Organisation | DEZERAECOX

Toolbox Talk: Notion

Sat, 04 Sep 2021 21:23:03 +0000

Toolbox Talk: Notion

Notion is the type of software that, if you know, you know. After hitting the scene only a few years ago, it has amassed a somewhat cult-like following among personal productivity buffs. For me, Notion is a love affair that started during Melbourne’s extended COVID lockdown in 2020. During this profoundly confronting time, where life seemed beyond control, I found solace in taking control of my tools and systems. A whole new consolidated and streamlined workflow emerged with Notion at its centre - and wow, do I have some thoughts! If you came purely for the Notion nitty-gritty, feel free to skip to the Getting Started section. Otherwise, for Notion newbies, here are a few of my feelings about digital tools for science and how Notion fits the bill for me.

Need a notion about Notion?

First and foremost, Notion is a blank canvas that you can make and mould into (almost) anything! In fact, its versatility is often something sceptics point to as a reason to steer clear. But really, this is where the magic happens. Unfortunately, it also makes Notion incredibly hard to describe! So, here goes.

First: think spreadsheets on steroids. At its core, Notion provides an architecture for building relational databases which are like spreadsheets that can be linked. But, **more than that, each entry itself is a ‘page’ that can contain another database. Which brings me to… Second: think lego! The second aspect of Notion’s design strategy is that all content is considered individual Blocks (even databases). This means that you can stack and link different types of content (from normal text, quotes, callouts, bulleted and numbered lists to more complex structures like embedded webpages, code blocks, equations, date reminders, embedded google drive files, and even databases). Layered on top of this is the ability to display databases as tables, boards, galleries or lists, plus filtering and sorting that makes sure you can see the information you need in the context you need it. Last but not least is the aesthetic! With a simple palette for labelling metadata, headings and text, coupled with optional icons and header images it is super simple to make pretty pages

What we arrive at is a highly versatile and customisable ecosystem that you can use to build and personalise any architecture you need, from a to a to a workplace wiki to a … The possibilities are endless! And for people like me, it presents the opportunity to unify all the disparate digital tools that we had cobbled together to take care of these functions in the past, like Evernote and . In this way, Notion for me embodies the principle of removing friction, by letting me focus on the work without context switching.

A simple sneak peek

In honesty, Notion is sometimes a tool you need to see to understand. So, here is a quick toy task management example. I’ve even provided this page as an template in case you want to try it out!

To start, databases can look just like a regular spreadsheet, but can also be displayed as a board ( think: Trello), list, gallery, timeline or calendar. Here is an example of two databases: “My First Database” viewed as a gallery, and “My Second Database” viewed as a table, placed on a single page titled “Example Relational Databases”. Each column of the table view shows some of the metadata for the individual elements. There are lots of types of metadata you can add, including dates, categories from a dropdown, checkboxes, formulas which calculate a property based on other metadata columns, urls, emails, attachments - so many choices!

Most importantly, we can link these two databases using a relational property, such that we assign Task 1 as associated with Project A. This opens up lots of possibilities, including new formula options called ‘rollups’ which let you see how many tasks for a project are complete.

Now, to this point most of these features you could fandangle out of a spreadsheet if you tried hard enough. But here comes the magic. Each of the entries in the database are themselves pages, which can contain any of the rich content blocks I described above, including more databases. It can also include filtered views of a database so, within a single project, you can overview associated elements.

Last but not least, one of my favourite time-saving functions - templates! You can add templates to any database, such that when you add a new entry to the database it can be prefilled with page content. This is a super-efficient way to capture essential and consistent information for each new entry beyond the metadata options. You can even pre-filter included databases, such that the filtered view automatically includes only related sub-entries.

Ok… But what about Notion for science?

In my 10 years as a scientist, I was not once introduced to the idea of “project management”, much less software fit for the task. It was mostly something that we were inherently supposed to do; keeping track of the overarching aim of our individual project, tracking goals and milestones and tasks. It wasn’t until my first post-doc, when suddenly the number of projects I was involved in exploded, that I found myself reaching for help in the form of digital project management tools.

In contrast, Electronic Lab Notebooks (ELNs) are a digital platform that is slowly permeating all levels of science. The available options seem to be multiplying at a steady rate, and institutional uptake is slowly increasing. Many of the front runner ELNs have connectivity covered, being accessible via browser or app across devices, and provide documentation processes, like versioning and witnessing, in line with funding body and research institution requirements. However, all of the many platforms I have tried suffer from similar issues: (i) they have quite a rigid structure for what constitutes an “experiment”, (ii) data storage size is limited, (iii) structured similarly to a paper notebook which treats experiments as a single entity, not just one of a number of specialised outputs researchers manage and produce, (iv) have no mechanism to track what stage in the experimental process that experiment is in (idea, design, data gathering, data analysis, summary and storage) and (v) are somewhat of an isolated island.

Needless to say, Notion has now alleviated most of these pain points. A few of the best bits:

It works where you do - in an app, browser, mobile, PC, Mac… Wherever you need to be, with synced content meaning everything is always accessible when and where you need it
It is less rigid than Windows file structures, taking full advantage of the interlinked nature of what we do as scientists, building a web of research
Allows you to automate some of the ‘boring’ (although I never find them boring!) organisational bits through templating
Functional web clipper to capture resources and info while you browse
Good selection of commenting, collaboration and automatic versioning features
(Almost) infinite customisability enables you to work in a way that works for you

This being said, there are some important caveats to bear in mind:

Funding bodies sometimes mandate data storage conditions, including the global location of servers for digital data. Notion may not always satisfy this criteria.
Similarly, Notion should not be used for confidential information such as clinical data
Due to the unique nature of Notion’s architecture, there is a limited ability to transfer to alternative systems - however there are substantial backup options to get your data out of Notion if you ever need to
Small number of direct integrations with Google products (like calendar) has been limiting, although the fledgling API will hopefully help this to thrive in the near future.
Some functionality has been slow to materialise - like the ability to natively add symbols outside equations, column-wise formatting within other blocks, and native drawing/writing/pdf annotation (I stick with the Notes app on my iPad, where the export-as-image and copy-as-text functions are my fired)

For me, none of these things were deal-breakers. But certainly, Notion is not fit for every purpose! Buyer beware, as they say.

My Notion Nitty Gritty

For my workspace, I started with the broad buckets of Science, Coding, Communication and Personal. Parallel to this are my Projects, Milestones, Tasks and Resources databases ( think: P.A.R.A.), where individual items are linked to their overarching bucket. From here, filtered views of each of the Project, Milestone and Resource databases form the basis of my daily work ecosystem. I can open a Project page and see each of the Milestones on the go for that project (manuscripts, experiments, funding applications), Resources pertaining to that project (like articles, funding, and ideas), and Tasks for that project (of course sorted by priority and due date). I treat all individual research outputs as Milestones; whether that be a single experiment, a manuscript I’m writing, a presentation I’m giving, a funding application I’m preparing, or a seminar I’ve attended. As well as linked databases, you can also ‘mention’ pages or people inline using the ‘@’ function (almost like a hyperlink) that helps to link together pages to create your very own web of knowledge.

To help with easy access and focusing, I also have a Dashboard page, with some of these @ links to my current priority projects, milestones and tasks - plus a filtered and sorted linked database with some friendly reminders to focus my day!

Some of my other favourite Science databases include my Virtual Lab Book (a filtered version of my Milestones database, which has separate properties for Experiments as they move from conception to data gathering to analysis to writeup), my Reading List (captured as a filtered database from my Resources), and my CV database with which I can filter to produce tailored versions of my CV for individual applications. I have templates set up for different types of Milestones, making it easy to create a new Experiment versus a Manuscript. On the personal front, a sneaky favourite of mine is my recipes database - drool worthy organisation if I do say so myself!

Tips for getting started

If you made it this far, I’m sure you’re thinking “Ok - you sold me. Now, where do I start?”. For many people, staring at the blank screen of a fresh Notion workspace will be quite daunting. If you’ve only ever used out-of-the-box systems, the requirement to create your own from scratch can be overwhelming! However, I truly believe this is where the magic happens. A few tips:

Start with stepping back - the first thing I recommend after installing Notion and creating your first workspace is to close the computer. Yup, put it away and find yourself a pen and paper. First, set to thinking about the broad buckets you want to encapsulate within the workspace. For this process, I found an adaptation of the . method of project management was a great place to start.
Remember to be flexible - your initial workspace should provide some guiding principles to start with, but should be fluid over time as you learn what works, what could be better and, most importantly, what you need. This is the true power of Notion - to grow with you.
Prepare for growing pains - changing to a new system (especially if you are planning a whole-life overhaul like I did!) will invariably present some challenges. But, it will be worth it. Stick with it, and pay attention to the pain points at what you need to adapt.
Face the future - with new systems, the temptation to retrofit your past outputs can be seductive. But (!) you should resist this temptation. Focus instead on ingesting only those things that you currently need into Notion, and leave the rest as the BN (before Notion) archive. You will know where to find things (hopefully) by sticking to the BN and AN line!

Once you have decided what your Notion might look like from a top-down point of view, it’s time to set to work creating the databases and entries that will comprise your workspace. If you’re still struggling with the basics, there are many great tutorials (like from the Notion team) and you can find plenty of inspiration, like and and .

Wrapping up

Wow, what a marathon! In my defence, I warned you I had plenty of feelings when it comes to Notion! My hope is that this post serves as a basic run-through of how I use Notion on a daily basis to capture my research process and enhance my productivity by providing a platform designed and curated by me. Beyond the infrastructure that I provide for myself in Notion, there are a host of strategies I use to link outputs across various other platforms, such that Notion serves as my catch-all and launch point, but I can leave more specialised operations like task management and writing code to specific apps that were tailor-made for those purposes.

