This is a mini-review (just highlighting some initial thoughts) of this preprint:

Compressive Pangenomics Using Mutation-Annotated Networks
Sumit Walia, Harsh Motwani, Kyle Smith, Russell Corbett-Detig, Yatish Turakhia
https://www.biorxiv.org/content/10.1101/2024.07.02.601807v2

This is an extension of the idea of mutation annotated trees which were successfully applied to SARS-CoV-2 in the UShER (and related) software. Phylogenies are stored as a sequence of mutations on each branch from the root, rather than keeping all sequences. This is not unlikely the use of ancestral recombination graphs to represent genotypes and evolutionary history in e.g. human genomes.

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 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.h aren’t supported on ARM CPUs, such as the M1/M2 seen in recent Macbooks. Fortunately there’s an easy enough three step solution, thanks to sse2neon:

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. Your character sprites sit on little tiles on an isometric battlefield and take turns in which they can make one move and one attack (an adjacent tile with a sword, or further with magic or arrows). Power for moves charges one point each turn.

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. I also very much enjoyed this video with Roisin Murphy:

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. I only have a bit of knowledge about them, and I think the talks covered a good range of questions on these charismatic genome elements: