John Lees' blog

Pathogens, informatics and modelling at EMBL-EBI

Powerpoint, Biorender and AI

This illuminating tweet from Michael Baym on how restrictive the biorender license is reminded me of a little post I’d meant to write. You’ve probably noticed a profileration of Biorender images in talks, papers, grants and especially graphical abstracts you’ve seen in recent years. I think I’ve seen these really increasing in prevalance over the past couple of years, maybe because of institutional subscriptions, maybe because we have been seeing increasing numbers of our peers using it and don’t want to be left out.

RapidNJ for M1 macs

RapidNJ is a really nice program for making neighbour-joining trees from distance matrices or alignment data. If you try and compile on an M1 Mac however, you’ll get errors that look like this: In file included from src/main.cpp:1: In file included from src/stdinclude.h:9: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/15.0.0/include/emmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture" #error "This header is only meant to be used on x86 and x64 architecture" These Intel intrinsics in emmintrin.

Video games in 2023 -- five good ones

This is the 2023 edition of my now yearly series of reviews of video games I’ve played over the last year (2020-2021, 2022). I’ve only played five games this year, to my slight surprise all of which were on the Switch. So this year’s post is a chronological list, and I’m going to start giving them ratings out of five. Definitely more great games this year than last. Triangle Strategy (RPG, turn-based) If you ever played Final Fantasy Tactics this type of game will be very familiar, and of course it has the same developer.

Mercury Prize 2023

The 2023 shortlist for the Mercury Prize is out, there is also a spotify playlist with a couple of headline tracks from each: Here’s my ranking. Or actually because I found it hard to rank them, more of a tier list: Winner: That! Feels Good!, Jessie Ware The one I looked forward to every time it came on the playlist, and I’ve listened to the whole album a few times. First came across her due to some remixes (Free Yourself is crying out for a higher BPM) but count me as a fan now.

Annual conference, Microbiology Society (2023, Birmingham)

This week was time for the Annual Conference of the Microbiology Society. This was my second time at this meeting, and I enjoyed it once again. There’s a committed core of attendees which gives a good community spirit, and the society is openly very keen on supporting PhD students attending. Favourite session – plasmids There was a great block of talks in the Genetics and Genomics session on plasmids that I thought fit together really nicely.

Rust take two -- I guess I'm a rust guy now?

About a year ago I had my first foray into rust, which I used to do advent of code. I wrote up my thoughts at the time, but in summary although there were some immediately nice features such as the build and dependency system, I wasn’t immediately convinced and decided to stick with C++. I also said I’d give it a go for my next WASM project. That time arrived at the end of last year, and what I intended to be a web implementation has turned into a full CLI tool where I used rust over C++.