It is an annual event on quantixed to post the papers I have selected for what is now called MD9A8 (the module formerly known as MD997 Frontier Techniques and Research Skills in Biomedicine). Previous selections are grouped here.

A quick post about a puzzle called Wordle that is currently taking over the internet. It’s a mastermind-like game where the object is to guess an unknown 5-letter word. Puzzlers are encouraged to share their results after completing a puzzle. Here is an example for puzzle 192. So how do you know if your performance on today’s puzzle was any good? Why not benchmark your effort against the crowd?

This recent tweet made me chuckle. It does seem that many structural biology papers have a title that begins “The structural basis of…”. I took a quick PubMed survey to look at its popularity. First a search of "structural basis"[ti] AND "journal article"[pt] gives us the number of research papers with “structural basis” in the title. This plot of the number of papers with this title each year is levelling off.

As 2021 draws to a close, it’s time to check back in on a previous post. As a recap, Garmin Connect offered four challenges to run 3 x 505 km and 1 x 505 km, one in each of the four quarters of 2021. Completing all four would mean running 2021 km in 2021 . I used an R script to check my progress throughout the year (available here). Each quarter gave a set of results, the final set for the whole of 2021 is shown here.

Here is a quick method for checking parity between two directories. Let’s say we have two directories dir1 and dir2. They are large and have thousands of files and subdirectories. How can we check that they have the same contents? I found myself in this situation recently during a server migration.

In early December, Spotify users received a list, known as Spotify Wrapped, of the tracks they listened to most in 2021. As a committed non-streamer, I was a bit envious of these lists; so I decided to assemble my own list using my Music database. This was possible by comparing two snapshots of my Music database in xml format* that were taken in 2020 and yesterday.

Every publication is assembling year-end lists of their selection of the best albums of the year. Well, quantixed did not want to miss out on the fun, so I came up with a list of my favourite 20 albums released in 2021.

Quantifying the degree of colocalisation of two signals in microscopy images is very tricky. Lots has been written on this topic, including in my book The Digital Cell. The focus of this post is on visualising colocalisation . One way to look at colocalisation is two think about two sets of objects and how many of each set overlap. This is sometimes referred to as co-occupancy or object-based colocalisation .

In a previous post, I described a coding challenge sent to me by my colleague. Here is the challenge again: My solution was… let’s say… over-engineered. He did tell me that the winner (the challenge was set in an international coding competition) solved it in a ridiculously short time. He didn’t tell me how short which I think would have led me to take a different approach.

A colleague sent me a coding challenge. This is a short post to describe how I tackled it. Edit: a follow-up post is here. This is the challenge: With an eye on b, and since I code fastest in Igor, I went with Igor over python or R. I knew this would lose me major points for c since Igor code is not very compact. It took me 22 minutes to write a solution, slowed down a bit by helping a small person with their homework.