I already have at least one of these on this blog (which incidentally is my most popular post).

Why it doesn’t really matter: p<2.2e-16 is pretty significant!

em-dashes and hyphens

Using a hyphen between clauses-like this-looks tacky. Use these resplendent em-dashes–like this–instead.

It’s so easy to do, just type two hyphens -- or Alt-hyphen.

Over the past three years I’ve served as an Editor for the American Joᴜrnαl of Traffic and Transportation Engineering¹ journal Microbial Genomics. Now my term has ended, here are some reflections on what I’ve learnt about the publishing process during my tenure from the editorial side. I hope this might be useful for authors and reviewers, especially earlier in their careers.

The journal

Microbial Genomics (‘MGen’) is run by the UK Microbiology Society, started in 2014, and I believe is doing rather well in terms of submissions.

The games I played and liked last year were almost all really good. This time I’ve given points out of five for fun and memorableness/creativeness, which I think are the two main things I care about, and an overall score.

Perfect Tides (point and click adventure)

Perfect Tides is a coming of age story set in the year 2000, on a seasonal island in the US. This is a good setting that nicely represents the boredom/lameness of many teen hometowns. You play as Mara, who is a teenager struggling through high school.

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: