will be familiar. If you’re a hazel user, you’re laughing.

### Using Smart rules with DEVONthink to Go for iOS

The iOS version of DEVONthink has a few hidden elements in the navigation menu that hint at what be available in future releases. By all accounts, there are plans to port the syncing of smart groups at least.1 In the meantime, we are left with workarounds. To be fair, as much as I like this stuff to just work out of the box, finding workarounds gives one an excuse to get familiar with the new functionality in DEVONthink 3.0. It doesn’t take long if, like I do me, you are simple people with simple needs.

I do most of my academic reading and annotation on the iPad, so settings up a smart group to pull readings across automatically would be ideal. However, as DEVONthink can create replicants of documents2, we can approximate this behaviour with a smart rule:

Then, in DEVONthink to Go we set the group to download always. Now anything I label for iOS is automatically synced to that group, and ready to read on my iOS devices. Better still, as DEVONthink supports edit in place, I can use any PDF app that can access the native iOS files and my annotations are automagically synced back to my Mac.

I have another smart group setup that groups all annotated documents once they are synced. I generally use the excellent Highlights app to export my annotations in Markdown when I review them, but I’m working on automating that part too.

1. Can’t say I’m entirely comfortable with the way this is communicated in the forums any times.
2. For the uninitiated, replicants are clever links to master documents that make it appear there is a copy without actually creating one. It’s a kind of spooky action for documents.

## Zotero iOS Shortcuts: Better BibTeX Citation Keys

This is the long awaited iOS Shortcut for Zotero to extract Better BibTeX citation keys for Pandoc. I know a fair few people have been waiting on this, apologies it has taken so long to post. If you need more detail, read on, otherwise the shortcut can be downloaded below.

### Zotero and Better BibTeX

There are a couple simple but important reasons I use Zotero, and the standard BibTeX support is not one of them. The web API allows me to build these shortcuts, but more importantly Zotero is an antidote to the closed and proprietary reference management systems of big academic publishers. 1

Despite the importance of both those things, if it wasn’t for the Better BibTex plugin I would almost certainly be using Bookends. The Zotero desktop app is a glorified browser, and an ugly one at that, whereas Bookends is a powerful native app. But I digress, the point is Better BibTex improves Zotero significantly, and I find it to be the best way of dealing with Pandoc citations. If you don’t use it already, you can look into it here.  Or if you want a visual guide, for anything to do with plain scholarship using Zotero I recommend the excellent tutorials by Nicholas Cifuentes-Goodbody

If you already use Better BibTeX and you’re looking for an iOS solution, you may find this useful.

### Notes:

• Better BibTeX  writes custom citations keys to an ‘extra’ field. For most people that won’t matter, but if have other plugins running there is always a chance the crude regular expression I have written to extract the keys will run into problems. 2
• Make sure your keys are ‘pinned’ on the desktop, if they have an asterisk next to them they will not get written to the web database, meaning the shortcut will break. This is the most common reason the shortcut doesn’t work
• Unlike the previous shortcuts, this version searches the entire library by default. It seems most users prefer that. If you want it to search a particular collection, it is easy enough to change the URL for the API call. The Zotero documentation includes examples of how the URL should look. You can also look at other versions of these Zotero shortcuts that use a collection instead of the library.
• If you want to use the shortcut with multiple text editors, delete the final ‘open in app’ action and use multitasking to paste the keys.
• The shortcut should run fine from the share sheet, but the best way to use these shortcuts is via the widget.

As always, any problems drop me a line.

Important: If you are an iOS only user, and do not maintain your Zotero database on a desktop, this shortcut will not work for you. You need to use one of the earlier versions.

1. e.g Mendeley has an API, but it’s made by Elsevier ↩︎
2. If anyone with actual RegEx chops wants to improve the expression, please let me know and I will update the shortcut ↩︎

## Plain Text Notes with The Archive and Zettelkasten

One of the most read posts on this site is a brief note praising Brett Terpstra’s wonderfully robust plain text notes app, nvALT. I’d wager the popularity owes much to a lack of alternatives. Note takers have never had so many apps to choose from, but nvALT still has significant advantages over most plain text note taking apps to come after it. There are very few native apps for macOS that leave notes unmolested in the file system. Fewer still that support features to make them noteworthy for academic work.