In short, Notion may be the broadest tool in my research organisation toolbox, but it is still only a tool that helps bring together other essential tools in the box. You could almost think about it as the toolbelt which keeps all my other tools handy!

That’s all for now. As organisation is intensely personal (what works for you will be very different to what I like and need!), I don’t think it is especially useful to go through my workspace in-depth here. If you’re keen to chat details, make sure to drop me a note on or on the page!

Happy organising 📚

Image credits: via unplash

Year in review: 2020 Edition

Sun, 14 Mar 2021 10:40:50 +0000

Year in review: 2020 Edition

2020 was… A year that felt like a decade, but with the productivity of a boozy long weekend. In case you haven’t been on planet earth for the entire year (hello friend, teach me your secrets), it was of course the year in which a coronavirus (specifically SARS-Cov2) emerged and rapidly took over the globe.

The ensuing pandemonium was slow to build, and even slower to resolve. In fact, most countries around the world are still living with some form of social restrictions aimed at controlling transmission and preventing severe infection. We’ve since entered a recession, predicted by many to be the largest since the global financial crisis. Most importantly, many people lost their lives to the virus, and many more still have a severe and long-lasting illness.

I am fortunate enough to live in a country with very low infection rates and virtually no community transmission, and so life has returned to a post-virus normal. But (of course, there is always a but) to achieve this hefty goal, we as a community endured the longest and harshest lockdown conditions seen anywhere around the globe for almost a year. Make no mistake; it was essential and worthwhile. However, it was also eye-opening, isolating, disruptive and challenging. And as well as being a bench biologist who couldn’t get to the bench, I faced the lockdown separated by state borders from my partner, family and friends. To say it was mentally tough would be a colossal understatement, and despite this I am well aware of many who faced worse than me.

So, in acknowledging that no two experiences of 2020 were alike, I decided to stick with my traditional by-the-numbers account of the past year. You’ll find wins few and far between, more than a handful of losses, and a list of goals that looked a little different from start to finish. Finally, I look to the future and set my sights on recovery in 2021.

Wins

A snapshot of the high points

I survived 2020. I think that certainly belongs in the win column, don’t you?
I read three books, and reviewed one.
I published five blog posts totalling 6500 words, which were viewed 1557 times by 833 different visitors from more than 10 countries
I contributed my first to an online publication
I published my first , providing analysis tools for researchers considering applying for NHMRC funding
I worked over 2500 hours, more than 40% of which went towards submitting my first first-author postdoctoral paper for review to a top-tier journal
Five manuscripts I contributed to were officially published
I slept an average of 7 hours and 5 minutes
I overhauled my entire organisation system, from code to experiments to publications
I created and published not but science-communication videos as part of my first official scicomm training worskhop
I organised and hosted 17 Departmental seminars from a diverse group of researchers spanning career stages and countries - and made a successful transition to virtual when the pandemic hit!
I gave 2 invited seminars, and attended 3 virtual conferences

Losses

A not-so-snappy shot of the low points

Another year with no published first-author manuscripts, despite furiously writing for most of the year
My first-author paper was rejected from 4 different journals before even being sent out for peer review
Almost one fifth of the hours I worked were spent on emails and other administrative tasks
I didn’t write a single grant or application
I downloaded 1084 papers, and read less than 10% of them
I started 4 books that I didn’t finish
I didn’t publish blog posts in 7 out of 12 months
My coding projects are still still in a state of disarray, in desperate need of a tidy and some documentation
I only averaged 3817 steps per day
I was, perhaps, 50% productive on any given day

Lessons

The bits I wish I knew at the start of 2020, but had to learn the hard way.

