So… I’m a University Research Lecturer

Very pleased to hear I’ve been conferred the title of Senior Research Lecturer here at Oxford. Applied five years ago and didn’t get it, so

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

Women in Computer Science Day

Last week I ran a small stall at the annual Women in Computer Science day run by the Department of Computer Science at the University

Twitter at #ECCMID

A bit over two years ago I was a guest blogger at the US Biophysical Society Annual Meeting in Baltimore. I was disappointed by the

Diagnosing antibiotic resistance: future trends?

It is Sunday, I’m in Vienna at the European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) congress. As is traditional at all large conventions,

BashTheBug.net Zooniverse Citizen Science project launches today!

My citizen science project, BashTheBug, is launched today. Head over to the website or go straight to the Zooniverse project page and help us start

BashTheBug.net Beta Testing Results

Zooniverse have finished beta-testing my BashTheBug citizen science project. To verify that the task is easy to do and the tutorial and help text understandable, the first version of the project was sent to a number of experienced Zooniverse beta-testers. Over a period of two weeks, 672 volunteers made 34,791

BashTheBug at the Science Museum

A group of us from Modernising Medical Microbiology went to the Science Museum in London to take part in one of their “Lates” events. I

Accelerating Oxford Nanopore basecalling

It looks innocuous sitting on the desk, an Oxford Nanopore MinION, but it can produce a huge data of data from a single sequencing run.

New Publication: Effect of SAO mutation on Band 3

There is a lovely story behind this paper just published earlier this week in Biochemistry. Reinhart Reithmeier came to visit Mark Sansom in Oxford whilst on sabbatical back in 2002. Now Reinhart, if you don’t know, is a world-expert on Band 3 which is the transmembrane protein in the membrane

Software Carpentry Workshop, Oxford, 9-10 January 2017

Earlier this week I instructed the first Software Carpentry workshop run by the Reproducible Research Oxford project. This is a one-year project supported by the

DTC Bioinformatics Module – Hackathon!

Last month I organised the Bioinformatics Module for the Oxford Interdisciplinary Bioscience Doctoral Training Partnership – this immediately followed the DTC Programming Module, which I also taught part of. This was the first year I’ve organised this three-week module and was fortunate that we had five teams of lecturers from

DTC Programming Module – Feedback

Last month I finished lecturing part of the Programming Course that all the Doctoral Training Centre DPhil students do at the start of their first year. It is the first time I’ve helped teach the course so I thought I’d record some of the feedback I collected here. Overall the

2017 PhD projects advertised

If you are interested in helping combat antibiotic resistance and want to work on an interdisciplinary computational project with the possibility of strong public engagement (through bashthebug.net), please check out this project Antibiotic resistance in Tuberculosis: Predicting de novo the effect of individual genetic mutations. Supervised by me and Sarah

bashthebug.net alpha launch

I’m planning to launch a citizen science project, bashthebug.net, in 2017 which has two distinct ways anyone can help combat antibiotic resistance. I’ve revamped and relaunched what will ultimately become the public-facing project website – please have a look. The first strand is closer to the light of day and

New Publication: Lipids can form anti-registered phases

When we think of lipids phase separating in a cell membrane we usually think of this process occurring symmetrically, i.e. with like on top of

New Publication: Proteins Alter the Stiffness of Membranes

Although there have been many studies of proteins whose primary function is to ‘sculpt’ the surface of membranes e.g. BAR domains, there have been very

New Publication: Membrane Compartmentalization Reduces the Mobility of Lipids.

Lipids are not free to diffuse around the cell membrane. Rather they are constrained not just by all the embedded proteins but also by the

Cheltenham Science Festival

A bit over a week ago I helped run the Modernising Medical Microbiology stall at the Cheltenham Science Festival. This was my first time helping

GROMACS in DOCKER: First Steps

DOCKER is cool. But what is it? From the DOCKER webpage Docker containers wrap up a piece of software in a complete filesystem that contains

Setting up a GROMACS cluster

Recently I’ve moved to the John Radcliffe hospital and my old lab kindly let me have some old servers that were switched off. This pushed me to learn how to setup them up as a compute cluster with a scheduler for running GROMACS jobs. I’ve wanted to learn this for

