Goodbye glados

Setting up my own computing cluster with a batch queuing system and then using it run large numbers of molecular dynamics simulations was one of

BashtheBug podcast

BashTheBug is a Zooniverse citizen science project I setup in April 2018 to help the large CRyPTIC tuberculosis (TB) consortium analyse the thousands of TB samples

Successful NIHR grant

Last year I coordinated a bid to the NIHR for capital to improve our research capacity to study antimicrobial resistance (AMR) at the Oxford Biomedical

Read Ellen’s Azure post

As I’ve described here, here and here, I ran a Hackathon instead of the more traditional project in the third week of the Bioinformatics module

New Publication: Predicting whether mutations confer resistance to an antibiotic

Due to the rise of antibiotic resistance, it is increasingly important that your clinician knows which antibiotics will work (and which will not). Traditionally, this is done in hospital microbiology labs by growing a sample taken from the infection site, and then testing how a range of antibiotics affect its

Automated detection of bacterial growth on 96-well plates (AMyGDA)

I am involved in an international collaboration, the Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC), that is collecting 30-50,000 clinical samples from patients with tuberculosis (TB). Although often viewed as a historical disease, TB kills more people globally than any other infectious disease, with 1.7 million people dying from

Azure. Can I break it? Yes you can.

In this post, I’ll spell out some of the problems we encountered using Microsoft Azure to run a 3-week course for about 30 postgraduates in

New Publication: Protein crowding affects the organisation of ion channels

Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes It is difficult to look at the dynamic spatial organisation of ion channels in cell membranes, but this is something coarse-grained molecular dynamics simulations can offer insights. This work, led by Anna Duncan, shows how

Azure, Hackathons and PhD students: Feedback

This is the second year that I have organised a three-week course on Bioinformatics from PhD students in their first year of the Oxford Interdisciplinary Biosciences programme. As last year, I run the third week as a Hackathon and in preparation the students had to choose a scientific paper in

A way of using Azure in computer-based practicals

Last year I took over coordinating a three-week Bioinformatics module for the Interdisciplinary Bioscience Doctoral Training Centre in Oxford. Much of the course is taken up with computational practicals which we usually run on the low-spec desktop PCs that they have in the DTC. This year though we have been

2018 PhD projects announced

As described here, one of the main ways of getting funding to studying for a DPhil with me is to apply for an NDM Prize

BashTheBug has won an NIHR Let’s Get Digital Award!

The National Institute for Health Research hold an annual competition, called Let’s Get Digital, to “recognise those people involved in NIHR research using video, photography, websites, infographics and online communities to promote research”. I was encouraged to enter BashTheBug back in June 2017 and was pleased to see in August