News

2026

New paper: Validation of an optimized Oxford Nanopore sequencing workflow versus Illumina for mycobacteria from primary MGIT culture

24 August 2026

Most genetic sequencing of Mycobacteria, including Mycobacterium tuberculosis, has for historical reasons used short-read technology, often from Illumina. Whilst effective and economical, newer long-read technologies, as exemplified by Oxford Nanopore Technologies (ONT), confer several advantages… more

New preprint: using genetics to analyse ESBL infections in a neonatal ICU ward

7 July 2026

In this preprint, Melody Parker as part of her DPhil, has analysed a series of infections in a neonatal intensive care unit. At the time there was concern that this could be an outbreak; if so the ICU team would want to improve their infection control measures. Whole genome sequencing can give yo… more

Fourth Dx4LMICs conference

7 July 2026

This year marked a change for the conference as Professor Lord Tarassenko took a step back and I took over chairing the Organising Committee. Based on feedback from last year’s conference we introduced several interactive elements borrowed, shall we say, from Unconferences. more

ESM Annual Congress 2026

26 June 2026

Earlier this week the 46th Annual Congress of the European Society of Mycobacteriology was held in Verona, Italy. Around 210 scientists from over 40 countries attended and the University of Oxford, through the MMM Unit, was unusually well-represented with 11 of us travelling to Italy. more

Oxford Public & Community Engagement Conference

12 June 2026

As part of the “Enriching Engagement - funding, culture and institutional legacy” session at the Oxford Public & Community Engagement Conference on Thursday 11 June, Philip Fowler presented how the funding helped support BashTheBug, a citizen science project that run on The Zooniverse from 2017 t… more

NIHR PPI In Action Webinar on BashTheBug

1 June 2026

As part of the NIHR’s “PPI In Action” series, Philip Fowler gave a webinar on Friday 22 May 2026 entitled: more

New preprint: ONT sequencing is comparable to Illumina sequencing for M. tuberculosis

9 April 2026

In this preprint, we compare the differences when Mycobacterial samples are sequenced with either long- or short-read sequencing and show that long-read sequencing (as exemplified by Oxford Nanopore Technologies) is now comparable to short-read sequencing (e.g. Illumina). As we are focussed on cl… more

Congratulations Dr Adlard!

7 March 2026

Dylan successfully defended his DPhil on Friday 6 March, well done. From what he said his examiners, Professor Sam Sheppard and Associate Professor Louis Grandjean gave his work a thorough examination. As luck would have it we received the reviews from the last manuscript to come out of his thesi… more

New paper: predicting pyrazinamide using a graph convolutional network

3 March 2026

This paper is the start of us, as a group, using deep learning methods to predict antimicrobial resistance whilst taking into structural and chemical features. You can read a more detailed description in an earlier post and notably it is our first paper in a special issue for a while. Dylan Dissa… more

New paper: Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

9 February 2026

Zam Iqbal, at the University of Bath, led this epic study published today in Nature Methods where we assembled all SARS-CoV-2 genomes deposited in the European Nucleotide Archive before 2 March 2023. In total a staggering 4,395,655 samples were processed. Since SARS-CoV-2 was almost always sequen… more

New preprint: evaluating a laboratory workflow for sequencing Mycobacteria using long-read sequencing

7 February 2026

In this preprint, we describe and evaluate a laboratory workflow for sequencing Mycobacterial samples using long-read sequencing (as exemplified by Oxford Nanopore Technologies). A key part of this manuscript is the development of a lab protocol that combines rapid, semi-automated DNA extraction… more

Gr-ADI consortium announced

22 January 2026

Pleased and excited to be a small part of the Gram-Negative Antibiotic Discovery Innovator (Gr-ADI) consortium which was announced today. Gr-ADI is a join initiative between the Gates Foundation, Novo Nordisk Foundation, and Wellcome. Our project is headed by Dr Annette von Delft and you can read… more

2025

New paper: how well can we predict AMR in tuberculosis samples?

16 December 2025

This paper just published in Microbial Genomics examines how well our software tool, gnomonicus, predicts to which antibiotics a clinical sample that has been whole-genome sequenced is resistant. To do so, it implements the second edition of the WHO catalogue of resistance-associated mutations (W… more

Congratulations Dr Brunner!

10 December 2025

Viki successfully defended her DPhil thesis on Tuesday 9 December 2025 - well done! I always tell everyone they will enjoy the viva after half an hour or so and I hope she did. Her examiners were Professor Tim Walker and Associate Professor Conor Meehan. more

New preprint: Predicting pyrazinamide resistance in M. tuberculosis using a graph convolutional network

29 October 2025

In previous work we’ve used “traditional” machine-learning approaches, like XGBoost, to learn and therefore predict which mutations in PncA confer resistance to pyrazinamide, one of the four first-line antibiotics used to treat tuberculosis. A key limitation is that because the data are presented… more

New paper: Evaluating 12 WGS analysis pipelines for MBTC

21 October 2025

Ruan Spies did a careful systematic analysis of the publicly-available pipelines that claimed to process raw genetics files from M. tuberculosis complex samples, including the pipeline available via EIT’s GPAS which we have written. more

New paper: What can subpopulations tell us about rifampicin resistance?

