If you have followed this site with any regularity, you will be aware it has been idle for a while. There are reasons, of course. It hasn’t been completely abandoned, but it became unsustainable to run it as it was. So it will be a little quiet while I look at changing things. The idea is to open it up. Whatever happens, there will be no hedging.
In the meantime, in case you missed it. DEVONthink has had its first major upgrade in a gazillion years. The public beta has been available for a little over a week. If you were ever on the fence due to the interface, those fears should be allayed. The new version has all the old power underneath, with all the modern polish of a slick native app. It still has some rough edges, and it remains as niche as ever. Still, if you have a lot of data to manage, and need advanced search functionality, there is nothing like DEVONthink for Mac users.
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.
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.
Download Zotero Better BibTeX Shortcut
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.
e.g Mendeley has an API, but it’s made by Elsevier↩︎
If anyone with actual RegEx chops wants to improve the expression, please let me know and I will update the shortcut ↩︎
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.
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.
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.
My apologies to anyone hoping for a meaningful update, the site has been quiet for a few weeks while. Time is hard to come by, nonetheless new material is not far away. In the meantime, I draw your attention to the annual WinterFest sale from Eastgate. Some of the best apps you will find anywhere for study and academic work are on the list, among them the most important software I own. These are the highlights:
One of only two reference managers I can recommend at present, Bookends is annoyingly good. I say that because I am currently invested in Zotero, while I continue to use the API for building iOS shortcuts. If it were not for that exercise, I would switch permanently to Bookends. It is everything I always hoped Papers 3 would be and never was. If you want a native referencing solution this is it.
I write in Markdown wherever I can, but there is nothing that comes remotely close to providing what Scrivener does for long form writing. I mean real long form writing. 1 If you're crafting a dissertation, a thesis, monograph, or a novel get Scrivener. Ulysses provides a well polished middle ground for writers, but Scrivener is much better suited for serious projects in my view. If you’re still writing in MS Word, do yourself a favour.
Another singular and irreplaceable tool. There are programs about that approximate some of its functionality, such as Keep-it, Eagle Filer, or Evernote in a pinch, but there is nothing that combines the powerful heuristic engine, security features and search capabilities. All of my data ends up in DEVONthink eventually.
I have all but forgotten how to type without TextExpander. By no means the only option for the job, though likely the best of them.
For the entire list, and more information check out the Eastgate WinterFest page. As far as I can see, there doesn’t seem to be any indication of when the promotion ends. However, the promo code is the same for all the apps: WINTERFEST2018
Sorry Apple Bloggers, long blog posts are not long form writing ↩
I shared an iOS Shortcut recently for opening academic journal articles via EZProxy. It’s a simple trick to short circuit the tedious cut and paste method . All it does is copy the EZproxy address 1 to the start of a url to give you access to resources via your own university library. Here are a couple of simple methods for doing the same thing using macOs automation tools.
Open Closed Access Journals with EZProxy and Keyboard Maestro
I am slowly coming to terms with some of the intricacies of macOS automation. Even so, I find Keyboard Maestro can be a little overwhelming at times. For one thing, it has a seriously misleading name, going well beyond the keyboard to hook into anything you could possibly want to do with macOs automation. The good news is you don’t have to be a coding grand master for it to be useful. This little macro is proof of that. Keyboard maestro can even simulate keystrokes, so using this method can even save you from hitting return.
Automate EZProxy with TextExpander
Built in Macros come standard with any decent text expansion app. I’m still using TextExpander, simply because there are no alternatives on iOS. As good as it is, the fact that I have Alfred on hand means TextExpander could probably be made redundant on macOS.
To make this work with TextExpander use the builtin macros to both grab the system clipboard macro and simulate keystrokes. My snippet looks like this:
Obviously, you need to copy the URL before you type the abbreviation so you’re a keystroke ahead with the Keyboard Maestro version, if that matters to you.
I already mentioned Alfred, which is easily as powerful as Keyboard Maestro. This would be a trivial problem to solve with Alfred, either by creating a workflow, or by using Alfred’s text expansion utility.
Another option is to use a clipboard manager. With Copied, for example, you can setup templates to transform the text you copy, and activate them with hotkeys. Similar functionality can be found in Pastebot. 2
Most university libraries, and some public libraries have an EZProxy address, it shouldn’t be too difficult to find one you can access. ↩
Unfortunately, neither app has been updated in a while, so I can’t vouch for their longevity. Copied is still working perfectly for me on macOS Mojave ↩
I intend to do this justice by covering it in more detail. In the meantime, Case uses machine learning to track medical research. Technically it is aimed at research beyond my own wheelhouse, but I have personal reasons for keeping up with specialist medical research so I have had cause to play around with the app. It is still developing, but the underlying technology is interesting and the app is very promising. If you are doing research in this area, Case is a worthy addition to your workflow.
Here's something I had forgotten about. A self-contained, and feature rich web app for transcription. It works pretty well for transcription on the fly, but don’t get clearing your browser cache or your work is hosed.
Yet another Markdown editor, this time with a specific focus on academic writing. I’ll be honest, I’m not sure if this is necessary given the excellent tools already out there. For academic writing in markdown, I recommend the powerful MultiMarkdown Composer1. Still, Zettlr might suit others who don’t mind Electron apps quite so much.
