How I’m using Milanote to write my PhD thesis

MilanoteA PhD thesis is a large piece of writing which compiles several years of research. As such, it needs a great amount of planning not only at the beginning but also during the writing process itself where thoughts might move to another section several times.

My PhD is in the field of nanophysic, exploring the possibility that single molecules could be used as the building blocks of new kinds of microprocessors. My work is based on numerical simulations that run on supercomputers where performance really matters, which could explain my obsession with finding the right tool for a given task.

The problem was that planning my thesis in a conventional text processor wasn’t working for me. Standard word processors are inherently linear, but my mind doesn’t think in a linear way. And while the auto-generated table of contents did describe the concept of my thesis, it was often too coarse and inflexible for my brain.

What I needed instead was an “architect’s plan” of my thesis. In this plan, my individual ideas would become bricks. The bricks would be organized into pillars, and these pillars could build into the sections of my thesis. In this system, writing a draft would be like playing the role of mental bricklayer.

In his book How to write a thesis, Umberto Eco suggests outlining a thesis with paper index cards. These cards were the bricks I was looking for! I created my first draft using this paper-based system. Working this way was extremely fast since a thought could fly out of your mind and appear on your desk in seconds. Adding print outs of my plots and figures made my thesis even clearer.

But as my draft started to grow it quickly got out of control. My index cards required a lot of physical space and transporting them between home and university was turning into a project of its own. Eventually the fact that none of my stacks of paper were backed up anywhere pushed me to look for a digital solution.

First I tried Trello. In essence, Trello is all about index cards enhanced with fancy features like checklists and due dates. But it turned out it was overkill for what I was trying to do. Moreover, in Trello categories are can only be moved horizontally (similar to text processors). This might be useful for project management but I found it drowned my creativity.

Another tool I checked out was PinUp, a virtual corkboard with post-its that can be pinned anywhere, giving you creative space to breathe. But because PinUp lacks any type of categorisation, the board I created for my draft quickly became a mess of post-its.

MilanoteFinally, I stumbled on Milanote—just like my paper index cards but made of bits and bytes! In Milanote I can easily maintain the flow of my thoughts by putting them down on a card (either during the draft phase or spontaneously while actually writing). If an idea doesn’t find its place on the board initially, then I leave it in the “Unsorted” section of the board in the meantime. The chapters of my thesis correspond to columns and their spatial arrangement represents the outline of my thesis. The minimal design of Milanote keeps me focused while I play with my ideas in a distraction free environment.

Being able to move columns around in Milanote lets me compare their content side by side in order to detect redundancies or discrepancies. In particular, I often move the introduction and conclusion columns next to each other to compare them (since these are the parts readers pays most attention to). Adding figures or graphs is simply a matter of dropping them into the board.  Having this sort of a plan in front of me lets me relate thoughts to each other much more effectively than if they were spread over a series of pages like they would be in a conventional document.

thesis milanote

But in my opinion the absolute killer feature is the nesting of boards. This lets me build creative subspaces anywhere I want with unlimited depth. For instance, while writing a particular section I realised it was overloaded with information. Being able to nest boards meant that I simply opened a new sub-board, moved the cards there and tackled the section separately.

In academia, publishing journal papers is an integral part of the business. With Milanote, any piece of writing can be drafted in a way that matches the way my brain actually works. And while it’s great for gathering data, interpretation and drafting that’s not all I’ve been using it for—I’ve also started using Milanote for meal plans, organizing events, and even writing this article 🙂

Go to to give it a try yourself.

Chriszandro HofmeisterChriszandro Hofmeister has a diploma (major) in Physics. He is doing a PHD in nano physics at the Friedrich-Alexander University in Erlangen, Germany, around the topic of Proton Transfer for conductance controlling in molecular junctions.



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