The aim of this post is to look at revisions of bioRxiv preprints. I’m interested how long preprint versions exist on bioRxiv. In other words: how long do revisions to preprints take? The data from bioRxiv is a complex dataset with many caveats as I’ll explain further down, but some interesting details do emerge. Consider this a sketch of the dataset rather than an in-depth analysis. I’ll walk you through the code.
This post is an update of a previous analysis on quantixed. We have covered publication lag times – the time it takes for a paper go from submitted (received) to accepted and published – a lot on here. It is possible to look at lag times, in R using data from PubMed. Previously my code performed these calculations using an XML file downloaded from the PubMed website.
As the COVID-19 pandemic continues, different countries are experiencing various restrictions including lockdowns. Some of these restrictions alter our ability to do science: by hindering lab access or taking time away from researchers for homeschooling. So, what impact has the pandemic had on scientific output? One way to look at this – for biology – is to look at newly deposited papers on bioRxiv.
Clathrin is a three-legged protein complex or triskelion that can assemble into lattice-like structures. Inside the cell, this assembly helps to create vesicles: tiny packages of membranes containing proteins and goodies for the cell to use. Incredibly our first view of assembled clathrin was made in the 1960s, with resolution improving steadily since then. The image below shows these improvements.
The scientific response to the COVID-19 pandemic has been astounding. Aside from efforts to generate vaccines, the genomic surveillance of the virus has been truly remarkable. For example, the nextstrain project has sequence many SARS-CoV-2 genomes. In fact, the rapid identification of multiple new strains and mutations by diverse groups of scientists has resulted in a nomenclature crisis.
Reading about someone else’s recovery-after-injury story can be a bit dull. At least that was my conclusion after pressing delete on my story a moment ago. Having spared you the details, the summary is: I got injured. It hurt. It took me a year to recover because I didn’t tackle the recovery properly.
We have a new paper out! I am a bit late with this post, since the accepted version went online in December 2020, and the final version appeared a few weeks ago. It will shortly appear in a finished issue of the journal so I can tell myself that I am not too late yet. What’s it about? A complex of TACC3-chTOG-clathrin-GTSE1 is important for stabilising the mitotic spindle during cell division.
Many running races and events have been cancelled or disrupted due to the pandemic. To fill the void, I’ve been taking on Garmin’s “Challenges”. In Garmin Connect, you can accept a challenge set by Garmin (I think users can challenge each other too). Completion of these challenges gives the user points, which I’ve become somewhat obsessed with.
The IQ Block game is a puzzle where the player must fit eight shapes into a square space. The challenge is to find as many ways as possible to do it. The IQ Block game The box says there are more than 40 solutions! So how many are there? I wrote a solver to crack the IQ Block game. The code is available here and a detailed description is at the end of the post. The solver found 264 solutions from 33 placements.
I have a long-running project to make timelapse movies using a Raspberry Pi Zero with camera module. I’m capturing a countryside view and have images for two years. The uptime on the Pi is seriously impressive, but nonetheless I wanted to upgrade the Pi so that it would send me updates of how it’s going, so that I would know if it image capture had failed. Here is my solution.