I wasn’t aware of this one until a fellow traveller brought it to my attention. It looks a little different to the now defunct Editorially, but one can only hope this will last longer than that platform did. I am yet to properly put it through its paces, but I'm looking forward to doing just that.
While we are on the topic, Draft has been my preferred option for online Markdown collaboration. If you can actually convince another academic to collaborate in earnest using Markdown, Draft is free to use. Although, it is still very basic. Penflip, is another option, or if you want something with client apps, Quip is probably the best option.
With the buzz around iOS Shortcuts, I thought it would be useful to do a round up of resources for sharing and discovering iOS Shortcuts, and for learning how to build your own. A number of galleries and exchanges have started to emerge in the past few weeks. Believe it or not, the app formerly known as Workflow was released back in 2014, so there are also a number of established resources worth knowing about.
This one looks very promising. The developer was clever enough to add an API, so users can incorporate actions to automate updates to complex Shortcuts. That feature alone should make RoutineHub the frontrunner.
This one was looking likely for about a week, until Routine Hub introduced its API. Still growing, just not as fast. They have started to run competitions for signups too, which puts me off to be honest. You may still find some interesting creations here
By all accounts, this was one of the first galleries. It was setup by users on the developer Beta, so they had a head start. Unfortunately, it is still locked down to new users, which means it is not as useful as other repositories at this point. There is some quality control, nonetheless the admins have missed an opportunity here by not trusting the community.
Anyone who has followed the Workflow/Shortcuts story will be aware of the role that Federico Viticci has played in popularising the app. More than that, MacStories has been a kind of vanguard of iOS Automation. In depth examples of advanced workflows and Shortcuts are shipped almost every week with Club MacStories. A membership will also grant you access to an impressive archive of Shortcuts.
I have my suspicions that Rose Orchard is not one person, but more like Inigo Montoya’s Dread Pirate Roberts. How else can you explain how she seems to be everywhere at once? This particular Orchard instance collates automation links. It has slowed down a little lately, but there is the Automators Podcast for would be automation disciples.
In the beginning there was Workflow which came with its own gallery. Once Apple acquired the app the gallery was one of the first things to be culled. Innovations like this one from Jordan Merrick help fill the gap for a time. I published a brief post about the directory, if you are so inclined. Otherwise, there is also plenty to learn on Jordan’s own site.
This site hasn't been updated in some time, but it still hosts a number of interesting workflows/Shortcuts that still work. I’m putting it here as it remains a little piece of Workflow and iOS Automation history.
Shortcuts for Students and Academic Nerds
There is a growing collection of Shortcuts on this very site. Some generic, and many more that are aimed at writing, research and study:
I recently shared an iOS Shortcut for scanning citations directly from the barcode of a book. Handy as it is, I have another shortcut I’m getting a lot of mileage from when I write on my Mac. Both Zotero, and Bookends1 can add references to your library directly by scanning different metadata, including any book’s ISBN. You can obviously search for the numbers, or type them out by hand, but this little trick can add items to your library by using an iOS device as a scanner.
The shortcut works by scanning the ISBN from a barcode of any book and copying it to the clipboard. If the Universal Clipboard is working properly, the ISBN will become immediately available on the nearest Mac to paste into Zotero, or Bookends. I have also set it to copy the number to my clipboard manager in case the universal clipboard fails, as it does far too often 2.
This version of shortcut is configured to use my favourite clipboard manager, Copied. You could also use the equally impressive Paste, which is included with Setapp. Or any other app with a URL scheme that uses iCloud sync, like Gladys or Yoink. You could even use Apples own Notes App in a pinch.
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.
I shared my Docverter Workflow recently. When I have the time, I will update it with a Stylesheet. In the meantime, here is a web service using Pandoc that has a few different styles for converting Markdown documents
File this under amusing. I’m not advocating you use it. In fact, it’s a shame to think of classes so boring the inspiration can’t be found to write the minimum. My problem was always the opposite, how to keep under the word limit.
Apparently it's fun with fonts week. I find this more interesting. It is designed to help you remember by making you work at reading your notes. Maybe an antidote to handwriting being the best cognitive medium for notes? Come to think of it, looking at my handwriting, illegibility may always have been the real advantage.
1Password runs a service called watchtower, which is built in to their apps. A basic version is available from their website, but the public version will only scan for affected sites, and not email address. This, from Mozilla, is more like a proactive version of Have I Been Pwnded. Mozilla's contribution to privacy and security has to be admired, the improvements to Firefox are making it more an more attractive give the developments with Chrome, and Apple's decision to cash in on user security.
As for Safari, not that long ago I praised its new security features. Unfortunately, for all its convenience I'm now looking at the browser sideways. Say what you like about Apple's commitment to user security, but they are not without choices in how they enact it. If you have extensions you already trust but no longer work, workarounds are available. About that convenience….
If you want a more nuanced approach for controlling ads, and you enjoy tinkering with Raspberry Pi, this could be for you. Incidentally, there are ways to do something similar on some routers (such as the Synology), or a blunt force approach can be to edit your hosts file.
More fun with web design and philosophy. This is an interactive, summarised and visualised history of philosophy. I will spare you the comments on auspicious absentees, or indeed on the philosophical decisions involved in drawing lines between names. Although, for philosophy nerds that will be half the fun. Enjoy.