I am having some fun running AlphaPulldown on a computing cluster. A requirement is to have input sequences in FASTA format. I found that I needed to get ~600 sequences. I had a list of the relevant Uniprot IDs. Surely getting the sequences for these proteins should be straightforward? Solution The Uniprot IDs can be converted – using the ID Mapping Tool on the Uniprot website – into any number of other IDs.

2023 has been a great year in running for me. Previous running round-ups are here (2022, 2021). My two main goals for 2023 were to run 3000 km and also to run 50 HM-or-more distance runs. I managed both with a couple of weeks left. I also bagged new PBs for 5K, 10K and half marathon as well as a handful of segments on Strava. I won no races but I did win two little running competitions at work.

Bands have been known to declare “No Synths!” on their albums. This statement was a badge of pride indicating that the artists hadn’t used any modern trickery in their recordings. Today, the growing use of artificial intelligence (AI) and large language models (LLMs) in science has created a similar scenario. Advocates argue that these tools improve every aspect of science, including the publication process.

It’s getting towards the end of the year so it is time to assemble a list of my favourite albums released in 2023. I have sporadically posted lists in the past e.g. here.

In the spirit of “if it took you a while to find out how to do something, write about it”, I will detail a method to approximate the surface area of a 3D shape. Our application here was finding the surface area of a cell but it can be used on any shape. We start with a 3D point set, specified by points of interest in a single cell imaged by 3D confocal microscopy.

In a previous post, I looked at how Google Scholar ranks co-authors. While I had the data available I wondered whether paper authorship could be used in other ways. A few months back, John Cook posted about using Jaccard index and jazz albums. The idea is to look at the players on two jazz albums and examine the overlap.

We have a new paper out describing how vesicles move inside cells. The paper in a nutshell In science-speak We analysed how small vesicles are transported in cells. In contrast to large vesicles and organelles, which move using motors inside cells, our analysis revealed that passive diffusion is the main mode of small vesicle transport. In normal language Inside cells, molecules are moved in tiny transport packets called vesicles.

On a scientist’s Google Scholar page, there is a list of co-authors in the sidebar. I’ve often wondered how Google determines in what order these co-authors appear. The list of co-authors on a primary author’s page is not exhaustive. It only lists co-authors who also have a Google Scholar profile. They also have to be suggested to the primary author and they need to accept the co-author to list them on the page.

Hopefully I will soon break out of this funk of posting about either Mastodon or Twitter. But not yet! This post is to say that: I made a static archive of tweets for @quantixed and for @clathrin. There, you can read all my posts, which ended in 2022. Edit: removed the archives in October 2024. How did I do it and why? I made the archive with this excellent tool written by Darius Kazemi.

Earlier this year I set up a bot on Mastodon. The bot, AlbumsX3, posts an album suggestion twice-a-day. Performance has been good. It has only missed a few posts due – I think – to server glitches. However, I have made a couple of tweaks to upgrade the bot since my last post, so I thought I would detail them here. Preventing duplicate posts In the last post I wrote: Well, it wasn’t long before I needed to revisit this issue.