14 October 2025

Last Thursday this work which we’d previously preprinted looking at looking at rifampicin-resistant subpopulations in clinical M. tuberculosis samples was published in JAC-Antimicrobial Resistance. If you want to know more please read the blog post we wrote when it was preprinted. A nice touch, h… more

New preprint: rapidly and reproducibly building resistant catalogues for M. tuberculosis

3 October 2025

The CRyPTIC project carried out many exciting research projects but it never quite got around to building a catalogue of resistance- and susceptible-associated genetic variants in M. tuberculosis, in part because near the end of the project we donated our entire dataset to the Seq&Treat project w… more

New paper: predicting rifampicin resistance via free energy simulation

23 September 2025

This work was carried out by Xibei Zhang, who is doing her PhD with Peter Coveney at UCL. It builds on earlier work I did using alchemical free energy methods to calculate whether individual mutations in the protein target of an antibiotic reduce how well the drug can bind, thereby conferring res… more

Third Dx4LMICs conference

3 July 2025

Most of us attended the third Diagnostics for Low- and Middle-Income Countries (Dx4LMICs) conference at Reuben College in Oxford over the last two days. I am a Fellow at Reuben College and helped our President, Professor Lord Lionel Tarassenko and several others, including Dylan Adlard, organise… more

I’m hiring!

26 June 2025

Thanks to funding from the OxCoD4TB project, I am hiring a postdoctoral research associate. This consortium pulls together expertise from all over the University, including in diagnostics, data science, drug and vaccine design, preclinical testing and clinical testing and brings it to bear on tub… more

CRyPTIC datasets available through new website

25 June 2025

The CRyPTIC project ran from 2016 to 2022 and collected \20,000 clinical samples from patients with tuberculosis. Each sample underwent whole genome sequencing and also was inoculated onto a 96-well plate containing 13 different antibiotics at a range of concentrations. We also collated some exis… more

ESM Annual Congress 2025

25 June 2025

Several of us attended the 45th Annual Congress of the European Society of Mycobacteriology in Lisbon, Portugal. This is probably my favourite scientific meeting -- small, friendly and with plenty of time to talk, including organised social events. more

New paper: automatically and reproducibly building a catalogue bedaquline resistance-associated variants

18 June 2025

Dylan Adlard’s paper describing how we can rapidly automatically build catalogues of bedaquiline resistance-associated variants using a tool he’s written, called catomatic has been published in Microbial Genomics. You can read a bit more about it here. more

New paper: a deep learning model that reads MICs from images of 96 well plates

26 May 2025

Our paper describing how a convolutional neural network model can determine the minimum inhibitory concentrations (MICs) from a photograph of the 96-well plate after two weeks incubation has been published in the Computational and Structural Biology Journal. You can get the model, which is called… more

New preprint: looking at rifampicin-resistant subpopulations in clinical samples

10 April 2025

Since clinical samples are usually grown in a MGIT tube for a while before some “crumbs” are harvested for DNA extraction, they are metagenomic in the sense that they can and do contain multiple colonies. This means we should expect subpopulations in our analysis but most bioinformatics tools and… more

New grant: Ox4TB

17 March 2025

Very pleased to announce that I am a co-investigator on the recently announced Oxford4TB project that has been funded by the Ineos Oxford Institute for antimicrobial research (IOI). The project will received £5 million over three years and the main aim is to develop new therapies for multi-drug r… more

Can medical microbiology become a big data science? Lessons from CRyPTIC

11 March 2025

The CRyPTIC project ran from 2017 to around 2022 and in that time collected over 20,000 clinical samples of M. tuberculosis. Each sample underwent whole genome sequencing and phenotypic drug susceptibility testing (pDST); the minimum inhibitory concentrations (MICs) of 13 different antibiotics wa… more

New preprint: a deep learning model that can read 96-well broth micro dilution plates

23 February 2025

The CRyPTIC project used bespoke 96-well broth microdilution plates to measure the minimum inhibitory concentrations (MICs) of 13 different antibiotics; to reduce the error in the measurements, photographs of each plate were taken after two weeks incubation and stored. Hence we have available ove… more

New preprint: automatically building a better bedaquiline catalogue

31 January 2025

A catalogue recording whether individual mutations confer resistance or not to specified antibiotics is a necessary component of genetics-based clinical microbiology. Such catalogues need to be not only accurate but also meet a number of minimum requirements if they are to be used widely. Dylan A… more

SARS-CoV-2 pipeline live on EIT Pathogena

28 January 2025

Back in the SARS-CoV-2 pandemic we worked closely with ORACLE Corp to build and deploy a bioinformatics pipeline in ORACLE Cloud that processes raw genetic files and infers what the consensus genome is and hence what lineage (e.g. BA.2) it belongs to. The heart of the pipeline is an amplicon-awar… more

Updated preprint: A validated cloud-based genomic platform for co-ordinated, expedient global analysis of SARS-CoV-2 genomic epidemiology

23 January 2025

In August 2022 seven laboratories across the world uploaded their SARS-CoV-2 genetics files for processing to an online cloud processing platform. Since then the pipeline that is run (the Tiled Amplicon Pipeline) has been updated and deployed in a new, more flexible cloud-based platform, EIT Path… more

Dylan Adlard is an SSI Fellow!

15 January 2025

Congratulations to Dylan Adlard for being appointed a Fellow with the Software Sustainability Institute for 2025! This Fellowship programme not only encourages good research software engineering but also gives you the chance to meet lots of interesting people in other disciplines. more

New preprint: comparing different genetics analysis pipelines for tuberculosis

13 January 2025

Ruan Spies has done a careful systematic comparison of the current genetics pipelines that purport to take raw genetic reads from a clinical sample containing M. tuberculosis (or Mycobacteria generally) and process them to produce a putative genome from which an antibiogram can be predicted. He c… more

2024

New preprint: validating antibiotic resistance prediction in our Myco pipeline

9 November 2024

Over the last 18 months or so we’ve been designing, coding and testing a Mycobacterial genetics processing pipeline (which we call Myco for short). This pipeline has been deployed on the EIT Pathogena cloud platform and is free for academic researchers and LMICs to use. One can upload raw genetic… more

New paper: Infection Inspection

10 September 2024

This paper is the cumulation of a lot of hard work by an interdisciplinary team drawn from both the Department of Physics and the John Radcliffe hospital in Oxford; at its heart is the idea that, by fluorescent staining and super-resolution microscopy, one can image individual bacteria and ones w… more