Take the popular notes app Bear. It is delightfully designed, aesthetically pleasing, and feature rich. Easily one of the best notes apps, perhaps even one of the better markdown editors for writing. At the same time, it is kind of cutesy and opinionated. Moreover, it is built upon a significant design decision that counts against it. By using a database to store notes, Bear is an ostensibly plain text notes app that ultimately obscures its data.

Bear is not alone in that of course, the same is true of other popular Markdown and writing apps, like Ulysses. Even the excellent note taking utility Drafts — which will soon be available on macOS — ties notes up in a database of sorts. 1 Where iOS is involved, CloudKit sync makes sense for these apps, especially given Apple’s mobile file system remains so half-arsed and piecemeal. 2 Nonetheless, the result is data that remains for all practical purposes beholden to those apps, in need of processing if you want to access it elsewhere. In a strange sort of way, it means more data tied up inside the Apple leviathan.

Put my discomfort at playing hide and seek with my data against the future proof and flexible plain text notes of nvALT. It should be clear why I claimed nvALT was still the best plain text notes solution. Now it seems, despite the affection I still hold for nvALT, there is finally a better option available for markdown notes. I believe The Archive has taken over the mantle of best plain text notes app on macOS.

### The Archive

I reached out to Christian Tietze earlier this year to review his other app, the markdown table generator, Table Flip. I was messing around with Deckset at the time, so I liked the idea of generating tables for presentations. As it happens I very rarely use Markdown tables for anything these days, so I can’t do Table Flip the justice it deserves. Having said that, if you should need Markdown tables regularly, it is exactly the tool you need.

I had heard of The Archive before that exchange, but I wasn’t looking for yet another way to take notes. I have grown weary of consumer geeks mistaking the tool for the work, and even more weary of the bizarro apple fan world in which notes apps are somehow second only to task managers for the tech mode du jour. I had seen a few posts about The Archive, but I overlooked it after a casual glance. I figured aesthetically it wasn’t for me. I was wrong.

Since then, between a realisation that my notes are an embarrassing shambles, and my curiosity with a growing enthusiasm among academic nerds for zettelkasten, I took another look. After downloading a trial and using it in earnest for about a week, I purchased it outright.

It’s still early days, but The Archive is exactly what it needs to be. An antidote to lollipop iconography, cartoonish design, and the electron powered assault on native apps. It is lean, purposeful, clean, and fast. A wonderfully native app built on plain text purism. I was wrong about the aesthetics. A simple and elegant templating system makes the Archive customisable in the right way. It was trivial to craft a theme of my own, crimping colours and fonts from apps like iA Writer and Drafts — and toning down the coloured aspects of the interface that put me off to start with. There are still some rough edges to be ironed out, but the app is still very new.

### Zettelkasten

The minimalism alone is enough to recommend The Archive, but the purpose of its design is what makes it really interesting. If I’m honest, it’s probably another reason I looked right past it initially. The Archive is built around the needs of a modern, digital approximation of the Zettelkasten. A structured note taking system descended from sociologist and functionalist, Niklas Luhmann.3 Luhmann’s work is not my jam — far from it — but, I hadn’t properly considered the virtues of implementing a suitably bespoke version. Or indeed, that the modern Zettelkasten is bespoke by default. 4

If that seems cryptic, a precise definition of zettelkasten is likely to be counterproductive. Short of saying it is a loosely defied method of constructing an archive of notes. An archive built upon layers of nodes and connections. If you want to know more, however, Christian and Sascha have a growing archive of their own at the Zettelkasten blog. In case you don’t already know how philosophical note taking can be, you have been warned.

There you will find examples of Zettelkasten built with apps as diverse as Sublime Text and Trello. You could potentially build a Zettelkasten with Bear if you felt so inclined, with some concessions to its idiosyncrasies it could work. I wouldn’t, but there you go. It has been done with Evernote, of course, but trust me when I say that’s a much worse idea. 5 Myself, I have no interest in locking up my data in either proprietary formats, rich text, or obscured databases. 6 Besides, if you are interested in crafting a Zettelkasten from your notes, why not build it with an app that was designed for the purpose. An app that, as it says on the box, is nimble and calm.

