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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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antimicrobial resistance clinical microbiology publication

New publication: Differential occupational risks to healthcare workers from SARS-CoV- 2

Very pleased and proud to be included on this manuscript, which has been published in eLife (and is also  available as a preprint); the observations are drawn from the large and comprehensive SARS-CoV-2 testing programme run by Oxford University Hospitals NHS Trust. I helped develop the internal website used by staff to book appointments and […]

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antimicrobial resistance clinical microbiology publication research

New publication: Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli.

Clinical microbiology often assumes a sample is resistant or susceptible. Making such a classification relies on applying a threshold (usually called a cutoff) to quantitative data, such as minimum inhibitory concentrations (MICs). If the MICs are strongly bimodal, then this is trivial and reproducibility is guaranteed. If the MICs are unimodal, then one is left […]

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antimicrobial resistance clinical microbiology publication research tuberculosis

New publication: Phylogenetically informative mutations in genes implicated in antibiotic resistance in Mycobacterium tuberculosis complex

Although the population structure M. tuberculosis is clonal, one must be careful when inferring the effect of individual mutations on the effect of an antibiotic. Purely because a mutation appears to define a phylogeny does not mean it has no effect on the minimum inhibitory concentration. Read more here (Open Access).

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antimicrobial resistance clinical microbiology computing tuberculosis

AMyGDA now available from GitHub

AMyGDA is a python module that analyses photographs of 96-well plates and, by examining each well for bacterial growth, is able to read a series of minimum inhibitory concentrations for the antibiotics present on a plate. Previously it was only available to download from this website (due to licensing) if you gave your email address […]

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antimicrobial resistance clinical microbiology computing GPUs molecular dynamics publication research

New preprint: rapid prediction of AMR by free energy methods

The story behind this preprint goes back to the workshop on free energy methods run by BioExcel in Göttingen in May 2019. I gave a talk, based in part on the work I’d previously published showing how alchemical free energy methods are able to predict which mutations in S. aureus DHFR confer resistance to trimethoprim.

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antimicrobial resistance citizen science clinical microbiology

BashTheBug Coordinator post advertised

We are advertising for a Part-time Citizen Science Project Co-ordinator to come and work with us in Oxford improving BashTheBug, in particular how the project engages, informs and educates its existing base of volunteers, as well as reaching out to new audiences. The closing date is Monday 25 November 2019. For more information please see […]

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computing GPUs molecular dynamics

GROMACS2018 on NVIDIA DGX-1s

HECBioSim advertised for proposals to use JADE, the new Tier-2 UK GPU high performance computer back in April 2019. JADE is built around NVIDIA DGX-1s, each of which contains 8 Tesla V100 GPUs. I’d previously run some alchemical free energy calculations on ARCHER, the Tier-1 UK academic supercomputer that has a conventional architecture, thanks to […]

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antimicrobial resistance molecular dynamics publication

New publication: Predicting resistance is (not) futile

Our “First Reactions” article has been published in ACS Central Science. We discuss the paper, Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches, by Matteo Aldeghi, Vytautas Gapsys and Bert de Groot, which is in the same issue of the journal. Aldeghi et al. apply a series of methods to try and predict the effect […]

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tuberculosis

Numpy v Biopython

Having only recently having to write bioinformatics Python code that e.g. interrogate GenBank files to find out the sequence of specific genes I’ve learnt a bit of Biopython. I’ve always wondered why (and I could be wrong) the bioinformatics community doesn’t make more use of numpy? For example the Seq class in Biopython seems to be […]