New preprint: predicting rifampicin resistance

16 August 2024

In this preprint we train a series of machine learning models on protein mutations found in rpoB -- this is the gene in the M. tuberculosis RNA polymerase complex where mutations can introduce resistance to rifampicin, an important first-line drug in the treatment of tuberculosis. Unlike pyrazin… more

New paper: Quantitative drug susceptibility testing for M. tuberculosis using unassembled sequencing data and machine learning

14 August 2024

This is the last paper from the initial set of CRyPTIC publications following the project’s data freeze in April 2020. The consortium takes a difference approach to that of (i) mapping the reads, (ii) look up the genetic mutations in a catalogue and (iii) return the predictions and instead traine… more

Updating the Grammar for Antimicrobial Resistance Catalogues

18 July 2024

This blog updates an old (and now out of date) post describing the grammar we’ve developed for tuberculosis resistance catalogues. It also includes elements from another post that advocated a set of requirements for all AMR catalogues. more

Dx4LMICs conference

3 July 2024

The whole group attended the second Diagnostics for LMICs conference at Reuben College on 2-3 July 2024. Was an unusually diverse meeting with talks ranging from lateral flow devices, including recent innovations like nano-diamonds to dramatically increase sensitivity, a study showing the forehea… more

FowlerLab at ESM 2024

1 July 2024

Three of us (Dylan Adlard, Dylan Dissanayake and Philip Fowler) attended the 44th Congress of the European Society of Mycobacteriology in Bruges last week. As ever was a very friendly, fun and informative conference with lots of familiar faces. Dylan Dissanayake had a poster and was also selected… more

Kafka and tuberculosis

21 June 2024

To mark the centenary of Franz Kafka’s death from laryngeal tuberculosis at the age of 40 in June 1924, the University of Oxford ran a series of events, including talks, an exhibition and a public reading of the Metamorphosis in the Sheldonian Theatre. more

New preprint: processing 3.9 million SARS-CoV-2 samples to make a consistent phylogenetic tree

7 May 2024

Martin Hunt, Zam Iqbal and lots of others have written an epic preprint where they describe their variant caller, viridian, that was written expressly for producing a consensus genome for a virus using tiled amplicon sequencing. We deployed viridian into our cloud-based sequencing platform during… more

New paper: predicting pyrazinamide resistance

20 March 2024

This paper has finally been published and you can find it here. It had a slightly tortuous journey from original preprint to updated preprint and now publication. In brief, we use a range of structural, chemical and evolutional features to learn which missense mutations in PncA (encoded by pncA)… more

Fitness compensation in M. tuberculosis: A game of genetic chess

11 March 2024

It was a pleasure to write this short blog post for the Microbiology Society, talking about my latest paper on fitness compensation in M. tuberculosis, and the process that led to this work. more

New paper: detecting compensatory mutations in the RNAP of M. tuberculosis

5 February 2024

In this paper, by examining testing the association between mutations known to be associate with resistance and other mutation in the M. tuberculosis RNA polymerase, Viki Brunner is able to identify 51 putative compensatory mutations. This is only possible thanks to the large CRyPTIC dataset cont… more

New preprint: processing SARS-CoV-2 genetics in the cloud

31 January 2024

In this preprint, we describe how in July 2022 for two weeks seven sites in six continents uploaded raw genetics files derived from sequencing SARS-CoV-2 clinical samples to our cloud-based platform, GPAS. Overall 5,436 samples were uploaded to GPAS and, unsurprisingly at that time, various Omicr… more

New paper: quantitative measurement of effect of mutations on antibiotics in M. tuberculosis

15 January 2024

The CRyPTIC project played a major role in the release by the WHO of their first catalogue of resistance-conferring mutations in M. tuberculosis by collecting and collating many thousands of samples. All the available resistance catalogues make a binary prediction (whether a sample is Resistant o… more

Our World in Data

10 January 2024

I didn’t know that Our World in Data was also based at the University of Oxford and it was lovely to see (via Twitter) that they’ve produced data and graphs for tuberculosis. I always say that tuberculosis has a bad PR agency as many people don’t know that more people die of TB every year than ei… more

2023

New preprint: Infection Inspection

12 December 2023

Some great work by Conor Feehily, Nicole Stoesser and others, including collaborators from the Department of Physics at the University of Oxford asking citizen scientists to help them classify images of E. coli which have been fluorescently stained and then treated with an antibiotic as either re… more

Updated preprint: predicting pyrazinamide resistance

21 November 2023

This study was performed by Josh Carter back in 2019 and we uploaded a preprint to bioRxiv and submitted the manuscript for review. Unfortunately the reviews came back just as the UK was going into lockdown in March 2020 and my memory was that the manuscript was rejected. The editor, however, had… more

Desirable features for any antibiotic resistance catalogue

31 October 2023

In the past few years a growing number of catalogues containing mutations associated with resistance (and susceptibility) to different anti-TB drugs have been published. Some are supplements to papers, some can be found in a version controlled repository and others are a mixture. more

Philip Fowler joins Reuben College as a Fellow

18 September 2023

Very pleased to announce that I’ve been elected an Official Fellow at Reuben College. The college was established in May 2019 and looks after graduate students; it has a particular emphasis on diversity and inclusivity. Reflecting the reality of many graduate students in Oxford, it is interdiscip… more

New preprint: compensatory mutations are associated with increased growth in resistant samples of M. tuberculosis.

