A day in the life (2018)

Today is Sunday, 20 May 2018.

I am an Edinburgh-Zhejiang lecturer at the University of Edinburgh (UK).

This is a day in my life.

4:00 am – I am woken up by birdsong outside my window. There is one particular bird whose song is very lovely.

Very lovely. Also, very loud. And very early in the morning. Stupid bird, I think, and fall back asleep.

9:30 am – I do get up and have a long and lazy breakfast

10:30 am – I usually avoid working on a Sunday because weekends are important, but I have two presentations to prepare for tomorrow.

The first presentation is for our departmental seminar tomorrow, It’s about building a framework that allows experimentalists and computational modellers to share data and information and construct and update models together. This is a collaboration with  Nisha Viswan, Gubbi HarshaRani and Upinder Bhalla at NCBS in Bangalore

Here is a simple workflow that illustrates what we want to do:


Our long-term aim is to use this framework for the collaborative development of models that would help us understand the molecular changes in the brain associated with some intellectual disabilities and autism spectrum disorders. (If you are interested in this topic area, check out the work done here in Edinburgh at the Patrick Wild Centre)

Noon – I have lunch.

1 pm – Back at work! This really isn’t a very good Sunday. (I blame the bird)

2:30 pm – Time for a run! I love going along the Union Canal, which goes all the way from Edinburgh to Glasgow (not that I’ve ever made it that far). It’s super lovely, and at this time of the year, the baby swans are out enjoying the sunshine.


5:00 pm – Back from my run, all stretched out and showered, I spend a bit of time on the phone and messaging with some of my favourite people.

6:00 pm – Dinner. As they say, “Eat pasta, run fasta”*

7:00 pm – And back again at my laptop. The first presentation is done, but I need to finish my second one, for the EMBL in the UK event tomorrow afternoon. Very much looking forward to this! I will be talking about our work on spatial stochastic modelling of molecules in the synapse. Here is a very short movie of a molecule called CaMKII diffusing around the postsynaptic neuron, and binding to NMDA receptors within the membrane.  This is based on simulations done by Susana Roman Garcia, as part of her Honours dissertation in our lab last year (using the MCell software). You can see the NMDA receptors are mostly clustered within an area called the post-synaptic density (PSD). In this video, unbound NMDA receptors are light green, and inactive CaMKII molecules are white. CaMKII can be activated by binding to another molecule called calmodulin (calmodulin-bound CaMKII shown in pink) or by phosphorylation (shown in purple). Active CaMKII can then bind to NMDA receptors (shown by colouring the NMDA receptor to whatever colour CaMKII it is bound to).

Anyway, I get carried away. The important thing is, this kind of simulation can help us understand the effect that spatial localisation has on the activity of some molecules, and this is important to understanding the dynamic regulations of synapses. Also, look! Pretty colours!


10:00 pm – In summary, not a great day for work-life balance. But a good day overall. I am going to turn in early, hoping that stupid bird doesn’t wake me again tomorrow. (And a little bit hoping it does – because I really like its song!)


*NOT a bioinformatics joke. What is wrong with you people?!






Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s