data science, dynamic simulation modelling, genomics, interactive visualisation, dashboards, image & video analysis

e: cnr.lwlss@gmail.com

t: @cnrlwlss

What proportion of fibres can we dissect from a section before it starts to disintegrate? Mitochondria are the parts of our cells that are responsible for generating energy. In the Wellcome Centre for Mitochondrial Research, we try to understand ways in which the function of mitochondria deteriorates in individual cells during the progression of mitochondrial diseases. There is a good introduction to mitochondrial biology and mitochondrial diseases in this blog post by Max Piotrowicz. ... Read more

I recently bought a copy of the latest edition of Darren Wilkinson’s book: Stochastic Modelling for Systems Biology because I’m interested to see what he has to say about Approximate Bayesian Computation (ABC). Browsing through, I am reminded of the very useful example in Chapter 11: Inference for stochastic kinetic Models, which describes a likelihood-free method for Bayesian inference of dynamic simulation model parameters. This approach involves using a bootstrap particle filter for marginal likelihood estimation. ... Read more

Autoregression models are a type of stochastic, dynamic process. They are a mathematical representation of some value that varies with time, where the variation includes a random, unpredictable component. Using a computer to generate (pseudo-)random numbers, we can generate a set of simulated values across time that are consistent with this kind of model. Stochastic simulations aim to capture the random component in the process and so are usually different every time they’re run. ... Read more

Recently, I have been analysing some functional genomics and drug screen datasets. The techniques I use are similar to those I developed while working on and using a method called Quantitative Fitness Analysis (QFA) (Addinall et al. (2011), Lawless et al. (2010)). QFA is a method for screening the health of up to tens of thousands of microbial cell populations (examples in picture above). It is typically used to search for genes interacting with a gene of particular interest. ... Read more

If you live anywhere away from the equator, you’ll be familiar with the fact that days are short in winter and long in the summer. There’s even a slight effect at the equator, but the farther away from the equator (e.g. the farther north you live in Europe) the more extreme this effect is. At the poles, there is a period in the summertime when the sun never sets, and similarly in winter, there is a period when the sun never rises. ... Read more