22 June 2023

In this preprint, Viki Brunner shows how, using the large CRyPTIC dataset, she can recapitulate the result that susceptible M. tuberculosis samples grow faster than samples that are resistant to rifampicin (and do not have any mutation that could compensate for that effect). more

New publication: detecting minor populations important for predicting fluoroquinolone resistance

5 April 2023

When predicting if an infection is resistant or susceptible to a specific antibiotic, it is all too easy to think that the infection is homogeneous and, in fact, many bioinformatic variant callers encourage that point of view. Or, at best, you can subvert the format of, say, a variant call file (… more

New publication: determining novel mechanisms of bedaquiline resistance

30 March 2023

A new paper with Lindsay Sonnenkalb as first-author has just been published in The Lancet Microbe. It is a collaboration between a number of groups, led by Stefan Niemann and in it we evolved resistance to bedaquiline in vitro. Sequencing revealed 265 genetic variants with 250 affecting Rv0678, w… more

DPhil in Computational Discovery

23 January 2023

I have a project advertised as part of the DPhil in Computational Discovery programme at the University of Oxford to start in October 2023. This programme is jointly run with IBM and benefits from their applied research in machine learning and other shared areas of interest. The project (Project… more

Congratulations Dr Brankin!

21 January 2023

Alice successfully defended her thesis “Predicting Fluoroquinolone Resistance in Mycobacterium tuberculosis” yesterday. Her examiners were Professor Philip Biggin and Dr Esther Robinson. Much of Alice’s research was done during various SARS-CoV-2 lockdowns and I doubt she thought at the start she… more

Philip Fowler appointed as Associate Professor

13 January 2023

More good news for the group! Philip was awarded an Associate Professorship by the Nuffield Department of Medicine along with two other researchers. more

2022

Viki Brunner wins poster prize

23 November 2022

The whole group attended the first INEOS Oxford Institute meeting on Multidisciplinary Approaches to AMR on Tuesday 22 November 2022. Great to hear how different research groups around Oxford (and elsewhere) are helping to tackle AMR. Best of all though, Viki Brunner won one of the poster prizes… more

New preprint: Including minor alleles improves fluoroquinolone resistance prediction

10 November 2022

Fluoroquinolones are used to treat both normal and drug resistant tuberculosis and therefore being able to work out if an infection is resistant or not to fluoroquinolones is very important. Sequencing the genome of an infection is increasingly used to rapidly return which antibiotics could be us… more

New publication: Predicting antibiotic resistance in complex protein targets using alchemical free energy methods

26 August 2022

In this paper, Alice Brankin calculates how different mutations in the DNA gyrase affect the binding of an antibiotic, moxifloxacin, and thereby potentially whether those mutations confer resistance or not. more

New publication: CRyPTIC Data Compendium

16 August 2022

The large and comprehensive dataset of clinical tuberculosis isolates collected by the CRyPTIC project is described in detail by this paper, just published in PLoS Biology. more

New publication: CRyPTIC GWAS of antitubercular resistance

16 August 2022

Since the primary goal of CRyPTIC was to map the genetic variants in M. tuberculosis associated with resistance to different antibiotics, this genome-wide association study is one of the key research outputs of the project. more

New publication: BashTheBug works!

20 May 2022

Yesterday eLife published the first paper from our citizen science project, BashTheBug, which was launched in April 2017 on the Zooniverse platform. (Update on 19 July 2022: the final formatted version of the paper has been posted on eLife). more

New publication: fast human read decontamination for SARS-CoV-2

16 May 2022

ReadItAndKeep is a new human-read decontamination algorithm that works by mapping the reads in a FASTQ file to the reference SARS-CoV-2 genome. This works because SARS-CoV-2 genetic variation is not so high as to lead to reads being incorrectly discarded and means the algorithm, which relies on m… more

Group photo

11 May 2022

From left to right: Dylan, Alice, Charlotte, Matty and Phil more

New refereed preprint: BashTheBug

31 March 2022

BashTheBug is a citizen science project hosted on the Zooniverse platform that we launched in April 2017 and asked volunteers to help us assess how well 20,637 clinical samples of M. tuberculosis grow on one of 13 different antibiotics. To help engage with the volunteers it has its own blog, that… more

New publication: WHO catalogue of Mycobacterium tuberculosis resistant mutations

28 March 2022

The CRyPTIC project collecting over 20,000 clinical samples of TB and for each, sequencing its genome and testing its susceptibility to 13 different antibiotics. A lovely unintended consequence of compiling such a large high-quality dataset is that CRyPTIC was invited to form part of the team tha… more

GPAS stopover on the ORACLE road trip

1 February 2022

You can listen to Philip Fowler talk about the Global Pathogen Analysis System (GPAS) as part of the ORACLE Road Show by clicking here. We hope in the long term to translate into GPAS the predictive models we are creating for tuberculosis. more

New preprint: Rapid decontamination of SARS-CoV-2 genetic reads

24 January 2022

This preprint by Hunt (2022) describes some software, ReadItAndKeep, that rapidly removes host (i.e. human) genetic information from a sample. This is necessary to ensure that a sample containing SARS-CoV-2 genetic reads cannot be linked to the individual who gave the sample whilst it is being pr… more

New preprint: Predicting antibiotic resistance in complex protein targets

4 January 2022

In this preprint, which Alice has been working on for several years, we show how alchemical free energy methods can predict whether an amino acid mutation confers resistance to an antitubercular, but only in cases where the change in binding free energy is large. This is mainly because the confid… more

2021

Alice Brankin wins NDM Prize

18 November 2021

Congratulations to Alice who last night was awarded an NDM prize for the work she’s done in the third year of her DPhil! more

New Publication: Structure of MmpL3

21 July 2021

Oliver Adams successfully elucidated the structure of the M. tuberculosis MmpL3 membrane transporter using cryo-EM and this has recently been published online in Structure00217-3). This was the main aim of his PhD studies in Simon Newstead’s group in the Department of Biochemistry here in Oxford.… more

Postdoctoral position advertised

17 May 2021

Through the CompBioMed2 EU Centre of Excellence project I have funding to appoint a postdoctoral researcher to develop machine-learning models to predict whether an infection is susceptible to an antibiotic. more

GPAS

17 May 2021

I’ve been working on this for the last few months and very happy that we can now share our plans. more

New preprint: Deciphering bedaquiline and clofazimine resistance in tuberculosis

22 March 2021

In this preprint we examine 14,151 clinical isolates drawn from the CRyPTIC dataset. Each isolate had its minimum inhibitory concentration (MIC) to bedaquiline and clofazimine measured and hence we were able to identify the transcription regulator Rv0678, as the current main source of elevated MI… more

New print: Epidemiological cutoff values for a 96-well broth microdilution plate for M. tuberculosis

5 March 2021

In this preprint, the CRyPTIC project proposes the maximum value of minimum inhibitory concentration (MIC) for 13 different anti-TB drugs below which a sample can be considered to be ‘genotypically wild-type’. more

Research position advertised

26 January 2021

Come and work with me on antimicrobial resistance! Advert here. Broadly the idea is to develop our work using machine learning and molecular simulation to predict whether individual bacterial protein mutations confer resistance to an antibiotic (or not). Any questions please get in touch. For mor… more

Adventures in online lecturing mathematics to biochemists. Part 3.

13 January 2021

In this post, I’ll describe the feedback I got from my students on my Quantitative Biochemistry course. It was delivered during October and November 2020 and comprised a dozen lectures and a series of seven examples classes, each led by a class tutor and containing 6-9 students. See here and here… more

Adventures in online lecturing mathematics to biochemists. Part 2.

13 January 2021

In the last post, I described how I’ve converted Professor Elspeth Garman’s lecture notes from OHP to jupyter-notebooks, which is quite a jump, but I had to do so I could record the dozen lectures making up the course which started in October 2020. more

New publication: Antibody Status and Incidence of SARS-CoV-2 Infection in Health Care Workers

13 January 2021

A second Covid-19 publication I’m proud to be (a small) part of has recently published been in the New England Journal of Medicine. Given the Oxford University Hospital’s Staff Covid testing has been running for months, as described in our first publication, the team was able to show that having… more

2020

Adventures in online lecturing mathematics to biochemists. Part 1.

20 November 2020

After one year of shadowing Professor Elspeth Garman, I’ve taken over lecturing the Mathematics course to the first-year undergraduates studying Biochemistry at the University of Oxford. more

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

20 November 2020

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 n… more

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

2 July 2020

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 w… more

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

30 March 2020

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 reprod… more

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

9 March 2020

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 m… more

AMyGDA now available from GitHub

27 January 2020

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 lice… more

New preprint: rapid prediction of AMR by free energy methods

15 January 2020

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 resis… more

2019

BashTheBug Coordinator post advertised

15 November 2019

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 Nov… more

GROMACS2018 on NVIDIA DGX-1s

27 September 2019

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 supercomp… more

New publication: Predicting resistance is (not) futile

21 August 2019

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… more

Numpy v Biopython

25 July 2019

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 t… more

Genetics and Tuberculosis: A Case of New Meets Old

12 July 2019

I was very pleased to be invited to contribute to this “Voices” article organised by the journal Cell Host and Microbe. You can read it here30296-3). more

BioExcel Alchemical Free Energy workshop

17 June 2019

Last month I was invited to give a talk on using alchemical free energy methods to predict antimicrobial resistance at a workshop in Göttingen organised by the Max Planck Institute for Biophysical Chemistry on behalf of BioExcel. You can read more about the meeting, which I hope will become a bie… more

Compression FASTA files natively in Python

23 May 2019

The M. tuberculosis genome is pretty small, only 4.4 million nucleotides, so storing all that as plaintext means each genome is 4.2MB, but when you have tens of thousands of genomes it starts to add up, particularly as I want to keep my data tree on my workstation so I can view the images produce… more

New preprint: Predicting pyrazinamide resistance by machine learning

29 April 2019

Usually, the protein that an antibiotic binds is essential for bacterial survival, which is how the drug has its effect. In this case, relatively few protein mutations arise that confer resistance, they are often subtle in nature and one can try to predict the phenotype of a protein mutation by c… more

2018

GARC: A Grammar for Antimicrobial Resistance Catalogues

25 November 2018

During the CRyPTIC project it has become obvious that we need a grammar to describe genetic changes that is readable by both human and code and avoids confusion but also allows for the rather sophisticated rules that are currently being developed. For example, in the supplement of the recent publ… more

New publication: Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of M. tuberculosis

26 October 2018

In this Microbiology paper we show how a Python package, called the Automated Mycobacterial Detection Growth Algorithm (AMyDGA for short), can be used to independently read a 96-well plate designed for determining the minimum inhibitory concentration of 14 different anti-tubercular drugs. AMyGDA… more

BashTheBug reaches one million classifications

4 October 2018

BashTheBug, a citizen science project I run that is helping us measure how different clinical samples of M. tuberculosis grow in the presence of 14 different antibiotics, reached its first million classifications earlier this week. To read more head over to its blog. The photo mosaic on the left… more

New publication: Assessing Drug Susceptibility in Tuberculosis

28 September 2018

A paper was published in the New England Journal of Medicine earlier this week by the CRyPTIC project, of which I am part, with help from the 100,000 genomes project. It demonstrates how whole genome sequencing can be used to accurately predict drug susceptibility for the four first-line anti-tub… more

Software Carpentry Workshop

10 September 2018

Last week on Thursday and Friday I helped run a Software Carpentry workshop in the Department of Experimental Psychology at the University of Oxford. This was organised by Research Reproducible Oxford (RROxford), a project of which I am member that aims to lay the groundwork for a culture of rese… more

New software: gemucator

4 September 2018

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. more

New software: pygsi

31 August 2018

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 bee… more

New publication: Validating a bespoke 96-well plate for high-throughput drug susceptibility testing of M. tuberculosis

