John Lees' blog

Pathogens, informatics and modelling at EMBL-EBI

Bot or not? Anti-research/University accounts on twitter

tl;dr I think it’s really hard to tell whether a twitter account is run by who it looks like on first glance, and what its intentions are. Maybe we should try and take more care before amplifying opinions of unknown actors. Just another angry tweet Recently, when scrolling through my twitter feed, I noticed some fairly aggressive tweets from the account @Help4StudentsUK, criticising Wellcome and some of its management. A typical example:

Some thoughts on bioinformatics software maintenance

Overall thoughts I released my first software package for bioinformatics about four years ago. I now have four, all of which see some usage, but certainly nothing like the heavy usage of the most popular utilities. Despite this, I would guess on average I spend around 20-30% of my time maintaining these packages. I love that people find our software of some use, and it’s still exciting getting messages from users from countries all around the world.

Plots that went wrong

There’s loads of these on https://twitter.com/accidental__aRt, here are some of mine from the past couple of years: The beach? You can never have too many violins A nice smooth likelihood surface Always good to see the zero contour ’terrible_dendrogram.png' Apply some smoothing then I’m sure it will be fine, right? R2 = 0.11, p < 10E-10 Let’s cram everything in to 1/10 of the space. 2) The ever so informative labels: ‘1’, ‘2’, ‘3’, … Machine learning (or would we call this AI now?

Paper summary – Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

This a summary of our paper on a joint pathogen and human GWAS that has just been published in Nature Communications: https://doi.org/10.1038/s41467-019-09976-3 This is the last bit of research from my PhD thesis. Also, this was the first thing I started working on back in 2014 (my first GWAS), and our collaborators have been collecting data since 2006 – so it’s good to see this one out! Overview We collected cases from pneumococcal meningitis patients enrolled in a nationwide Dutch cohort.

Readthedocs failing to build: module 'setuptools.build_meta' has no attribute '__legacy__'

As we all know, it’s critical that your code’s github README.md However, to my horror, I noticed one of my many nice green badges signalling my professionalism had turned an alarming shade of red. What were potential users to think, seeing that the docs for my most recent commit had failed to build on readthedocs The horror Looking at the build logs, one of my dependencies (in this case hdbscan) was failing with the error message:

Conservation of core genes in S. pneumoniae

A question I am sometimes asked is whether a gene of interest, usually being studied in vitro or in vivo, is conserved. Although the availability of population genomic datasets allows this question to be answered, it can be hard to find this kind of analysis in the literature, and doing it yourself is not trivial. This post hopes to be an easy way to access this information for S. pneumoniae.