How to setup a Gramble

This is a Gramble, which of course is short for a GROMACS Bramble, or, in other words, a Raspberry Pi 2 model B cluster running GROMACS. Given the ARM processor in a Raspberry Pi 2 does not allow SIMD instructions like the more complex (and expensive) Intel chips, why would

I’ve moved…

Today is my first day as a Senior Researcher in Modernising Medical Microbiology in the Nuffield Department of Medicine at the University of Oxford. Practically I’ll be based at the John Radcliffe Hospital in Oxford. I was a Postdoctoral Researcher in the SBCB Unit at the Department of Biochemistry for

New Publication: Predicting affinities for peptide transporters

PepT1 is a nutrient transporter found in the cells that line your small intestine. It is not only responsible for the uptake of di- and tai-peptides, and therefore much of your dietary proteins, but also the uptake of most β-lactam antibiotics. This serendipity ensures that we can take (many of)

GROMACS on AWS: compiling against CUDA

If you want to compile GROMACS to run on a GPU Amazon Web Services EC2 instance, please first read these instructions on how to compile

GROMACS on AWS: compiling GCC

These are some quick instructions on how to build a more recent version of GCC than is provided by the devel-tools package on the Cent

GROMACS on AWS: Performance and Cost

So we have created an Amazon Machine Image (AMI) with GROMACS installed. In this post I will examine the sort of single core performance you

GROMACS on AWS

In this post I’m going to show how I created an Amazon Machine Instance with GROMACS 5.0.7 installed for use in the Amazon Web Services cloud. I’m going to assume that you have signed up for Amazon Web Services (AWS), created an Identity and Access Management (IAM) user (each AWS

Dr Firdaus Samsudin

Congratulations to Firdaus Samsudin who successfully defended his DPhil thesis on Tuesday 10 November 2015. His thesis is titled “Improving Oral Drug Delivery: Computational Studies

New Publication: The Extra-Cellular Domain of PepT1 and PepT2

PepT1 is a nutrient transporter found in the cells that line your small intestine. It is not only responsible for the uptake of di- and tai-peptides, and therefore much of your dietary proteins, but also the uptake of most β-lactam antibiotics. This serendipity ensures that we can take (many of)

Analysing Simulation Data CECAM Workshop, Jülich, 14-15 October 2015

This two day workshop on Analysing Simulation Data was part of the larger CECAM Macromolecular Simulation Software Workshop at the Forschnungzentrum, Jülich that I co-organised. It was the second workshop and immediately followed an introductory Software Carpentry workshop. Prior to a few years ago I analysed all my simulation data

Software Carpentry Workshop, Jülich, 12-13 October 2015

Last week, myself and David Dotson from ASU, ran a 2 day Software Carpentry workshop to kick off the CECAM Macromolecular Simulation Software Workshop at the Forschnungzentrum, Jülich. The idea was to give participants who were less well versed in python and working collaboratively with e.g. git a crash course

CECAM Macromolecular simulation software workshop

I’m co-organiser of this slightly-different CECAM workshop in October 2015 at the Forschungszentrum Jülich, Germany. Rather than following the traditional format of 3-4 day populated by talks with the odd poster session, this is an extended workshop made up of six mini-workshops. Since it is focussed on python-based tools for biomolecular simulations, of which there

Running GROMACS on an AMD GPU using OpenCL

I first used an Apple Mac when I was eight. Apart from a brief period in the 1990s when I had a PC laptop I’ve

New Publication: Alchembed

In much of my research I’ve looked at how proteins embedded in cell membranes behave. An important part in any simulation of a membrane protein is, obviously, putting it into a model membrane, often a square patch of several hundred lipid molecules. This is surprisingly difficult: although a slew of methods

Is Software a Method?

Last month I went to the Annual Meeting of the US Biophysical Society. As a Software Sustainability Institute fellow I was interested not only in my

Lectures, Clickers and Quizzes

It’s 9.40am. You are sitting in a nice warm lecture theatre. There are no windows. The lecturer is talking, their slides projected onto a big

New publication: Nothing to Sneeze At – A Dynamic and Integrative Computational Model of an Influenza A Virion

In this paper we show how we built and then simulated a model of the influenza A virion. Rather than model every atom of every lipid, a “coarse-grained” representation (MARTINI) is instead used which replaces roughly every four atoms by a single coarse-grained bead. Microsecond simulations then start to give