28 August 2018

This paper, published in Antimicrobial Agents and Chemotherapy, determines the reproducibility and accuracy of minimum inhibitory concentrations for a panel of 14 different anti-TB compounds using a specifically designed 96-well plate (called UKMYC5) manufactured by Thermo Fisher. Since the UKMYC… more

So… I’m a University Research Lecturer

10 August 2018

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 I guess perseverance does pay off! more

Goodbye glados

11 July 2018

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… more

BashtheBug podcast

4 July 2018

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 it is collecting over the next few years. To determine its drug susceptibility and resistance profile, each sample is being grown on… more

Successful NIHR grant

29 June 2018

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 Research Centre. We were successful and were awarded £1.8 million to fund several different activities, including developing vaccines to prevent… more

Read Ellen’s Azure post

26 January 2018

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 Pasterna… more

New Publication: Predicting whether mutations confer resistance to an antibiotic

5 January 2018

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… more

2017

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

11 December 2017

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… more

Azure. Can I break it? Yes you can.

3 December 2017

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… more

New Publication: Protein crowding affects the organisation of ion channels

3 December 2017

Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes more

Azure, Hackathons and PhD students: Feedback

2 December 2017

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 th… more

A way of using Azure in computer-based practicals

1 December 2017

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… more

2018 PhD projects announced

27 October 2017

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 Studentship. There is a competition held each year and the successful applicants have all their fees paid and get a generous £18,000 pa tax-free stipend. The deadline is 12 noon… more

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

4 September 2017

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 201… more

Going tubeless

27 August 2017

Bit off top-topic, but without my bikes it would be a whole lot harder to get to the John Radcliffe hospital. Decided to bite the bullet and try going tubeless, especially after I realised my Shimano Ultra 6800 wheelset was “tubeless ready” (the inside of the rim is completely smooth with the end… more

Women in Computer Science Day

21 June 2017

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 of Oxford. Fortunately being neither a woman nor a computer scientist proved to be a problem. The event was aimed at female Year 10 students (and therefore would b… more

Twitter at #ECCMID

27 April 2017

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 lack of Tweeting at the conference - there were 208 tweets using the bps15 hashtag when I wrote a blog post in which I speculated that, one day, there might be a tip… more

Diagnosing antibiotic resistance: future trends?

23 April 2017

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, I’m sitting on the floor outside one of the halls because the organisers have put one of the most popular sessions (Gram-negative re… more

BashTheBug.net Zooniverse Citizen Science project launches today!

7 April 2017

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 classifying bacterial growth and fighting antibiotic resistance! Alternatively, read the news article on the University of Oxford website or see how… more

BashTheBug.net Beta Testing Results

5 April 2017

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. more

BashTheBug at the Science Museum

29 March 2017

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 took BashTheBug for its first public outing prior to launch earlier next month. Head over to the BashTheBug.net website to find out more. more

Accelerating Oxford Nanopore basecalling

26 January 2017

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 is com… more

New Publication: Effect of SAO mutation on Band 3

12 January 2017

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 of… more

Software Carpentry Workshop, Oxford, 9-10 January 2017

12 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 IT Innovation Challenges Fund and the Social Sciences Division. It is led by Laura Fortunato and I’m a member of the project team. One… more

2016

Shimano Ultegra 6800 Wheelset: an evidence-based review

28 December 2016

Earlier this year I bought some new wheels for my commuting bike. They certainly felt like they made it faster, but did they? Since I record all my rides on Strava and go the same route between Witney and Oxford everyday I have a good dataset. In theory, changing the wheels was the major differen… more

DTC Bioinformatics Module - Hackathon!

12 December 2016

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 h… more

DTC Programming Module - Feedback

9 December 2016

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 course introduces C… more

DTC Programming Course

31 October 2016

Advanced Resources for the Curious more

2017 PhD projects advertised

3 October 2016

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 more

bashthebug.net alpha launch

3 October 2016

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. more

New Publication: Lipids can form anti-registered phases

23 September 2016

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 like (this is described as a registered phase). If we consider the simplest case of two lipids, one saturated (A), one unsaturated (B), then if their leng… more

New Publication: Proteins Alter the Stiffness of Membranes

23 September 2016

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 few investigations of what effect regular membrane proteins have on the stiffness of membranes. Here we show via very large simulations, using th… more

New Publication: Membrane Compartmentalization Reduces the Mobility of Lipids.

23 September 2016

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 cytoskeleton, which, it has been suggested, corral the lipids. In this paper, we show by very large coarse-grained simulations of a realistic model of the pla… more

Cheltenham Science Festival

22 June 2016

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 explain about antibiotic resistance to, well, anyone and everyone. As I come from a molecular background and we didn’t have any information about protei… more

GROMACS in DOCKER: First Steps

23 May 2016

DOCKER is cool. But what is it? From the DOCKER webpage more

Setting up a GROMACS cluster

28 April 2016

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 years, having used many clusters… more

How to setup a Gramble

14 April 2016

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 want to do such a th… more

I’ve moved…

14 March 2016

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 Biochemist… more

New Publication: Predicting affinities for peptide transporters

29 January 2016

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)… more

GROMACS on AWS: compiling against CUDA

27 January 2016

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 b… more

GROMACS on AWS: compiling GCC

27 January 2016

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 OS based Amazon Linux AMI. (currently GCC 4.8.3) You may, for example, wish to use a more recent version to compile GROMACS - that is my interest. If so, then the… more

GROMACS on AWS: Performance and Cost

17 January 2016

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 can expect and much this is likely to cost compared to other compute options you might have. more

GROMACS on AWS

13 January 2016

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 account can have… more

2015

Dr Firdaus Samsudin

18 November 2015

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 of Proton Dependent Oligopeptide Transporters”. He has been published one paper and another has been accepted. more

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

2 November 2015

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

28 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 Softwar… more

Software Carpentry Workshop, Jülich, 12-13 October 2015

23 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… more

CECAM Macromolecular simulation software workshop

14 July 2015

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 focu… more

Running GROMACS on an AMD GPU using OpenCL

10 July 2015

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 used them ever since. Until last year I had an old MacPro which had four PCI slots so you could add a GPU-capable NVIDIA card, although you were limited by the power supply. A GPU can ac… more

New Publication: Alchembed

12 June 2015

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… more

Is Software a Method?

