My Software as a Phd Student: Planning, Writing, Tracking

In social science/humanities we may not require super-computers, but all knowledge work demands a way to organize knowledge in a useful and pleasing way. For me, a great design is just as important as functionality of applications. Perhaps that’s why these are mostly Apple-only apps with a minimalist design.

The apps below help me trick my brain into doing the work with sleak design, helpful emojis and interruption blocks. My apps here are not specific to any data analysis type, but general purpose apps for planning, writing, etc. I will have to do another blogpost on specialised apps for analysing qualitative data. Also, I am not affiliated with any of these apps.

My conspicuous desktop wallpaper is a colourised photo of an African shaman.

OmniFocus (project management)

OmniFocus is the brain of my research system. I'm not sure I would have been able to cope effectively with the intensive demands of a PhD project without OmniFocus's ability to sort out my thoughts and deliver the right information to me at the right time. If something is not in OmniFocus, it might as well not exist for me. I even have an agenda list for stuff to talk with my wife about. It really is my extended brain when it comes to planning and executing tasks - and everything else actually. It does take a lot of time to set up the app just right though - mostly because you (in my opinion) have to understand the Getting Things Done (GTD) methodology, according to which all my lists and tags are organised. GTD have a PDF guide specifically for OmniFocus too, which helps. My absolute favourite thing about OmniFocus is the capture shortcut. I’ve set up quick capture shortcuts on my Mac and iPhone, as well voice capture on my Apple Watch. The idea is to make it effortless to always get ideas off my mind. As you can tell, I'm also a big fan of emojis for a quicker overview of projects and tags.

Ulysses (writing)

If OmniFocus is my extended brain, then Ulysses is the place where my actual brain does most of the thinking. Over time, Ulysses has become my hub for EVERYTHING writing related: Idea notes, personal notes, course notes, book notes, manuscripts, quotes, planning documents, journaling etc. I even have a folder with jokes — there’s a single sad joke in there that’s too awful to share here. Ulysses is a space for all writing in one place and features distraction-free experience with text and text only. It’s mainly used by authors and writers I think, but it fits scientific writing perfectly too - especially the qualitative analysis that I do. There’s even a workaround for using Endnote references. The only problem is no collaboration features on documents, so if you are writing with other scientists, you need to move your manuscript to Word at some point. But for writing first drafts and building arguments, the app is unmatched. An alternative app is Scrivener, but Scrivener lacks the clean, modern design of Ulysses. Ulysses also has built-in grammar check and it works fine. For articles, I sometimes also run them through Grammarly too for extra safe grammar check.

Fantastical (calendar)

(The above image is a sample calendar, not my own) Fantastical is basically a pro version of Apple Calendar. The interface is built for more heavy use. For example, it takes one click to set event alerts instead of two clicks in Apple Calendar. It’s filled with small improvements like that for professional users. It also has a lot more customisability than Apple Calendar. Fantastical also works great on Apple Watch, as I have described here.

Mindnode (brainstorm, planning)

I use mindnode and a versatile thinking and planning tool. I’m a big follower of David Allans and his insight that “we need more casual planning”. Many times, I will use Mindnode for casually sketching out project plans, and that will be the only project planning that I do. Only for the most demanding project, I will use Excel and other tools for keeping track. Mindnode also works well as a brainstorming or inspiration board tool, such as this one I made on 3 Zones for the Home Office.

Freedom (focus)

Many times, my fingers will trick my brain and open up YouTube or some news site. To avoid this, I use Freedom.to to block YouTube and other interruption sites when I’m writing. I schedule Freedom to block everything in my prestige writing time from 6 am to 8 am.

Timing (time tracking)

Timing tracks everything you do on your computer and assigns a productivity score to the time you’ve spent. While I only review the app on a monthly basis or less, Timing has one extremely useful feature. The little score icon in the top menu bar. If you have not been productive during your day, the score is below 50% and red. It feels good to look up at a green 90% productivity score at the end of the day, signalling that 90% of your computer time was spent on productive tasks. I’ve set Timing to count writing tasks as 100% productivity and playing computer games as 0%. Just try to not look at the score during weekends.

Apple Mail and MailButler (email)

I use Apple mail for the simplicity. All my tasks are tracked in OmniFocus, so I keep nothing in mail: there’s no folders, no nothing. Only a inbox that I clean up every day. I use a Plugin called Mailbutler that I was attracted to for the ability to stick yellow notes on emails. I don’t know what happened, but they removed that feature 🤦‍♂️ Now I use Mailbutler for the ability to undo emails 10 seconds after they are sent. Mailbutler holds the email and gives you a summary of recipients and attachments to review. Mailbutler can also scan outgoing emails for clues, such as the word “attached” or “file”, and then ask you if you’ve forgotten to attach something. This has saved me a couple of times.

Word, Powerpoint & Excel (editing, presentations, graphics, figures)

For cooporation with other researchers on articles, I use Word. I don’t like the design, but it’s the only tool for cooperating effectively on texts. I use Powerpoint for presentations and making quick graphical mockups. Powerpoint is actually quite powerful for graphics and I used it for many image on this blog. I use Excel for tables, e.g. time planning, PhD course list, budgetting, funding plan, etc.


Other apps that I use (not my favourites, but still useful) are Endnote X9 for reference management, Apple Books for ebooks, Apple Memos for interview recordings, Paintbrush for quick image editing, Apple Preview for quick image annotation, Grammarly for serious grammar checks and Zoom/Teams for video conferencing.

I love that OmniFocus and Fantastical syncs to Apple Watch - i've written about that here.

Malte Lebahn-Hadidi

Malte Lebahn-Hadidi