Research Workflows and Tips (Primarily Oriented at Academics)

Liz recently had a conversation going on Facebook where some academic workflows came up. This is the sort of thing I love to read and then run my mouth about, particularly about software and methods of organizing the things that end up getting collected because I think it’s especially relevant to the ABDs.

I had some bookmarks on Pinboard that I hastily shared but I wanted to grab a few more things and put together a more tailored list.

Caveat: Since she and I both are firmly ensconced in the Apple Family, most of these are directly related to iOS and OS X software and I will make no apologies for that. There are many exceptional options for research and organization of information that favor OS X and iOS, and that’s where I spend the majority of my time so my sources are slanted that way.


The problem I had in putting this list together is that in some cases my bookmarks are a few years old, and things move and change quickly. Because of technology being such a fast-moving target, some of this will be a little different (or a lot different), but this shouldn’t be too distracting since, as best I can tell, most academic researchers commit to something and don’t fiddle with it nearly as much as I do.

General Workflows and Notes for Researchers and Academics

“There’s more than one way to skin a cat, and more than just a few tools for creating a paperless workflow for academic research and writing. I’ve noted some of the possibilities on the Affordable Mac apps for academic tasks page.”

Goes into some detail with various tools like Sente and DEVONthink, including the workflow they use for research, drafting, and polishing their work. Scrivener fan, too.

Luc Beaulieu

The e-Office series has some interesting workflow and notes relevant to academic research.

He’s also got some interesting Academic templates for DEVONthink Pro.

More about DEVONthink

I love DEVONthink Pro Office so much I want to marry it. Some notes I’ve found dealing specifically with DEVONthink are bound to happen. Luc’s templates are interesting but I’ve got tons of links!

DEVONthink is great at a lot of things, but honestly I don’t find it that exceptional for collecting — especially when I’m away from the computer. I prefer Evernote for that sort of thing.

Evernote Stuff

Rabbit-hole warning: Numerous outbound links here for other workflows

Sidebar: the Creating Personal Flow article on doing research lead me to a neat post about Commonplace Notebooks, which LL may like.


Thoughts and observations on software and workflows for more-productive academics.

Sidebar: I must tell you that I love Ulysses 3 and use it for writing projects all the time. It’s pretty awesome.


A lot of good notes about Scrivener but other interesting tidbits as well.

Academic workflows: revisited

It’s been a year since I wrote this post on academic workflows. The way I work has changed a bit since then – some apps have gone out, some have been added, and the relationship between some of them have changed, primarily affecting my literature review work flow. Here’s a little post on my current set up.


Fuck this shit, I’ll use paper

Go see my friend Patrick, and do not pass Go and do not collect the USD$200. You won’t need it anyway. Paper based markup systems!


My more complete archive of things I scrape away for later is pretty large, but some especially relevant items include but are not limited to things I tag as:

You’ll notice that many of these use tags for platform, e.g. iOS and OS X.

Byword is doin’ it right

iOS 7 has some great features that I could go on and on about somewhat endlessly, but one of my favorites is being able to designate which apps on my iPhone can use my wireless operator’s LTE data connection and which ones can only use WiFi.

App Store is a great one to disable, given some apps are quite large.
App Store is a great one to disable, given some apps are quite large.

I’m not on an especially frugal data plan or anything, but I generally like to avoid lecherous network access from the dozens of apps on my phone especially when LTE in my neck of the woods isn’t exactly blazing fast consistently but also due to general anxiety about battery life. So I disable a lot of background data access, geofencing is only allowed for a few selections like OmniFocus, and some software that I am happy to work with offline and sync up later. App Store is a great one to disable, given some apps are quite large.

There is a huge problem with this however. The majority of software I use is painfully stupid about this and absolutely annoying about it. This is compounded by push notifications still working over LTE and then either absentmindedly or accidentally opening a notification that launches an app that I prefer only work over WiFi. When you launch an application that you don’t allow to use the mobile operator’s data network, some of them spam several dialog box alerts such as games that require a login to play online. 

This small wall of shame will illustrate my point better:

But there is one app in particular that I noticed today was behaving much better than the rest — Byword! It uses a polite and quiet notification in the bottom of the screen just to tell you that it’s happy to let you write away on a draft of an article or document but that you are, in fact, offline. I like that far more than the nagging dialog boxes telling me that I disabled the cellular data connection. No shit it’s disabled — I’m the one that disabled it! Rather than talking to myself on the bus about how stupid pop-up alerts are, Byword let me grind out a draft of a document without giving me grief about not being able to reach Dropbox and even smartly cached my documents from the last time I ran it.

Byword is doin' it right
Byword is doin’ it right

Savvy readers will note that Byword’s data access is enabled in the first screenshot I posted — on the bus ride home I needed to make sure my documents were updated with my mobile edits before I got back to a computer. That’s right! I can even decide to turn access back on again whenever I want!

These types of hand-waving alerts are something that iOS should either let the user disable entirely or developers should take the initiative and follow the fine example set by Byword — these types of interruptions are second in frustration only to endlessly interrupting me in order to ask me to write a one-star review on the App Store.

I salute you, Brett Terpstra. Salute him yourself on @ttscoff  or use TweetBook, if you’re not into the whole ADN thing. And after you buy a copy of Byword for iOS or OS X, buy MarkedApp2. You’ll thank me later.

Correction! 20131120

Brett Terpstra is not the author of Byword — I don’t know where I got it into my head that he was responsible for it! The recommendation to buy his MarkedApp still stands, however. I use MarkedApp2 with vim, BBEdit, and Ulysses, in addition to previewing my Byword documents.

(Sincere heart-felt apologies to MetaClassy’s Jorge and Rúben, obviously I think you’re awesome. Just apparently not awesome enough to learn you were the authors until @ttscoff told me that I’ve made a huge mistake.)



I’ve encoded a collection of IRIX 6.5 sounds from the 4dwm desktop environment suitable for use on iOS devices. Now you can amaze your friends and colleagues with an iPhone alert of the 4dwm file manager’s “rm” sound! Relive the glory days of BUGTRAQ, where new local root exploits for your Indy were available on a weekly basis!

Anyway, even if you are completely disinterested in or don’t know what IRIX is, these are nice discrete tones for alerts.

[button link=”” color=”green” size=”medium”]download IRIX Tones[/button]


iOS IRIX Alerts


iPhone can now IFTTT!

There is now an iPhone app for IFTTT, allowing you to create new recipes for automatic actions and event logging. Rather than relying on a third party notification service you can now opt to use notifications to the IFTTT App.

IFTTT1 is one of my favorite web services — I use it to dump ADN2 and Facebook status messages I’ve written into a Google Drive document, send CERT advisories to my iPhone via Prowl, and one of my favorites: starred posts on ADN, pinboard3 bookmarks marked “to read” and saved articles in Feedly get saved to Evernote and Pocket.

Having said that, IFTTT is my current achilles heel and I am hoping that they find a way to make sure some reasonable continuity of business is in the cards through some sort of service model. I would pay for the service as it is, especially now that my hot selfies can be auto-posted to my tumblr.

As with everything IFTTT, you’ll have to get creative to truly take advantage of the service’s three new channels: Photos, Reminders, and Contacts. For example, you could have IFTTT create a new Google Calendar event every time you add a contact, so you can keep track of when you meet people, or you could have IFTTT post every selfie you take to a Tumblr blog you’ve created. Yep, there’s an IFTTT trigger that activates only for photos taken using your phone’s front-facing camera. You can optionally receive push notifications when any of your recipes run their course.
The Verge

  1. if this, then that: 

  2. – 

  3. Great bookmark service: