One of the most enjoyable aspects of my PhD was the experimentation. To my mind, there were two important types: 1. the experiments related to my research; 2. the experiments on myself. My time as a PhD candidate provided ample opportunity to see the effect of different eating habits, coffee intake, work hours, sleep patterns, and most importantly working styles. Up until early in my undergraduate degree, I had managed to get by on doing the work when it was needed. When I was now defining what was needed, that approach no longer worked. After much experimentation, including tweaking up to the day I write this post, the following is a snapshot of my productivity system.

The concepts

Getting Things Done (GTD)

David Allen’s guide - or more specifically the philosophy behind the guide - applies to everyone and anyone. When I first heard about it, I dismissed it as irrelevant as I was not a business person. However, after reading Zen to Done, I found that aspects of the concept applied to my situation.

1. Capture
   This was revolutionary. The simple act of noting down thoughts/ideas/information as it presented itself made me much more productive. At first I was somewhat haphazard, and had multiple capture locations, but have found that having a discreet set of inboxes for capturing ideas works much better. I know I have only three potential places to check and clear: my standard notes inbox (see below), my wallet post-it note, or my whiteboard.
2. Clarify
   The inbox contains many types of content. Some are ideas, some information, some thoughts on existing projects, some are just passing thoughts. These get clarified into actionable information (which then goes into a relevant list for tracking), reference information (either events or phone numbers - mostly zoom links now), or ideas: either well-formed ones which get put into the asset folder for the relevant project, or initial concepts that need time to simmer or be reviewed before it is usable, which get put into a review list.
3. Carry-out
   During my weekly review, I use time-blocking to schedule my big rocks, as well as my meetings. I then whittle down my next actions list to ones I would like to get done that week. This means two things: 1) I make time for the bigger tasks that would otherwise slip through the task-churning cracks. 2) I save myself a fair amount of cognitive effort by pre-deciding on a smaller number of tasks for that week.

Time-blocking

I was a late-comer to both time-blocking and its extension time-boxing. David Allen’s GTD method is a good foundation for approaching work. Capturing ideas, translating them into discreet and pre-decided next actions, and then working through that list in the slots of time available around the sacred calendar of meetings. Time-blocking allows me to plan out my week in more detail. I find that devoting a chunk of time to work on a more involved project makes sure I actually do that work. I also time-box¹ the ‘shallow work’ that is necessary: checking email with a time limit ensures I don’t waste an afternoon responding when fifteen minutes would have sufficed.
I have found that I need to be realistic with my time blocks, and recognise that I cannot do more than about four hours of truly deep work. Rather than burn myself out trying, I have time-blocks for hard work, with time blocks for mental refreshers. I also try to alternate the type of work that I do every ninety minutes or so. Reading, writing, and editing require different modes of thought. I limit myself to two ‘blocks’ of one activity type, usually with a proper (e.g. lunch) break between them.

The Pomodoro Technique

For me, the Pomodoro Technique is a game-changer. I use it in two main ways: to get started, and to limit how long I can work on something. In terms of tools, I have three depending on where I am. Most simply I use either my phone or computer to set a timer. This is for when I am working from anywhere and don’t have access to my preferred tools. At home, I use a mechanical ‘time timer’. The tactile nature of setting the timer, coupled with the background clicking, has an inspiring effect on me. It is like a tangible commitment to my work session. The red wheel gives me an at-a-glance vibe of how long I have left - both when I am wanting to stop and hurrying to finish. However, the ticking and the alarm of the time timer are not appropriate for a communal office, so I made my own version.
Using some neopixels and an ATTiny85, I made a silent time with a strip of 6 lights. One is either purple or blue, to indicate work or break respectively. The other five count down the time by flashing on and off at one-second intervals. When in a work mode, each of the five LEDs are red and indicate 5 minutes. So after 5 minutes of the first LED flashing, it turns off and the next LED starts to flash and count down its 5 minutes. The change from a work to break mode involves a quick flash of white to grab my attention. Then the five LEDs (now green) count down 1 minute each.

I use the pomodoro technique in combination with time-blocking. I can forget about keeping an eye on the time when I know an alarm will sound (or flash) when I’m done. I also take note of how many successful 25 minute blocks of deep work activity I complete in a day. If I was interrupted, or lost focus, then I don’t include that pomodoro in the tally. Tracking this metric keeps me honest with myself about my productivity, which helps me set realistic plans for the week. I also get a sense of what aids my productivity and what hinders it.

The tools

Standard notes

There are many alternatives, but I selected StandardNotes to be my GTD tool of choice. It is secure, simple, and syncs between my phone and computer. There is some tagging ability, but no reminders, no automated transfer of tasks. It is distinctly manual, and I kind of like that aspect too.
The core of the GTD methodology is, after all, keeping lists. Standard Notes is my selected tool for that job. I clear out completed tasks during the weekly review - my GTD lists are actionable items and current reference material, not a history of what I have done.

