John Lees' blog

Pathogens, informatics and modelling at EMBL-EBI

Using the new Microreact API

(the excellent) Microreact has recently had a major new release which has a few breaking changes. One that hit me is that the API has changed. The previous API was pretty simple, and allowed anonymous POST requests with a blob of CSV, tree and optionally network to return a stable URL. The new API requires a token for authorisation and addition to your account (which seems sensible), and also adds deletion and updating of instances (which is also useful).

Annual conference, Microbiology Society (2022, Belfast)

I recently attended the Annual Conference of the Microbiology Society, which was held in Belfast. This was my first time attending this meeting, and I was a bit nervous that as a genomics researcher/someone who wouldn’t know a colony from his elbow I might not be able to follow much. This proved to be unfounded, and I was really happy to see that genomics is becoming a routine part of many microbiology studies, rather than a separate area (machine learning if anything seems to be the new bogeyman – I look forward to the hype settling down).

Model flexibility and number of parameters

This post is some thoughts I had after reading ‘Real numbers, data science and chaos: How to fit any dataset with a single parameter’ by Laurent Boué. arXiv:1904.12320 The paper above shows that any dataset can be approximated by the following single-parameter function: $\sin^2 (2^{x \tau} \mathrm{arcsin} \sqrt{\alpha})$ Where $x$ is an integer, $\tau$ is a constant which controls the level of accuracy, and $\alpha$ is a real-valued parameter which is fit to the dataset in question.

Quantify everything, all of the time

I recently read the article by Wu et al in Nature Biotechnology (you can also find similar articles in pretty much all of the Nature journals) which analysed data on participants at some virtual meetings over the past couple of years, and came to the conclusion that ‘Virtual meetings promise to eliminate geographical and administrative barriers and increase accessibility, diversity and inclusivity’. Which sounds great! Of course there are certainly some good things to come out of virtual meetings, and many unresolved issues with in person conferences.

Did 1.27M people die from AMR in 2019?

I would answer ‘I don’t know’. If I was being less trite, I would add that I’m more confident saying that it was between 100k and 10M – whichever way you look at it, vast numbers that are growing larger, and which require action on multiple fronts. The authors of the study ‘Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis’ (also called ’the GRAM study’) have actually attempted to estimate this.

Delete your tweets

Each year I delete all my old tweets. Disadvantages to keeping your old tweets around: No-one reads them. They’re difficult to search through. They’ve probably lost most of their context. You might have changed your mind, or they’ve become outdated. Shitposting is usually a lot less funny in retrospect. Advantages to keeping your old tweets around: The dubious ability to quote tweet an old take/prediction that turned out to be true.