The tools of my PhD trade: referencing, reading, writing, and productivity

Photo:Todd Quackenbush

Recently , I’ve invested a bit of my time in organising my reading, research, and writing work-flows and digital tools. I am acutely aware that I need to get these habits and practices bedded down soon to avoid breakdowns, flare-ups, and run-arounds later on in the doctoral journey.

Here’s a quick run-down of the main elements of my toolbox.

Zotero for reference management

I’ve used Endnote and tested several others (Endnote, Mendeley, Paperpile, Citavi, Docear), but I’ve settled on Zotero for a couple of reasons.

  1. It’s free, open-source, and developed by the Roy Rosenzweig Center for History and New Media, an organisation that has education, access to information, and democracy at the core of its mission. As opposed to, let’s say, Elsevier, who owns Mendeley and is known for its rapaciousness.
  2. I have set it up, with an add-on called Zotfile to download citations, along with the full-article .pdf, from academic databases, store the files in Dropbox, and rename the file and the Dropbox folder according to my set style, all in one click of the mouse.
  3. I have also set it up so that I can open the .pdf, annotate and highlight it, save it, and then extract those notes and highlighted sections as plain-text files to be stored in the Dropbox folder as the .pdf and attached to the citation record in Zotero (see image below).
  4. It just does citation management, .pdf wrangling, and light .pdf annotations. Other tools include deeper .pdf annotation and note taking, social sharing, mind-mapping, writing, and all sorts. But I kind of prefer to take a one-tool for one-job approach.
  5. Zotero works well with the plain text approach that I’ll speak more about. I can export my library as Bibtex and any annotations are plain text. This means that I am not beholden to any one system: plain text can be read by pretty much anything.
  6. I dislike the things I dislike about Zotero less than I dislike the things I dislike about the other reference managers that I use.

Drawboard for  Reading and annotating .pdfs

When I bought a Microsoft Surface recently, a demo copy of Drawboard came pre-installed. I usually consider this bloatware and will uninstall it immediately, but I bought the surface specifically for reading .pdfs, so thought I’d give it a spin. I agree with the good reviews it gets: it’s an easy to use, simple, and effective .pdf reader. It’s designed especially for use in tablet mode, with a stylus.



Writemonkey for note-taking and early drafts

For a while there I was trying to use Scrivener, the preferred tool of many academic writers, for my writing, but I just couldn’t get past the overwhelming interface and array of options. I’m a minimalist in many areas of my life, and I’ve decided to go with a plain text editor, Writemonkey.

Plain text has many benefits over many more complex writing software tools. Most importantly, it is open and ubiquitous: it works on all operating systems and can be opened in any number of apps. The simplicity of plain text, free of all but the most basic formatting, makes it perfect for note-taking, generative writing and early drafts. Plain-text editors are microscopic in comparison to more developed (one might say bloated) software. This makes them lightning fast and portable.

Writemonkey works for me for a couple of reasons:

  1. It’s fully portable: the whole program lives in Dropbox or on a USB stick. This means I can run it on any windows computer without needing to install it or otherwise impact that computer.
  2. It is as simple or complex as you want it to be. If you choose to, you can get into Markdown , use Regex for navigation and filtering, or even use the Writemonkey API to  develop plug-ins.
  3. Some writing software that I have used is extremely obtuse about where your work lives on your computer. As with everything else, I like my stuff to be in Dropbox, and Writemonkey doesn’t fight me on that.
  4. Built in Pomodoro timer to encourage and track productivity, white noise generator to help focus, and clicky-clacky typewriter sound effects, which I thought were a gimmick but are actually kind of motivating to hear, indicating lots of precious words being written.
  5. Writemonkey is owned and developed by one person. It’s nice to use something that isn’t the product of some vast corporation, but rather the fruits of one person’s vision and labour. I know I’m straying toward hipster artisan territory with that.

Microsoft word for final drafts

There’s no getting around it. At some point you’ll have to send a .docx file to someone. In my case, I can use plain text up until the point I need to send a draft to my supervisor, share anything with my colleagues, submit an article to a journal or an abstract to a conference, apply for a scholarship, or… any number of other things. Luckily, plain text makes this as simple as select all, CTRL+C, and CTRL+P.

Todo lists and light project management

Plain text again. I’ve lost count of how many productivity apps I’ve tried and abandoned. Some proved very tricky indeed in extracting my data from in any usable form. I’ve also found that the more feature-rich the app, the more likely I am to spend my time fiddling with it (I prefer to say “optimising it”) than actually doing the stuff I’m listing in it.

So my todo list is just one text file living in Dropbox. If I open it in a plain old text editor, it looks like this:

Which is a perfectly functional, if tricky to read and use, todo list. But if I open it in an app that recognises the todo.txt formatting rules, such as the tiny, portable, and lightning-fast, it looks like this:

The trick is that by appending + for projects, @ for contexts, or (A) through (Z) for priority, I can filter or sort in a million useful ways.

Keeping it simple

A clear theme of these tool choices is my desire to keep things simple. I prefer one tool for one task. Plain text and Dropbox go a long way to keeping the integration of these parts simple. In the past I’ve searched for the one comprehensive tool to rule them all, but all tools that claim to do that either suck badly or require their own PhD to learn how to use them.

I’m sure this set-up will evolve somewhat, but I hope by not too much. I no longer have the time to mess around tinkering with my system, I’ve got a PhD to write.

Reading, writing, reps: Waitangi Day edition

It’s both Waitangi Day and Bob Marley’s birthday. If I were in New Zealand I’d be enjoying a day off and hopefully getting some writing done. But here I am in Melbourne, so I’m at work. Nonetheless, I’ve made some good progress on a key project.

REading and writing

My supervisor and I a co-writing a chapter on Dialogical Self Theory in Career Education. My contribution is basically a potted-history of key approaches to career education: Cognitive Information Processing, DOTS, career-learning theory, and what I’ve termed dialogical career-learning theory. This last one is where Frans Meijers, Reinekke Lengelle and others have integrated Dialogical Self Theory into Laws’s career-learning theory, arguing that “the development of a career story must be understood not only as a cognitive learning process but as a dialogical learning process as well” (Meijers & Lengelle, 2012, p. 169).

We’ve completed a first draft and are now editing for cohesion. The last step will be an introduction and conclusion and then we’re done. All going well, this will be the first publication for me in this doctoral project.


I enjoyed a morning in the gym yesterday. I have been trying a new rep scheme from this article by Dan John:

Do a single, rest a bit, do a double, rest a bit, then do a triple. That is six total reps and the quality should all be excellent. For a solid workout, run through this three times: 1-2-3-1-2-3-1-2-3.

Yesterday I did this with:

  • BB squats: 1,2,3 for 3 times around
  • Bench: 1,2,3 for 3 times around
  • Bent over barbell rows, 1,2,3 for 3 times around
  • Single arm landmine rows: 3×10

I also had a short ride on my new bike.