Workflowy

Workflowy is a fantastic service. The ability to zoom into a given bullet is amazing for focus. I use workflowy to skeleton ideas, and track solo project progress. I do not use it for archival purposes. Anything in workflowy is ‘live’.

Trello

Trello is good for collaborative project tracking. Workflowy does have collaborative features (sharing a bullet point), but I have found Trello to be better for working with others - particularly as my university has an enterprise license. There is a lower barrier for entry, and the ability to easily assign at task and due date keeps everyone on track.

BulletJournal or BuJo

I use a simple gridded notebook. I like the B6 size ones from Muji. They are nice paper, not too expensive, and just the right size for me ($8 AUD and it fits a year and a half). My only wish is for a 5 mm grid instead of the 6 mm. My bullet journal is nothing fancy. It is essentially a diary laid out exactly as I want it. On each two page spread, I only have Monday to Friday with a free space for sketching ideas. For each day, my time-block schedule goes on the right hand side, and next actions/events go on the left. The BuJo serves as a log of what I did in a given week more than anything.

Laboratory book

I am very lucky, as early in my research career (a special project during my second year of undergrad) I had a fantastic mentor who instilled me with a love of a well kept lab book. A lab book serves as somewhat of an external brain. My lab books are kept chronologically, mixing projects freely. The title gets a shorthand project reference, followed by an informative title. This helps me quickly sort cross-references where relevant. Aim, reagent origins, method, rough data interpretation, and conclusion/next steps/ideas. My lab book get scanned every few weeks, and I take a few minutes to add the new experiment page numbers and experiment titles into my zettelkasten (this could equally be a list in my GTD system, but I try to keep ‘archival’ type content out of standard notes). This practice, both scanning and keeping a digital list of titles has been incredibly handy now that I’m WFH. While I have missed the tactile nature of flipping through the pages, I am able to write up and process all of my experiments easily.

A scratchpad

As a complement to my bujo, I have started using a ‘scratchpad’ for hashing out ideas and plans. I use a simple spiral bound notebook with removable pages. I prefer to use a mechanical pencil as sketching occurs quite often - mechanisms, figures/schemes, preliminary design ideas for 3D printed parts. The key concept, and one that took me a while to truly embrace, is that this book is ephemeral. Much like my GTD system not being a log of my work, this book is not a reference. It is my short term memory. This allows me to use it freely; something that never felt quite right in a bujo - what if I fill it up before the end of the year?

Zettelkasten

There are few ideas that radically change how I work. Most of the methods, tools, and structures provide improvements on how I work. A few changed the game for me. One was the idea of ubiquitous capture. A more recent one is the idea of a zettelkasten (“slip box” or “box of notes” in German). I first read about the idea in How to take smart notes. My decision to go paperless precluded trying to implement a physical zettelkasten. I have selected Zettlr as my zettelkasten software, and am very happy with it. I use Zettlr for drafting documents (markdown is quick to write and there are fantastic export options), taking or transcribing meeting notes, and - most importantly - building my zettelkasten. I find that two stages of writing notes are needed for the zettelkasten: first, writing summaries, notes, and drafts ideas. These are kind of scratch, working documents. Second, extracting the ‘zettelkasten’ elements from the summaries, which need to be robust and timeless. As a quick example, I summarise a paper once a week. I select an interesting - though beyond my current level of understanding - paper and take careful notes as I read it (often several times before I fully comprehend the concepts). These summaries are kept in a ‘literature summaries’ folder. After writing the summary, I extract any key concepts and ideas, and try to place them into the web of information I already have, slowly growing my zettelkasten, and also pointing me in new areas that are ripe for exploration.

Data management

There are three parts to my data management approach.

1. Consistent file naming
   For my various data forms, I have defined file naming protocols. I name experimental data files INSTRUMENT_DATE_LABREF, where Instrument is an identifying code for the particular instrument, DATE is in YYYYMMDD format, and LABREF is my laboratory book page (my initial, book number, 3-digit page number e.g. 014 for the 14th page) plus whatever identifier is relevant (_1 for the first run, or _sm for starting material)
2. Sync platform
   All of my experimental data goes into a folder named DATA. Within DATA there are folders for the data types, and then folders for each data folder. That DATA folder lives in onedrive (university run, stored within Australia, and approved for data retention). My supervisor has access to the folder, and when I leave I will upload it to the research data storage drive.
3. Version control
   Data goes into two folders: raw and processed. The raw data is copied directly off the instrument, and the processed folder is where I analyse the data, including any plotting and interpretation. Some forms of data generated (e.g. modelling) will have so many iterations, that I prefer to use git to track the versions. That lets me keep a tidy processed folder, with all of the steps that led me there retained for posterity. Manuscripts are the same. I ‘commit’ the major versions of a manuscript so that I can review them if needed. This is far nicer than looking at a folder full of draft_1, draft_1_with_edits, draft_latest and so on. The key for me is being descriptive with my commit messages.

Conclusion

My productivity setup is constantly evolving. The most important requirements are: to keep it as frictionless as possible, keep my data accessible, and to have clear guidelines so that minimal mental muscle goes into how to use the system.