The Appademic https://appademic.tech Technology, productivity and workflows for academics, students and other nerds Fri, 25 Jan 2019 22:35:27 +0000 en-US hourly 1 https://wordpress.org/?v=5.0.3 https://appademic.tech/wp-content/uploads/2017/09/cropped-android-chrome-512x512-2-150x150.png The Appademic https://appademic.tech 32 32 Zotero iOS Shortcuts: Better BibTeX Citation Keys https://appademic.tech/zotero-ios-shortcuts-better-bibtex-citation-keys/?pk_campaign=feed&pk_kwd=zotero-ios-shortcuts-better-bibtex-citation-keys Fri, 25 Jan 2019 07:44:58 +0000 https://appademic.tech/?p=2965 Permalink: Zotero iOS Shortcuts: Better BibTeX Citation Keys

Zotero Ios Better Bibtex

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 ... Read more

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Permalink: Zotero iOS Shortcuts: Better BibTeX Citation Keys

Zotero Ios Better Bibtex

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.

Download Zotero Better BibTeX Shortcut

Ios Zotero Shortcut
Zotero Better BibTeX

 

 

 

 

 

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 ↩︎

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Thoughtful Plain Text Note Taking with The Archive and Zettelkasten https://appademic.tech/zettelkasten-thoughtful-plain-text-note-taking/?pk_campaign=feed&pk_kwd=zettelkasten-thoughtful-plain-text-note-taking Sun, 06 Jan 2019 22:53:46 +0000 https://appademic.tech/?p=2945 Permalink: Thoughtful Plain Text Note Taking with The Archive and Zettelkasten

Plain Text Note Taking

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 ... Read more

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Permalink: Thoughtful Plain Text Note Taking with The Archive and Zettelkasten

Plain Text Note Taking

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.

Downloads

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)  

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Academic Software on Sale at Eastgate WinterFest 2018 https://appademic.tech/academic-software-eastgate-winterfest-sale-2108/?pk_campaign=feed&pk_kwd=academic-software-eastgate-winterfest-sale-2108 Thu, 27 Dec 2018 01:38:34 +0000 https://appademic.tech/?p=2934 Permalink: Academic Software on Sale at Eastgate WinterFest 2018

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 ... Read more

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Permalink: Academic Software on Sale at Eastgate WinterFest 2018

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:

Bookends

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.

Scrivener

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.

DEVONthink Pro

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.

Scapple

Scapple was designed as a companion tool for Scrivener, but works just as well as a standalone utility. It is the simplest, most freeform mind mapping utility available on macOS.

TextExpander

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.

WinterFest 2018

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

    1. Sorry Apple Bloggers, long blog posts are not long form writing

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MacOS Automation: Accessing Academic Resources https://appademic.tech/macos-automation-accessing-academic-resources/?pk_campaign=feed&pk_kwd=macos-automation-accessing-academic-resources Wed, 07 Nov 2018 03:48:38 +0000 https://appademic.tech/?p=2918 Permalink: MacOS Automation: Accessing Academic Resources

Keyboard Maestro Textexpander.png

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 ... Read more

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Permalink: MacOS Automation: Accessing Academic Resources

Keyboard Maestro Textexpander.png

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.

macOS Automation Keyboard Maestro
Keyboard Maestro can simulate system shortcuts and keystrokes so one hotkey can do all the work

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:

http://ezproxy.auckland.ac.nz/login?url=%clipboard %key:return%

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.

macOS Automation
TextExpander's builtin macros can add the system clipboardd to a snippet, simulate keystrokes, and more

Other Options

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

  1. Most university libraries, and some public libraries have an EZProxy address, it shouldn’t be too difficult to find one you can access.
  2. 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

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Show and Tell — 29 October, 2018 https://appademic.tech/show-and-tell-29-october-2018/?pk_campaign=feed&pk_kwd=show-and-tell-29-october-2018 Mon, 29 Oct 2018 00:21:48 +0000 https://appademic.tech/?p=2899 Permalink: Show and Tell — 29 October, 2018

Web discoveries for researchers, students and writers Research Tools ‎Case Medical Research | the App Store 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 ... Read more

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Permalink: Show and Tell — 29 October, 2018

Web discoveries for researchers, students and writers

Research Tools

‎Case Medical Research | the App Store

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.