Selfish isn’t a dirty word - for much of 2020 I struggled with the feeling of being a bad friend, bad partner, bad lab mate, bad family member as I weathered the storm of Victoria’s lockdown alone. I was lonely, unhealthy, unmotivated and struggling to keep my head above water and still I felt uncommitted to the many relationships in my life I let languish during this period. But in reality, I didn’t have anything to give - and I needed to be selfish, to rebuild my own mental health, to redefine my sense of self in this weird and wonderful (?) new world we were suddenly inhabiting. And it took me a long time to be ok with this idea of a self-centred approach to wellbeing. After all, you can’t pour from an empty cup.
Working from home and living at work are two entirely separate things - At the start of 2020 there was an abundance of tips about productive workspaces, setting routines, engaging in your normal ready-for-work activities, setting aside time each day to step away from work…. As someone who has had the luxury of a few work-from-home days in the past that yielded astounding levels of productivity, I was initially optimistic about the opportunities a few onths of working from home presented. It was only a few weeks into what would turn out to be a year long work-from-home order, before I realised how sorely mistaken I was. This was not the quiet, focused time I had enjoyed pre-pandemic, but clouded, overcast and gloomy time spent doom-scrolling, feeling unengaged and unenthusiastic about the prospect of another day spent alone in my home-office. It was a few months in that I came across the phrase living at work, and it struck home how insidiously this transition had happened. Despite having a separate work space, work never really left my home space in the way that I could leave the work office, and I came to realise how important the role of our choice is in this regard.
Variety is the spice of life - Ok, I know this one is a little cliché. And yet, if you’d asked me a year ago I would have adamantly told you that I am a person who is fond of organisation, planning and routines. From breakfast meals to shampoo brands to pens to friends - I am a creature of habit. I know what I like, and I surround myself with it. I structure my time. I plan and organise weeks, months, years in advance and I work toward goals with almost singular focus. And yet, this year almost every single one of those things was thrown completely out the window. It was impossible to plan a week in advance (or even a day sometimes). I found myself missing those spontaneous interruptions to my calendar or walks for coffee with random colleagues during the day. I missed the variety of faces on the tram each morning, and instead sought out variety in walking routes to new cafes for lunch as a poor surrogate. Most vividly I missed the usual spontaneity of a week in bench research science. Normally, each day is subtly different - a different experiment, or technique, this meeting versus that meeting, a new piece of code to work on or a new manuscript to write. Instead of this variety, life became a blur of zoom meetings, trudging forward on a single manuscript, and trying desperately to halt my doom-scrolling as we awaited daily case numbers and press conferences. I will never again take for granted the motivation a varied work day brings to my passion for science.

Goals

As with much about 2020, my goals unfortunately went promptly out the window around June. Even still, I finally submitted the first of three first-author postdoctoral research papers, and successfully created a growing community of Happy Hacker scientists who are learning to code. I started semi-regular yoga and implemented a new morning routine focused on engaging mindfully with the day ahead. While my writing here lagged severely, those posts I managed to write and publish are some of those I am most proud of. None of these things went according to plan, and it certainly wasn’t a glamorous insta-worthy road to ticking boxes. And yet, here we are, moving forward ever so slightly. So where to from here?

Papers are paramount. Déjà vu aside, with drafts still floating around in various states of disarray the first half of 2021 demands some serious focus on wrapping up the next two manuscripts. Using structured writing time of at least twenty hours a week, my goal is to have submitted the remaining two manuscripts before starting my next postdoctoral position mid-year. While last year writing sessions were often sidetracked by more ‘pressing’ needs, this year I will plan each session in advance, using calendar entries for accountability and a master task list for assigning goals and tracking progress.
Revamp the reading routine. Last year I hinted at a timely review of how I consume scientific literature. I’ve often pushed reading to the end of my to-do list and settled for skimming daily email alerts or saving an article or two from Twitter with some handwavy expectation of actually reading them. Instead, I want to not only find time for an engaged reading practice but also give myself space to really think about what I am reading, parlaying this into more (and better!) scientific insights. I will implement two reading sessions per week, drawing pre-selected articles from my ever-growing pile of exciting new material. This will be tracked using a database, which simultaneously enables detailed cross-connection between individual resources and developing insights and ideas within overarching project themes.
Commit to coding cleanup. One of the few positives to come from a year of working from home, coupled with a freshly-submitted manuscript combing computational analyses of wet-lab experiments, was a rapid expansion and solidification of my amateur coding skills. I am often pleasantly surprised when I realise just how far these skills have developed, and it makes me even more excited to pass them on during Hacky Hours each week. And yet, two packages I first wrote more than four years ago still languish, lacking love and in desperate need of refactoring. This is the year I commit to cleaning up these packages. I will spend an hour each week tackling small chucks, which will be tracked using GitHub issues and measured in milestones.
Invest in intentional. Sometimes a week can pass by and I barely realise due to a blur of endless triaging. These type of weeks tend to feel like an old-school cartoon where my wheels are spinning yet the car is going nowhere fast. My goal is to understand (and correct) my balance between the urgent but unimportant tasks that often fill my day (hellloooo email, I’m looking at you…), and the essential but non-urgent tasks that will be of most tangible benefit long term. Beyond task management, I will start each morning by writing down three intentions for the day, using these to anchor how my time is spent and as a record for reflection. I will also frame these intentions within the time management matrix, to ensure I am investing in long term progress by hitting small milestones each and every day.

2020 was without a doubt challenging and confronting and, just between you and I, 2021 was not looking to be off to a great start. After handing over my role in Melbourne and leaping out of my comfort zone, I landed in limbo - awaiting a revised start date for my international Fellowship, unemployed and uncertain of my direction for the first time in over a decade. And yet, here I am daring the universe by setting goals for the year ahead. From here, 2021 is about regrouping, recovering and recalibrating, readying for reentry to the world post-COVID. And I couldn’t be happier to have you along for the ride.

Image credits: @brookelark via

Learning to code: it's as easy and as complex as that.