1 April 2015

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 research area, but also in how my community viewed software. Were there talks and posters on how people had improved important pieces of community s… more

HackDay: Data on Acid

31 March 2015

Every year the Software Sustainability Institute (SSI) run a brilliant meeting called the Collaborations Workshop, usually in Oxford. This is an unconference lasting two days. At first glance it doesn’t look like it would be relevant to my research, but I always learn something new, meet interest… more

Lectures, Clickers and Quizzes

23 March 2015

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 screen. You’re feeling sleepy but this course doesn’t seem too hard - you can always learn the key concepts from the lecture notes before the exams. And so… more

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

6 March 2015

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 s… more

BPS15: Yes! Yes! But why? But why?

11 February 2015

As part of my series of guest blogs at the 59th Annual Meeting of the US Biophysical Society I wrote some thoughts on the National Lecture by Klaus Schulten that was last night. To find out what the quote refers to, you’ll have to follow this link... Update: you can now watch the National Lectur… more

BPS15: Twitter and conferences: an ideal match or a nuisance?

9 February 2015

I’m at the Annual Meeting of the US Biophysical Society Meeting in Baltimore which is large (6,500 scientists) with multiple parallel sessions. You might have thought that Twitter would be the ideal platform for providing a feed for all the questions, reactions and suggestions but very few people… more

BPS15: Where shall we have lunch?

7 February 2015

The most useful and enjoyable part of coming to the Annual Meeting for me is not the talks, nor is it the poster session nor even the free T-shirts. It is meeting up and talking with fellow scientists. But one must first solve an important question that Douglas Adams describes better than I ever… more

BPS15: I’m (guest) blogging..

7 February 2015

I was pleased to be chosen as one of the guest bloggers. for the Annual Meeting of the US Biophysical Society in Baltimore that runs from today to Wednesday 11 February. You can read my posts, as I write them, here. more

New publication: Gating Topology of the Proton-Coupled Oligopeptide Symporters

3 February 2015

[bibshow file=http://dl.dropboxusercontent.com/u/7762003/mypub.bib template=av-bibtex highlight=“P. W. Fowler” ] This paper [bibcite key=Fowler2015] is the result of a large collaboration between several groups. Since all the current crystal structures of peptide transporters are open to the… more

New publication: Insights into the structural nature of the transition state in the Kir channel gating pathway.

2 February 2015

[bibshow file=https://dl.dropboxusercontent.com/u/7762003/mypub.bib] We recently examined how Kir1.1, an inwardly-rectifying potassium channel that is found in the kidneys, opens and closes in response to being stimulated by changes in pH or the presence of absence of PIP2, a signalling lipid … more

Software Carpentry Workshop, Oxford, 13-14 January 2015

16 January 2015

So how did the workshop go? I thought it went a bit better than the first day, but, hey, I’m a bit biased. To get a better idea I sent the participants a similar questionnaire to the one I sent to the Software Carpentry workshop I organised before. Nearly all the participants (95%) agreed with th… more

Software Carpentry Workshop in Oxford, Day 1

13 January 2015

Today I’ve been instructing on a Software Carpentry workshop at the Wellcome Trust Centre for Human Genetics in Oxford; it’s the first time I’ve been lead instructor on a bootcamp. Today Kwasi Kwakwa and myself covered the shell and basic python; more python, then git and SQL tomorrow. So what we… more

2014

Installing GROMACS with MPI support on a Mac

5 December 2014

GROMACS is an optimised molecular dynamics code, primarily used for simulating the behaviour of proteins. To compile GROMACS you need, well, some compilers. I install gcc using MacPorts. Note that this requires you to first install Xcode. Then it is easy to install gcc version 4.9 by sudo port in… more

A simple tutorial on analysing membrane protein simulations.

3 September 2014

I’m teaching a short tutorial on how to analyse membrane protein simulations next week at the University of Bristol as part of a series arranged by CCPBioSim. As it is only 90 minutes long, it only covers two simple tasks but I show how you can do both with MDAnalysis (a python module) or in Tcl… more

Goodbye Hans Krebs Tower

12 August 2014

When I first started in Oxford our lab was based on the top floor of the Hans Krebs tower. Since 2008 we have been in the imaginatively named “New Biochemistry Building” which is actually only half a building, but that is another story. To make room for the other half, the Hans Krebs Tower is fin… more

New Publication: State-Dependent Network Connectivity Determines Gating in a K+ Channel

27 June 2014

In an earlier paper we showed that the closed state of Kir1.1, a important potassium ion channel found in the kidneys, was stabilised by a single hydrogen bond. This paper builds on that work by looking for any interactions that stabilise either the open or closed state of the channel by systemat… more

Getting an ext3 Drobo 5D to play nicely with Ubuntu 12.04

25 June 2014

Our lab has recently bought two Drobo 5Ds to give us some large storage. They work out of the box with Macs but getting them to play nicely with Linux, specifically Ubuntu 12.04, has been a bit more work so I thought I’d share the recipe that, for us at least, appears to work. Much of this has be… more

New Publication: NRas slows the rate at which a model lipid bilayer phase separates

