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antimicrobial resistance clinical microbiology computing distributed computing grants

GPAS

I’ve been working on this for the last few months and very happy that we can now share our plans. Through a very generous donation by ORACLE, a group of researchers led by ModMedMicro at Oxford, are developing a cloud-based clinical microbiology genetics processing service, called the Global Pathogen Analysis System (GPAS). GPAS is still […]

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antimicrobial resistance computing distributed computing GPUs molecular dynamics publication research

New publication: how quickly can be calculate the effect of a mutation on an antibiotic?

The idea for this paper arose during talking over coffee at the BioExcel Alchemical Free Energy workshop in May 2019. We’d previously shown that alchemical free energy methods could successfully predict which mutations in S. aureus DHFR  confer resistance to trimethoprim (and crucially, which do not). That is all well and good, but to do […]

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distributed computing teaching

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 course for around 30 students from the University of Oxford Interdisciplinary Biosciences programme in November 2017. One of the students, Ellen Pasternack, wrote a guest blog post for Microsoft which […]

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distributed computing teaching

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 a typical “computer lab”. As you’ll see, a group of cloud-naive highly intelligent postgraduates are capable of breaking nearly anything and, perhaps, might constitute the perfect resilience test for your […]

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distributed computing teaching

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 the first week, form teams […]

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distributed computing teaching

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 fortunate to receive a grant […]

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antimicrobial resistance clinical microbiology computing distributed computing GPUs

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. Since the nanowire works by inferring which base is in the pore by how much it reduces the flow of ions (and hence current) through the pore, the raw data […]

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citizen science computing distributed computing

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 will help the international Tuberculosis […]

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distributed computing molecular dynamics

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 everything it needs to run: code, runtime, system tools, system libraries – anything you can install on a server. This guarantees that it will always run the same, regardless of […]

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computing distributed computing GPUs molecular dynamics

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 an AMI without CUDA. These instructions then explain how to install the CUDA toolkit and compile GROMACS against it. The first few steps are loosely based on these […]