Sun, 05 Jul 2020 15:12:56 +0000

Learning to code: it’s as easy and as complex as that.

Many life scientists have used their time under pandemic-induced lockdown to learn their first programming language. Yay! Coding has many many advantages (reproducibility, more complex analyses, reusability, time-saving) that I have espoused all too many times before.

Many people start with a tutorial or two, then jump straight in and analyse a dataset. They get a plot, maybe a few statistics and voila! They are now scientists who can code.

Kinda.

See, the thing is there is more (much more) to implementing programmatic workflows in a biological context. Unfortunately, these are the skills that intro-to-programming courses often fail to teach you (or sometimes even mention) - but without them, adding scripts to your workflow can often make your work less reproducible, not more. For the sake of the argument, lets pick one.

Version control.

Imagine a bowl of spaghetti (lots of lines of code), which you admire briefly before throwing at a canvas (your interpreter). You create a beautiful work of art (your plot), and stand back to admire your handiwork. Maybe you show it to a few friends, and they are super impressed. (Awesome!). And then they ask - how did you do it? Not just the throwing motion, or the rough distance between the bowl and the canvas. They want to know the precise location of every single strand of spaghetti in the bowl before you threw it at the canvas. They want to know the recipe you used for the sauce, down to the precise number of grams of oregano.

Now, of course, we aren’t actually talking about a bowl of spaghetti - we are talking about your code. So - of course - you can simply show them the script! Huzzah! The precise instructions that enabled you to make that very specific plot. But here’s the kicker. The code is not static. In fact, chances are that you poured over it for hours (maybe days) adjusting, tweaking, changing, testing and rerunning - all to get the glorious, awe-inspiring plot at the end.

By this stage, you’ve probably made over 100 spaghetti-splattered-spectacles (plots) and your house is starting to smell like an Italian Pizza joint. If I asked you to produce the exact recipe, down to the very position of each strand of spaghetti, for plot number 47 - could you do it?

My guess is probably no.

Conducting experiments is at the heart of science. However, without the essential extracurricular activities like maintaining backups, organising your results files and optimising project management systems, you wouldn’t last very long in academic research. The same is true of coding. Learning to write a functioning script is just the tip of the iceberg when it comes to implementing reproducible computing workflows in biology.

So, with this in mind, what are those all important skills you ask? Well, luckily, far more experienced scholars than I have written on this topic and provided guides (like and ) for those starting out in the computational space. These are highly applicable to biologists learning to code, and I encourage you to check them out before you stray too far down the spaghetti-on-the-wall path (like I did). As with any system, it is easiest to implement new routines before you have become to set in the old ones! At the very least, here are a few things to consider:

, including Github/GitLab/BitBucket
, including efficient folder layouts
and docker containers
practices
, including repositories and citing software you use

For more, make sure you check out the resources below.

Oh, and one last thing.

Unfortunately, this type of organisational work is not typically measured as a key performance outcome for biologists. Your number of git repositories or test coverage for an analysis suite is unlikely to come up in an award nomination or promotion application. And yet, it is entirely crucial as we move toward bigger and more complicated data and analyses - and so I encourage you to take the time to learn anyway. Maybe one day it will be recognised as essential work by the powers that be - but until then, at the very least, it remains essential for anyone wanting to do good reproducible science. And who doesn’t want that?

Final thoughts

So you want to learn to code? Yes - do it, 100%. I honestly couldn’t recommend or encourage it more. But please do so mindfully. If you want to have the best possible chance of integrating this wonderful tool into your scientific ecosystem in the long-term, you have to lay solid foundations and develop sustainable practice/methods.

Have you used any of these techniques as a budding bench-to-bytes biologist? Find me on or head over to the to tell me more!

Resources:

Image credits: Tomwsulcer via & olamishchenko via

A year in review: 2018 edition

Tue, 15 Jan 2019 09:52:30 +0000

The last few weeks have seen a flood of people posting their 2018 achievements, promoting the academic currency of papers published, grants won, students mentored and conferences attended.

Without taking away from these achievements, I wanted to focus on viewing myself as more than my work, and especially more than the ‘publish or perish’-driven manuscript list. And so, here lives my reflection on the year that was. Lessons remain a crucial part; after all,

“If a man looks at the world when he is 50 the same way he looked at it when he was 20 and it hasn’t changed, then he has wasted 30 years of his life,”

Muhamed Ali

Of course, I would be remiss not to celebrate the high points - but I have tried to temper the ‘gloating’ with a few honest low points. Finally, I take a look to the future. By defining goals which will drive my personal and professional life in 2019, I hope to kick off a fulfilling and smooth-sailing year with the course charted and the wind in my sails.

Wins

A snapshot of the high points

I received my first personal scientific project funding through an Early-Career Researcher Grant
I had four papers published, including the last of my PhD research, and landed travel funds for an international conference
I was priviledged to give too many conference presentations to count (Lornes, ABS-ABA, Winter School..)
I developed and grew this page, with 20 blog posts including tools, conference reviews, book reviews and scicomm
I produced hundreds (maybe thousands?) of lines of brand new code - but more importantly, saw a significant improvement in my ability and confidence when programming which has allowed me to assist others
I attended my first PyLadies meetup, where I met people like me (in science, learning python independently) and some less like me (employed full time in programming or data analysis positions)
I developed closer relationships with family and friends, as I worked harder to maintain and build these ties
I read two more books than last year
I consistently, regularly exercised, losing 15 kilograms
I hit a saving milestone and we bought a house

Losses

A snapier shot of the low points

I worked for two months on experiments that were to resuscitate one of my major projects
I’m now left with no papers in the pipeline, leaving lots for the year ahead to wrap up these projects
My coding projects are in somewhat of a state of disarray, in desperate need of a tidy and some documentation
I only read 2 books, and put 8 kilograms back on
I spent more than 50 hours writing six grants, all of which were unsuccessful
I was quick to judge others and less approachable than I would like to be, letting my stress seep to the outside
We unbought a hous

Lessons

The bits I wish I knew at the start of 2018, but had to learn the hard way

Have the hard conversations - with your boss, your partner, yourself
Self-care is about what you need - not what everyone else’s definition of rest and relaxation tells them (and they, therefore, tell you) you should be doing
“There are less qualified people than you doing what you want to do, just because they decided to believe in themselves. Period.”
Make a positivity folder and actively collect the warm fuzzy moments: emails, photos, messages, compliments, congratulations…
If you want to do something, really want to, then make time. Do it. No one else is going to do it for you, and your schedule will not magically clear. Life is never going to get less hectic or stressful.
Every day, hour, minute you spend wishing your way to the next thing (job, house, friend, partner) you will equally spend wishing you had taken the time to value what you had, to revel in it.
Prioritise, prioritise, prioritise

Goals

Hopefully to help me meander with purpose through 2019

It might be a little meta, but a big goal of mine this year is to learn to set SMART goals. Not so much “new years resolutions” - but personal and professional goals that I would like to work towards every day.
If you’ve never heard of the SMART goal concept, you can find a more detailed description , but in a nutshell SMART goals are:
- S - specific, significant, stretching
- M - measurable, meaningful, motivational
- A - agreed upon, attainable, achievable, acceptable, action-oriented
- R - realistic, relevant, reasonable, rewarding, results-oriented
- T - time-based, time-bound, timely, tangible, trackable
With this in mind, I have the following goals for 2019:
- Yoga at least two days in a fortnite during 2019. A flexible body -> flexible mind -> clarity of ideas, increased alertness and engagement with the task at hand. I would like to be able to better calm my mind when distraction threatens. I will track this goal via a calendar which records each session.
- Land the next job - be strong enough to throw myself into the applications and let go of the guilt of not chasing (limited) Australian funds. This will be measured via my application for at least 3 more Fellowship programs.
- Attitude adjustment - I will track this goal via weekly mini-reflections, where I will focus on (1) Learning to take control of what is within my reach, and to more rapidly accept that which is outside my control and move on, (2) Doing one self-positive task per day - learning, physical activity, kindness, and (3) Fostering self belief to replace self doubt, in personal relationships, professional settings and long-term career prospects
- Prioritise, prioritise, prioritise!

And with that, it’s time to say sayonara 2018 - bring on 2019.

May science be kind to you!

Image credit: @brookelark via

Toolbox talk: Trello

Thu, 30 Aug 2018 12:34:06 +0000

As an early-career researcher, I am still figuring out the best way to get stuff done. Every day it seems like my to-do list gets longer and longer, for every item I tick off two more take its place and I have no doubt it will only get worse. I am all about finding the best, most efficient and connected technologies to help alleviate some unnecessary legwork. After my first , I have decided to write more on the programs, apps and integrations that I use every day starting with one of the newest additions: Trello!

The basics: What the Tr-hell-o is all the fuss about??

Trello is fundamentally a project management application with a simple but sophisticated hierarchical interface consisting of boards, lists and cards. Trello thrives in settings suited to organisation. In the context of Trello, kanban is most often laid out as three stages (lists) - to-do, doing, done - and each element (or card) of a project (board) is represented within a list according to its state of completion. Elements progress through each list, giving a simple, visual overview of the project’s overall state.

This style works well when you work alone on individual projects - but it is also something you could easily accomplish with a chalkboard and some post-it notes. Where Trello really comes into its own is the ability to share and collaborate, such that individual tasks can be assigned to different people, comments can be added to cards specific for that task, and everyone can know at a glance the current big picture.

Trello is free (for the basic version, which is all I have needed thus far!), and accessible via the web interface, PC and iOS apps. It also integrates with all manner of other productivity apps, including GoogleDrive, GitHub, Dropbox, Slack, Evernote, OneDrive… Together, these features enrich the functionality of boards, providing a kind of dashboard from which to tackle projects and giving unparalleled flexibility for teams with diverse computing and file storage preferences.

Trello in action: managing your research projects

First things first: keeping track of experiments. There are many many electronic lab notebooks currently on the market, and I have tried more than my fair share. If you are not stuck in your ways (like I am) I highly recommend shopping around and picking one that you can integrate into your work as soon as possible. Unfortunately, I am a control freak and I am yet to find one that fits seamlessly with my workflow, and so I have resorted to building my own system using Trello!

The basic elements include lists for Ideas, Planned experiments, Lab work in progress, Analysis in progress, Ready to writeup, and Complete. Each new experiment or idea gets a card, for which I quickly note the purpose, reagents to be used, techniques and instrument details, and any pertinent references in the description. I then link this card (using the GoogleDrive powerup) to the folder containing the full experimental plan, results, analysis and write-up. The card then gets moved across the columns (lists) as each stage of the experiment is completed. For similar types of experiments, I have a checklist that allows me to easily track specific small elements of the experiment (e.g. plating cells, collecting results etc). If I complete a particular action for the experiment, I will also note in the comments any details specifically about that action. These comments are date and time stamped, helping to keep track of my activity on a day-to-day basis.

Another awesome Trello feature is the ability to label cards with a customisable category, which appears as a coloured bar on the front of the card. I use this feature here to label experiments with which one of my (many) projects it is specifically associated with.

This brings me to my second board - my project board. This is a board with which I track all of the ongoing projects I am involved in. There are lists for my individual projects (think: first author work), students projects I am involved with, collaborators projects, and ideas to keep in mind. The cards on each of these lists refer to a specific project, which can then also link to another Trello board or card which contains information, ideas and important references specifically for that project. That’s right baby, it’s Trello-ception!

Along similar lines, I have a board for manuscripts which tracks each manuscript I am involved in (cards) as they progress from the first draft to submission to revision to (if I’m lucky!) acceptance. In this case, labels are assigned to indicate my author position, and whether my contribution is required to move the article to the next stage. Individual cards link to additional Trello boards for each manuscript (normally only those for which I am the first author) where I can store more detailed information and ideas, tasks etc in a kanban layout.

By starring the top-level boards for Projects, Manuscripts and my Virtual Lab Book (starring is an inbuilt Trello function that allows you to favourite boards to be displayed at the top of your home page) I can easily get an overview of current progress, then by clicking a specific project or manuscript card I am automatically linked to all the more specific information I might need when working on that project, article or experiment.

The bigger picture: managing your science

When I first started with Trello, the ability to modularly (and very visually) manage and monitor my projects was a great tool. Since then, I have expanded my use of Trello boards to include the peripherals necessary for managing life as an ECR. Things like how to prioritise your workload, manage your short-term and long-term goals and keep on top of your reading list all become easier using Trello. My most recent addition was a prioritisation board, based on the priorities list shared by Corey J. A. Bradshaw in his amazing book “The Effective Scientist” (stay tuned for a book review - I really cannot recommend this book highly enough!). In short, Bradshaw runs through an exemplary list of how to prioritise the many competing interests vying for the time of an academic to get the maximum bang-for-your-buck in terms of career returns. These include things like writing articles, doing experiments (duh), helping students and colleagues, social media and writing grants.

When I first filled in all of the elements of the board, I realised just how unbalanced I have been in allocating time to each of these aspects. It was a great way to put into perspective where I should be spending the majority of my time and revisiting this structured big-picture priority list once a fortnight has helped refocus my research output.

Resources

That’s enough from me for now - if I have convinced you to give Trello a go, there are a couple of handy links below. I have included template examples for each of the board types that I mentioned above: feel free to use, abuse, copy and manipulate them to fit your own workflow, I honestly believe one of the best assets of Trello is it’s customisability - so don’t be afraid to make it your own. Just be sure to let me know if you find it helpful!

Template boards:

Additional info (from those who’ve said it better than me!):

Happy organising!

Image credit: @sidneyperryphotography via @unsplash

My toolbox: 2018 Edition

Tue, 28 Nov 2017 10:27:50 +0000

After coming back from a wonderful conference, I feel refreshed. I heard a lot about the state of my field of research, the cutting edge ideas and the direction our research is taking. You can read more about it .

Of course this aspect of science is important - the research outcomes, equipment and techniques we use are all critical pieces of information that make up the substance of oral and poster presentations. However, this year’s conference brought with it a stark realisation. I feel there is a large part of the conversation that is missing that is equally as important.

In fact, I think it is the true essence of how it is that we do what we do.

How do we, on a daily basis, manage a varied and conflicting schedule with experimental, administration and personal demands? What are the tools and techniques the help us balance these elements with efficiency and efficacy, ensuring nothing falls through the cracks?

I guess in a sense what I am talking about is a best practice discussion for the practicalities of doing research. Not a one size fits all approach, but at least a discussion of how the tools I use are beneficial and what I think I could use or need more of. While this may not fit a conference panel, here is my current toolbox.

This one is definitely top of the list, one of the more recent additions but easily the most life changing. This is essentially my digital brain, the place where I collect, sort and store information. Everything from web clippings (using my handy integrated chrome extension), papers of interest, post ideas, project ideas, meeting notes to shopping lists - it all lives here. Completely synced across all my devices, and easily searchable. All of the major ’life’ aspects have a notebook folder (e.g. manuscripts I’m coauthoring) with notebooks for each element (e.g. “Paper Name #327”), and individual notes for each idea or aspect of that element (e.g. introduction ideas, responding to reviewers comments etc). I think of this as a virtual brain dump - so that as long as I remember a particular piece of information is in evernote, I know it will always be there when I need it.

My digital assistant. I use Calendar to manage meetings, equipment bookings and deadlines. In addition, the daily tasks feature keeps track of experiment steps or analysis projects. For me, this is one of the most crucial features, for a couple of reasons. First, tasks can be assigned to a specific day and live above that day in the calendar. This makes it easy to see what I need to do for the day, as well as what times I will have to play with. Second, I get to tick off completed tasks! I have found the most effective way to keep momentum is to break everything into small, manageable elements, so 8-10 specific tasks that give me a sense of accomplishment each time I tick off something. Finally (and most importantly) tasks are easily reassigned to other days using drag and drop. This means that it is so easy to be flexible, and doesn’t require tasks to be rewritten as with typical hand written to-do lists.

Drive at the moment is simply my backup storage place that provides some functionality when my hard drive is not plugged in. In some situtations it is really helpful to share documents and easily manage sharing permissions, although I dislike having to download and resync non-google files. I am still figuring out how best to incorporate this into my workflow.

Basically a freeware version of adobe Illustrator, I use Inkscape for all figure preparation. This includes figures destined for manuscripts, posters, or presentations. But also just as a neat way to collate image data from experiments. I am yet to come across something that I have wanted to do with a figure that Inkscape can’t handle. There is a relatively steep learning curve, but for a piece of free software it is remarkably versatile. One thing I will note is that it does not play well with iOS (admittedly this is not from personal experience, but from colleagues who have had a tough time getting started), however windows works well.

& : As a self-taught python enthusiast, I am always looking for the best way to write, edit and run code to analyse my ever-growing data sets. This is my current configuration (although I have been through many others - Spyder, Jupyter, Sublime to name a few) and I am happy with the ease with which I can run scripts within atom, as well as manage my git commits with a few keyboard shortcuts. As someone relatively new to git version control, being able to see the folder layout and files which require an updated commit is incredibly helpful. Also, the ability to test, then tweak my code using attached iPython kernels within the editor is a great time saver.

Until very recently, I was an EndNote purist. I was first given access during my Undergraduate degree, and it did a wonderful job at managing my bibliography compared to the manual method. So I amassed a reference library, despite many issues leaving me disgruntled, and established a pipleline that included downloading the referencing file, downloading and saving the pdf separately, and then linking the two together using EndNote. To find articles, I would search in EndNote then locate the pdf and open it to view my notes and highlighted sections. If I lost you there - apologies - but it goes to illustrate my point: long and tedious. I have recently rediscovered Mendeley, and in terms of accessibility to my articles and notes, and ease of import, Mendeley beats EndNote hands down: click the Mendeley extension in my browser (or drag and drop to import a pdf), add notes/highlight and that’s it. All managed and searchable within a single program, again synced across all my devices. There are still a few kinks to work out (sometimes the imported reference information is a little clunky) but overall much more functional.

I have recently come across the idea of ‘story-boarding’ an article during the initial planning and write-up phases. Coming into a new lab, my writing style was at odds with my new boss and needed a little TLC - I am great at the technical reporting language but struggle to tell a narrative. The basic idea behind story-boarding is to layout the elements of a manuscript as discrete chunks and move them around like puzzle pieces to get the flow right. This also helps to identify holes - more experiments or more detailed analysis etc. I am using Trello as a way to trial this concept - each manuscript gets a ‘board’, the lists correspond to ‘Intro’, ‘Methods’, etc. and cards are tiny chunks - text prompts for the intro, individual figures or panels for the results. While this is the newest addition to my workflow, and firmly still in the trial phases, I am pleased with the outcomes so far. It has encouraged me to think about what papers I am working towards (helping to focus my research), as well as getting me thinking about the story to go with it.

So there you have it - my toolbox. It’s worthwhile noting that many of these I adopted from watching/hearing how someone else achieves a particular goal and making it work for me. I hope you find something new and useful, or maybe you have some ideas for something better? Feel free to let me know in the comments - I’d love to learn from you!