Turn the Web Into a Database | Mixnode

An interesting idea, and a potentially excellent research tool for analysing data from the web. You can get free credits to check it out, before you start blowing your funding.

Transcribe Interviews | oTranscribe

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.

Markdown Tools

Zettlr | Home

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 Composer 1. Still, Zettlr might suit others who don’t mind Electron apps quite so much.

HackMD | Collaborative markdown notes

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.

Draft | Write Better

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.

Create a Webpage With Just Markdown | Oscarmorrison/md-Page

If you want to create a simple online bio without coding or dealing with a database, this ought to work.

Web Tech

GitHub Actions | GitHub

Github is opening the beta for their new workflow automation platform. More evidence that Microsoft sees a move toward open collaborative systems as profitable.

Hello P5.js Web Editor! | Processing Foundation

This looks like a lot of fun. P5.js is an online editor for learning to code in a visual way. It helps students learn JavaScript, HTML, and CSS by creating graphics with code.

Photo by henry perks on Unsplash

  1. Also writing by an academic

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A Roundup of iOS Shortcuts Galleries and Resources https://appademic.tech/ios-shortcuts-galleries-resources/?pk_campaign=feed&pk_kwd=ios-shortcuts-galleries-resources Sun, 21 Oct 2018 23:49:55 +0000 https://appademic.tech/?p=2889 Permalink: A Roundup of iOS Shortcuts Galleries and Resources

Ios Shortcuts Galleries And Resources.png

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 ... Read more

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Permalink: A Roundup of iOS Shortcuts Galleries and Resources

Ios Shortcuts Galleries And Resources.png

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.

New iOS Shortcuts Galleries and Exchanges

RoutineHub

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.

Shortcuts Gallery

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

Sharecuts

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.

Shortcut Station

May or may not be the newest of the bunch, but the one I learned of most recently. Expect this one to become popular, as it was shared in the recent edition of the MacStories Newsletter.

Helpful Resources for iOS Shortcuts and Automation

r/Shortcuts | Reddit

The Shortcuts sub on reddit is by far the best place to find information about Shortcuts. You might have to wade through some inane posts, and silliness at times, but it is worth enduring.

Automating iOS: A Comprehensive Guide to URL Schemes and Drafts Actions | MacStories

Although this guide is focused on Drafts, learning how URL schemes work will take your Shortcuts game to another level. The post has aged well, the author was a big loss to the site.

Club MacStories

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.

Hacking around with JavaScript and Shortcuts in iOS 12

One of the more exciting additions to Shortcuts is the ability to run arbitrary Javascript on a web page. This has opened up all kinds of possibilities, as demonstrated in this post from Chris Hutchinson

Workflow Help | Official Documentation

I don’t often recommend official documentation. The Workflow documentation, however, was always very comprehensive. Curiously, Apple have not yet bothered to update the guide.

Other Repositories and Sites Worth Visiting

Automation Orchard

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.

Workflow Directory

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.

One Tap Less | Actions

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:

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iOS Shortcuts: Clipboard Shortcut for Bibliographic Data https://appademic.tech/clipboard-shortcut-for-bibliographic-data/?pk_campaign=feed&pk_kwd=clipboard-shortcut-for-bibliographic-data Fri, 19 Oct 2018 23:32:28 +0000 https://appademic.tech/?p=2881 Permalink: iOS Shortcuts: Clipboard Shortcut for Bibliographic Data

Ios Shortcuts Book Scanner.png

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 Bookends 1 can add references to your library directly by scanning different metadata, including any book’s ... Read more

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Permalink: iOS Shortcuts: Clipboard Shortcut for Bibliographic Data

Ios Shortcuts Book Scanner.png

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 Bookends 1 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.

Zotero Quick Add.png
Zotero can add items to your library automatically using metadata, such as the ISBN

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.

Download the shortcut and adapt it to your needs here: IBSN Scan To Copied

 

  1. These are the two I recommend, but other reference managers will do this too 
  2. I have lost hours troubleshooting the universal clipboard when it stops working, it’s not worth it.

