Categories
computing skills software carpentry teaching

Software Carpentry Workshop

Last week on Thursday and Friday I helped run a Software Carpentry workshop in the Department of Experimental Psychology at the University of Oxford.

Categories
antimicrobial resistance computing tuberculosis

New software: gemucator

Short for “Genbank Mutation Locator”. A simple Python3 package that if you pass it a mutation it will give you the location in the specified genbank file. > gemucator-run.py –mutation rpoB_S450L rpoB_S450L: 761153 t 761154 c 761155 g (H37rV.gbk for M. tuberculosis is loaded by default). Or you can go the other way > gemucator-run.py –location […]

Categories
antimicrobial resistance computing

New software: pygsi

Whenever a paper involving sequencing the genome of bacteria (or other species for that matter), the researcher is obliged to deposit the (usually short reads) in either the European Nucleotide Archive (ENA) and the Short Read Archive (SRA) along with some metadata. Sounds good, but there has been a flaw until recently; whilst one could […]

Categories
computing

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 the more satisfying things I have done professionally. The compute nodes were Apple Xserves from 2008 and 2009. Myself and Ben Hall won the first seven of these nodes from […]

Categories
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 […]

Categories
antimicrobial resistance molecular dynamics publication research

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 growth, or, ideally, kill it. […]

Categories
citizen science clinical microbiology computing research tuberculosis

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 it in 2016. The ultimate […]

Categories
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 […]

Categories
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 […]

Categories
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 […]