### On Using the Zettelkasten

The Zettelkasten blog is a kind of sprawling object lesson. Part demonstration with a whole lot of reflection on research based note taking. There is a post overview if you’re looking for a front page, although by design there is no how-to guide as such. At the same time, the most succinct and recurring advice is this: start taking notes and your archive will take shape. If the move from thinking of your notes as singular annotations, to both particular and part of growing whole is subtle, it is also more than enough method.

The forum has examples of Keyboard Maestro automations, snippets and other innovations to help you along. The beauty of both the system, and The Archive as an app is there is nothing to lock you into a particular way of doing things. I found looking at examples of notes to be useful for getting started. You will find a baseline at Zettelkasten.de, and Dan Sheffler has posted one as a GitHub gist.

My own setup is very simple at this point. My notes consist of front matter, body, and a reference section. I currently use Zotero to manage my references, with a combination David Smith’s applet  and Dean Jackson’s mind boggling ZotHero workflow for Alfred to insert the citations. Users of TextExpander can download my snippets below for both front matter and back matter to use as a guide, but I recommend building your own, or at least adapting these to your own needs. There is also a shamelessly basic Alfred workflow for opening the Archive with a search query. There is little point in creating one for note creation as the app already comes with a very useful hot key function for quick entry.

### Reclaiming the Object of Note Taking

Evernote did a lot to confuse the object of note taking with their everything-bucket aesthetic. The push back against that has been encouraging for both the purpose of privacy, and in the rediscovery of a more deliberate practice of thoughtful note taking. nvALT, the long-time anathema to the hoarding elephant, received its last official update a little over a year ago. There have been whispers of a commercial replacement for some time, but the developers have other projects to keep them busy. I have no doubt it will be an outstanding candidate should it eventuate. In the meantime for all you plain text nerds, the Archive is worth a proper look. Even if you share my distaste for all manner of functionalism and its scions.

Text Expander Snippets

Simple Alfred Workflow

1. Although, given the history and purpose of Drafts as a sort of weigh station for text it makes more sense.
2. Frankly, iCloud Drive on macOS is also a mess in need of hacks to make it usable
3. I don’t have much time for the kind of sociology Luhmann practiced, and there has been some suggestion the method is implicated in the ideas.
4. And again,  not to confuse the subject and the object
5. I cannot put it better the Christian, who writes in the forum: ‘proprietary file formats do serve the devil’
6. It is for that reason I recommend Notebooks for anyone who wants a feature rich, multipurpose notes app (not for Zettelkasten)

## Digital Privacy at the Border with 1Password and DEVONthink

For whatever reason, people think of my country as progressive. A recent change to customs law might go some way to challenging that. Customs agents in New Zealand now have the power to demand security information including passwords, PIN numbers or biometric access to digital devices. They call it a ‘digital strip search’. If New Zealand has long been thought of as pioneering, I’m embarrassed to list this among our firsts. Assurances from customs that the threshold for search is high make no difference, the fact remains, the law exists. 1  What follows are some suggestions for apps and services that can help protect your digital privacy at the border.

First, note this is not legal advice, neither am I qualified to offer any. I am also basing this upon New Zealand customs law, which only covers the search of physical devices, and does not compel anybody to provide access to cloud services. 2 To state the obvious, you would do well to know the laws the that govern your border crossings, no matter where you travel. For the U.S, you could do worse than familiarise yourself with the recommendations from civil liberties group, the Electronic Frontier Foundation.

### Digital Strip Search, an Apt Phrase

Most Academics have cause to travel often, and many carry sensitive information with them of one kind or another. My own work might be considered seditious in some parts of the world, 3 and I know plenty of academics and even grad students working under embargo, simply because that is how universities operate. To say nothing of our actual ‘private’ lives; iPhones with photos of family, personal messages, journal entries, medical information and so on. The phrase ‘digital strip search’ is apt, being submitted to such an invasion of privacy would make anyone would feel naked. If you would rather not put yourself through such an ordeal, 4 there are steps you can take to protect yourself.

