John Lees' blog

Pathogens, informatics and modelling at EMBL-EBI

Favourite video games 2022

I think the last post I made on video games has been one of the most popular I’ve written on this blog, so thought I’d update you with some more recent favourites. I didn’t play as many video games in 2022 as the past couple of years, but there were still a fair few I enjoyed. Though, looking back, there weren’t any games that really knocked my socks off like the previous list I made, and in general I haven’t felt like there were as many games coming out that I wanted to play.

One hundred days and one hundred lines of code

Last week I attended ‘100 days and 100 lines of code’, which was organised by the Epiverse team at LSHTM. The overall idea was to think about when the next pandemic happens, what the first 100 lines of code written would be (I think more as a cute reference to similar thoughts about vaccine development, rather than a totally serious concept). The format was over three days: Talks from academics, public health and field epidemiologists on their thoughts and experiences with epidemiology software.

mamba saved my CI

We moved from Azure to github actions to run the continuous integration tests in PopPUNK about a year ago. It’s been working pretty well and wasn’t too bad to set up, and integrates nicely into the pull requests. However, in the past month two things happened: joblib v1.2 introduced a breaking security change which meant that hdbscan errored. Solving a conda environment pinning joblib to 1.1 takes about 12 hours (😱) to solve (longer than the 4 hour github limit).

Goodbye Wordpress

I originally set up a free wordpress (https://leesjohn.wordpress.com) in 2013, which I updated slightly when I moved it to some cheap hosting on www.johnlees.me in 2019. The hosting was fairly unreliable and every year’s renewal I thought about moving. Maintaining a wordpress also takes a bit of effort and I also worried about eventually allowing it to lapse. Finally, I’d grown increasingly frustrated with the wordpress style of editing, which had made it difficult to write code and embed HTML, and really wanted to move to something more like text to write posts.

Host/pathogen data for 'Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis' available on EGA

I have recently gotten round to adding the human data (and links to pathogen data, which has been available on the ENA since publication) to the managed access European Genome-Phenome Archive. The sharing of human genotype data is a little more fraught than bacterial genome data due to patient ethics and other issues, but the EGA offers a good solution for protecting this while making the data as open as possible.

WE, Arcade Fire (2022) – A reverse in trajectory?

The first three (Funeral, Neon Bible, The Suburbs) I first saw Arcade Fire performing Neon Bible at Glastonbury (though sadly only on the BBC broadcast). At the time it was released, I was working at the local supermarket at the weekends pushing trolleys around in the car park. I had a cheap – iRiver if I recall – MP3 player with space for a handful of albums that I would illicitly listen to.