13 June 2014

Here we examine by computer simulation what effect adding a small cell-signalling protein does to a model ternary lipid mixture that has been shown before to phase separate. This paper was presented at the 169th Faraday Discussion meeting in Nottingham in May 2014, the theme of which was Molecula… more

Trying to stop lectures from being so zzzz…Part 2

21 March 2014

Last time, I wrote about the tactics I was planning on trying out in my lecture series this year. Well, the lectures are done, I’ve collected some feedback and so here are the results. more

Trying to stop lectures from being so zzzz…

6 March 2014

Why are lectures so sleep inducing? I remember well the effort required to keep your eyelids apart after 35-40 minutes. So, now that I am the lecturer, how can I keep my students at least awake, and hopefully interested? I am not going to talk about the most obvious point, which is to be an enthu… more

Rushing here and there: planning an itinerary for a large scientific meeting

24 February 2014

I’ve just returned from the 58th annual meeting of the US Biophysical Society in San Francisco. With around 7,000 scientists, multiple simultaneous sessions of talks and nearly a thousand posters every day, it is a large event, but not as big as many. Even so, working out what talks and posters y… more

GROMACS 4.6: Running on GPUs

11 February 2014

I mentioned before that I would write something on running GROMACS on GPUs. Let’s imagine we want to simulate a solvated lipid bilayer containing 6,000 lipids for 5 µs. The total number of MARTINI coarse-grained beads is around 137,000 and the box dim… more

Windows Azure for research

3 February 2014

I recently attended the first training event in UK by Microsoft on how to use Windows Azure for research. A perspective I wrote for the Software Sustainability Institute has been posted on their website. more

2013

The Oxford Software Carpentry Boot Camp … one year on.

19 December 2013

In October 2012 I organised a Software Carpentry Boot Camp at the University of Oxford. I’ve previously posted the feedback I gathered immediately before and after the boot camp, but thought it would be interesting to see if all that enthusiasm actually translated into deeds i.e. did the attendee… more

So…. I’m a Software Sustainability Fellow

19 December 2013

I’m pleased to announce that I am one of the Software Sustainability Fellows for 2014. I met all the other fellows when we were being selected and it is an amazing group with very diverse research interests and backgrounds. This means I have a responsibility to try and improve the development and… more

New Publication: Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY

8 November 2013

In this paper we examine how the lactose permease, LacY, changes its structure to shuttle molecules of lactose across a cell membrane. The change in conformation is modelled usinga biased computational method called dynamic importance sampling (DIMS) and the results compared to the results of som… more

New Publication: Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels

31 October 2013

Can we predict the conductance of a potassium ion channel from an experimental structure? In this paper we examine the kinetic barriers experienced by potassium ions (and waters) as they move through the narrowest part of two different potassium ion channels. We examine the reproducibility of our… more

GROMACS 4.6: Scaling of a very large coarse-grained system

23 October 2013

So if I have a particular system I want to simulate, how many processing cores can I harness to run a single GROMACS version 4.6 job? If I only use a few then the simulation will take a long time to finish, if I use too many the cores will end up waiting for communications from other cores and so… more

GROMACS 4.6

18 October 2013

GROMACS is a scientific code designed to simulate the dynamics of small boxes of stuff, that usually contain a protein, water, perhaps a lipid bilayer and a range of other molecules depending on the study. It assumes that all the atoms can be represented as points with a mass and an electrical ch… more

Crowd-sourced computer networks

15 October 2013

Crowd-sourced computer networks Blog post on something I’ve been interested in for a while; how to create and use networks of everyday computers to solve interesting problems in biology. Links to the website of the Software Sustainability Institute. more

New Publication: Detailed examination of a single conduction event in a potassium channel.

15 October 2013

What can we learn using computational methods about how potassium ions and water molecules move through the narrowest part of a potassium channel? In this paper, we calculate the average force experienced by three potassium ions as they move through the selectivity filter of a voltage-gated potas… more

Habits of Highly Productive Academic Writers

21 May 2013

Not my title, but the title of the half-day workshop I’ve just attended led by Helen Sword, an academic from New Zealand. It was extremely thought-provoking and has made me question how I write. Please see her webpage, Writer’s Diet for more information and resources. I’d especially recommend the… more

How (not to) present a poster at a scientific conference

6 February 2013

Ok, so you are presenting a poster at a scientific conference. You’ve done the research, prepared and printed the poster and pinned it to the board, the poster session is approaching and you really want some feedback on your results and ideas. How do you maximise the number of people you talk to?… more

Good science

4 February 2013

“There was some good science in that seminar.” “Yes? Sorry I feel asleep shortly after the first slide of maths.” Familar? I expect every scientist occasionally gets the feeling that perhaps the person speaking is saying something interesting and important in say at a conference but why can’t the… more

2012

Top Tips for hosting a Software Carpentry Boot Camp

6 November 2012

I’ve written a post for the Software Sustainability Institute (who kindly provided the instructors for our boot camp) describing my top tips for hosting a Software Carpentry Boot Camp. more

Software Carpentry Feedback

1 November 2012

As well as asking the attendees how they thought the workshop had gone, I sent them a questionnaire before the workshop. The idea was to see what their expectations were and if the workshop then met them. For example we asked “How would you describe your expertise in the following tools?” and the… more

Improving Software Carpentry workshops

1 November 2012

Aron Ahmadia who helped run the Software Carpentry course has written a nice blog where he e.g. discusses some of the ways the course could be improved. more

Running my first Software Carpentry workshop

1 November 2012

“Can you email me that script you used to do your analysis?” “Sure. It isn’t very well commented but you should be able to work out what it’s doing. I’ve tested it on a few things and it seems to work.” Sound familiar? Of course, the story normally ends happily but…. Teaching some of the tools… more

This blog…

31 October 2012

...is where I shall put thoughts that at least might be of interest to other people. Any opinions are my own and are not representative of my department or university in any way. more