### Apps and Services to Manage Digital Privacy

This assumes you are traveling with iOS devices and not a Mac. That is not to say this cannot be done with a Mac, just that the entire process is more involved for Mac users. The principles still apply. If you’re travelling with a laptop, you could do worse than follow the advice of Bruce Schneier. Either way, it is getting to the point where traveling with as little tech as possible is the right way to go, even if it is impractical. And what gear you do travel with should be kept as clean as possible. Time willing, I may come back to the idea of travelling with a Mac.

I cannot bang the 1Password drum loud enough. In my experience it is the best password manager available. It actually includes a feature called Travel Mode, designed for this situation. There is a school of thought, however, to suggest it is a nice idea that is a bit misguided in practice. Whether or not you decide to use it, it is a nice option to have.  Although it’s not obvious that travel vaults are missing, that the feature exists is not a secret, so I do understand the argument.

At the same time, if you have a subscription to 1Password, the cloud vaults provide a better option by making it possible to remove the app entirely and download everything at the other end. This way you are not setting a flag that advertises you are ‘hiding’ something.  It does mean holding on to an extra piece of information, as you will need the encryption key, as well as your password to set it all up again. See below for places you might put that.

### Secure Private Data with DEVONthink’s Strong Encryption

I have written about using DEVONthink for this purpose. DEVONthink goes beyond being outstanding software for managing data by including strong AES 256 bit encryption. Again, you hold the keys, which means anything you put inside a DEVONthink database can be locked behind first class encryption. DEVONthink can store practically any kind of data or document, making it ideal for this scenario. Syncing is easy to setup with your choice of providers, including iCloud Drive.

Among DEVONthink’s strengths is its ability to compartmentalise data in different ways. Whether you do that by group, or you setup a separate database for the documents. It can give you granular control over what you sync and when. It will even let you use multiple cloud services simultaneously as it sync’s each database separately.

You can work out for yourself how best to set this up, but my preference would be to setup a special database and download it to my device when I need it. That way I can be deliberate about what data I need, and organise it accordingly. I can also avoid using excess data.

### Boxcryptor and Sync.com

If you have no use for DEVONthink, you might consider using encrypted cloud storage. If you’re serious about privacy, using DropBox or  iCloud is not enough. In the past I have happily endorsed Sync.com for approximating the convenience of Dropbox while offering much better security with end-to-end encryption. I still hold that service in high regard, especially now the app has better integration with the iOS Files app. They offer 5Gb of storage for free, which should be plenty for this scenario.

If you prefer the flexibility of sticking with your existing cloud storage service, then take a look at Boxcryptor. It is free to use if you only need to secure one service, but you will need a paid account to encrypt file names so bear that in mind when naming your files.

### A Method for Digital Privacy at the Border

Once you have handed over your passcode, or consented to unlock your device with TouchID or FaceID, anything on it is fair game. Many apps provide an extra security layer, but the passcode is all that is needed to change either the finger, or face to get beyond most of them. The safest approach is to have nothing on your device. Setup these apps before you leave, and remove everything from your device. Myself, I would even setup a different iCloud account altogether.

#### Before you leave

Back everything up, obviously. Now do it again. Don’t rely on iCloud backup alone. Ideally you will have at least a secondary location. I use iMazing for this, and all my backups are included in my Time Machine Off-site clone, and my Backblaze continuous cloud backup. Incidentally, if you use Backblaze you have another means for client-side encrypted storage. You can retrieve anything you need to on demand from your Backblaze locker. The way I figure, that even leaves me room to make the kind of screw ups that come with having attention madness.

If you’re an iOS only user, I would seriously consider investing in some external storage to add a secondary backup. The Sandisk iXpand Drives tend to be the best, not only for the drive quality but they include software to handle the backup.

Once you are backed up, setup a new iCloud account. Note, your devices can be logged into more than one account for different services. For example, you can log into the App Store with one iCloud account, and use a different one for Photos, iCloud Drive and so on.

#### When you Arrive

This should be obvious. Either download the necessary apps to your alternate iCloud account, or log back into your ordinary account and do the same. This is time consuming and annoying — and it will cost you data — but consider the alternatives. In this part of the world, it now means a choice between being digitally naked or a NZ$5000 on the spot fine for refusing access. Considering how you will maintain your digital privacy at the border is no longer optional. Photo by Matt Artz on Unsplash 1. New Zealand customs have form that should make anyone wary 2. Anyone with eyes can see how stupid this makes the law, so stupid it hurts. 3. Posting this probably doesn’t aid my cause 4. And you don’t have a spare$5000 to throw at the problem

## Automate Referencing on iPad with Shortcuts and Zotero

Update (2019-01-26): If you’re a Better BibTeX user, there is a new shortcut available to extract your citation keys

### Citation Management on iOS

For as long as the iPad has been an excellent device for focused writing, it has never been good for citations and referencing. Referencing on iPad remains the final, stubborn piece of the puzzle to fully untether iOS from the Mac for academic writing. It appears, without exception, the iOS is not yet viewed by developers of referencing software as a fully fledged computing platform. That leaves us with a choice between poorly designed companion apps, or hacking together a solution of our own. I have opted for the latter, by configuring different workflows using Apple’s Shortcuts app and the excellent Zotero API.

What follows is not a primer on referencing, rather it is a means for managing citations on iPad, or even iPhone in a pinch. It assumes some knowledge of Zotero, but that is not difficult to acquire. These tips will be useful regardless of whether you work with both macOS and iOS, or do everything on an iPad. With a little help from iOS Shortcuts, referencing on iPad is that little bit less painful.

### Getting Material into Zotero on iOS

Maybe one day we’ll get extensible browsers on iOS. Until then, we still have JavaScript bookmarklets. Most of your research is done online anyway, so using the Zotero Bookmarklet in a web browser works just fine. The only real caveat is you want to get your references from a source that Zotero will recognise. That will usually mean a university library, and my EZProxy shortcut can help with that.

Another convenient option is to use the WorldCat Catalog. The WorldCat option has the added virtue of not needing a login, which makes it a hassle free way to get full bibliographic records. I have setup a shortcut that can be invoked from the widget to send a search query to WorldCat, and open the results in Safari. 1 Once you have the bibliographic record up, as long as you are logged in to Zotero, the Bookmarklet will scrape everything you need to populate your library with that record. Download the shortcut here:

WorldCat Web Search Shortcut

### Cite as You Write on iOS

There are different ways to come at this. The method you choose will depend on a few variables. The biggest distinction is likely to be whether you work iOS only, or you also operate a Mac. However, there is also a question of how complex your work is, and whether or not you want to automate the process entirely, or you’re happy to manage a few aspects manually. If you are looking for the more comprehensive option, see the section below on rendering a bibliography.

If you write exclusively on iOS, and all you want to do is insert references from your Zotero library as you write, the following shortcut will do that. Invoke it from the widget to search your collection, and it will place a formatted in-text citation on the clipboard, eg. (Dickens, 1837, p. 21) 2

Zotero Cite as You Write Shortcut

See below for how to automate the creation of your reference list.

### Cite as You Write on iOS for macOS Users

If you are also using a Mac, you only need to know how you intend to process your finished works so you know which cite key style to use. If you intend to use Zotero’s own RTF scanner, your citations must be enclosed by {curly braces}. If you’re a Pandoc user, no doubt you already know you need [square brackets], among other things. 3

Zotero RTF Shortcut

Zotero Pandoc Shortcut

### Automate Rendering a Reference List or Bibliography

Depending on the complexity of your needs, this is where it can get tricky. If you’re writing anything genuinely long form — a dissertation, thesis, or a book — then this is the last remaining task where it is useful to have access to a Mac, or PC if necessary. That doesn’t mean you need to own one. Workarounds exist to make this possible from an iPad.

#### The Simple Method

For the most simple version of this, Zotero can produce a bibliography online, but it’s not pretty. Fortunately, Shortcuts can retrieve a formatted reference list from the Zotero API. If you want to use the Cite as You Write shortcut from above, you can retrieve the reference list, or bibliography from the relevant collection with the following shortcut.