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Digital Privacy at the Border with 1Password and DEVONthink https://appademic.tech/digital-privacy-at-the-border/?pk_campaign=feed&pk_kwd=digital-privacy-at-the-border Mon, 15 Oct 2018 23:01:43 +0000 https://appademic.tech/?p=2862 Permalink: Digital Privacy at the Border with 1Password and DEVONthink

digital privacy at the border

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 ... Read more

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Permalink: Digital Privacy at the Border with 1Password and DEVONthink

digital privacy at the border

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.

1Password

 

1password Digital Privacy At The Border
1Password's Cloud Vaults provide security and convenience for border crossing

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.

Devonthink Digital Privacy
DEVONthink's iOS app can help maintain privacy with its strong encryption and flexible syncing

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

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Show and Tell — 8 October, 2018 https://appademic.tech/show-and-tell-8-october-2018/?pk_campaign=feed&pk_kwd=show-and-tell-8-october-2018 Sun, 07 Oct 2018 22:06:41 +0000 https://appademic.tech/?p=2852 Permalink: Show and Tell — 8 October, 2018

Collected links for academics, students, and other nerds Markdown Converter | OU Libraries Tools 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 Times Newer Roman ... Read more

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Permalink: Show and Tell — 8 October, 2018

Collected links for academics, students, and other nerds

Markdown Converter | OU Libraries Tools

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

Times Newer Roman Is a Sneaky Font Designed to Make Your Essays Look Longer | the Verge

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.

Sans Forgetica | RMIT

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.

Firefox Monitor | Mozilla

 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.

Why I'm Done With Chrome | a Few Thoughts on Cryptographic Engineering

Speaking of Chrome,  here's Google again. It appears the time has come to delete Chrome. Sadly, like so many of these things that will be easier said than done

Bypass ‘Safari no Longer Supports Unsafe Extensions’ in Macos Mojave | George Garside

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….

Troy Hunt: Mmm… Pi-Hole…

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.

How to Build a Low Tech Website | Low Tech Mag

Another one for the tinkerers, I fancy this idea for a class project.

A Visualized History of Philosophy

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.

 

Photo by Andrew Neel on Unsplash

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Automate Referencing on iPad with Shortcuts and Zotero https://appademic.tech/referencing-on-ipad-zotero/?pk_campaign=feed&pk_kwd=referencing-on-ipad-zotero Thu, 04 Oct 2018 09:27:57 +0000 https://appademic.tech/?p=2840 Permalink: Automate Referencing on iPad with Shortcuts and Zotero

Zotero Shortcuts Referencing On Ipad.png

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 ... Read more

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Permalink: Automate Referencing on iPad with Shortcuts and Zotero

Zotero Shortcuts Referencing On Ipad.png

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.

Shortcuts Referencing On Ipad

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.

Zotero Shortcuts Referencing On Ipad

 

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

Referecing on iPad

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

You can download a workflow for either here.

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.

Beyond Referencing on iPad

Zotero’s Web API with the Shortcuts app is presently ās good as it gets for referencing on iPad. I’m not exaggerating when I say I have tried everything else, nothing comes close where iOS is concerned. From its communal, open source development, to its stance on privacy, Zotero is an antidote to the proprietary systems of giant academic publishers. 5 I cannot speak highly enough of the Zotero service. If you can spring for it, I recommend upgrading the storage option for both the utility, and to support their work. US$20 will buy you 2GB for a year, which is plenty for PDF documents.

For Mac users, Zotero is not the only solution I can recommend. I have started testing the native macOS referencing solution, Bookends, recently. I can tell you, it is impressive. I will post a proper review at some point, but there is a free trial available. Both these solutions, Zotero and Bookends, offer and excellent alternative to EndNote, Mendely, and the other big commercial referencing solutions. But at this point, for academic writing on iOS, Zotero is the best option we have currently. Whether you use these workflows, or shortcuts as they are or adapt them to your needs, I hope you find them useful. If you need any help configuring them, don't be afraid to contact me via one of the methods to your left.

Happy writing.

 

 

  1. If you use an alternate browser, you can change the final action to open the results there.
  2. If you are using footnotes, I have a post in the works to cover that
  3. I have a follow up post that will cover using Pandoc on iOS. It includes a shortcut for extracting citekeys for the Better BibTeX Plugin
  4. Unfortunately, the RTF scanner is a plugin, so it isn’t available online or through the API.  
  5. EndNote once sued Zotero for having the audacity to offer users a means for transferring their data. Mendely is run by similar ghouls. 

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