Zotero Bibliography Shortcut

Note, these workflows don’t know what references are in your document, there is no way to automate that via Shortcuts. They are by no means perfect, so proof your work carefully.

#### Run the Zotero RTF Scanner from an iPad (almost)

Should you wish to automate the process completely, you will need access to a desktop to scan your work through the Zotero RTF scanner. The good news about keeping your references in Zotero, being a web service you can make use of on demand computing. You don’t need to maintain your Zotero library in a local database, it remains in the cloud. That means you only need temporary access to a desktop for the sole purpose of running your work through Zotero. 4

#### Amazon Workstations

If you cannot access a desktop directly, there is always Amazon Workstations. It’s free to set one up, and you’ll only need it briefly. Be careful to choose an option available on the free tier though, or you could be in for an unpleasant surprise when a bill arrives. The iPad app for Amazon Workstations is useable enough for this. You can manage your referencing on iPad with Zotero, then setup a workstation to run the finished project through the scanner.

#### Portable Apps Zotero

Often on campus it is easy enough to access a desktop, but installing software can be a problem.  For that situation, the unofficial Portable Apps version of Zotero should do the trick.  Install it on a portable drive and run it on demand. To be honest, I like this option more than using AWS.

### Bonus Features

#### Windows version

This might not seem a big deal for iOS and Mac users, but Windows is everywhere. Apple users tend to forget this. Microsoft devices have improved dramatically recently, and there are plenty of other reasons for cross pollinating platforms.

#### Private Wifi Syncing and WebDAV support

I would like to see Notebooks add iCloud, and support for the iOS Files App, but the existing syncing options work well. Particularly pleasing is the consideration for privacy coded into the app via the Wifi option. If you have good reason for avoiding Dropbox, syncing can be managed across a local network. WebDAV support means Notebooks can also be synced via Synology and other private cloud solutions.

### The Question of Handwriting

Devices like the iPad Pro are finally delivering on the long promise of matching the cognitive advantages of handwriting to digital convenience. At the same time, where handwriting recognition and inking engines have improved out of sight, the apps that deliver these tools can be limited. As such, I have come to think of handwriting apps as an interface for capturing notes. Notes ultimately end up elsewhere, in Notebooks, DEVONthink, or Keep-It.

I have flipped between Notability, MyScript Nebo, and GoodNotes for handwriting. Nebo unquestionably has the best handwriting recognition, but the app hasn’t had much attention 7. Notability is a good self contained app if you can work with its limitations. However, I have returned to GoodNotes since it started generating searchable notes on the fly. Between the now instant OCR, and one of the best drag and drop implementations, GoodNotes is currently my favourite handwriting companion for Notebooks. Once a note is written, I open Notebooks and drag it from GoodNotes in slide over. The notes are preserved perfectly with the searchable layer.

Handwriting is the most obvious missing feature of Notebooks at present, but it’s likely to be added in a future version. If and when that happens, this already excellent tool will become a bonafide killer app. Until then, I still recommend it as a better place to store handwritten notes, and GoodNotes has the most compatible feature set right now.

#### Final Remarks

I say final, there is another post following with Workflow and url scheme automation. Despite this relatively lengthy post, there remains a lot I haven’t covered. Nonetheless, I believe these highlights make Notebooks, in my opinion, the best general purpose note taking app on iPad for academic use. There is room for improvement, no doubt. I expect that handwriting will arrive at some point, and while the hooks are already deep in iOS further integration

I have a final superficial qualifier. If I am going to spend any amount of time working in an app, I want it to look good. No problems here, the understated minimalism and use of whitespace make Notebooks a handsome app.

1. The scope of the article covers iOS. However, Notebooks is cross platform, with excellent versions on macOS and Windows.
2. Liquid Text has function for working with two documents, but it work vertically. Besides, Liquid Text is a world unto itself, so a subject for another time,
3. As opposed to dictating notes to text
4. If you know what MathJax is, chances are you have no problem with editing a few lines of HTML
5. I’ll be honest, I wish the app cost more since I have come to reply on it. Given what it can do, I feel it is seriously under priced.
6. It seems to get more buggy as iOS is incrementally updated.