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 […]
Ten Years vs The Spread II: Calculating publication lag times in R
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 […]
The Rise and Fall: impact of the COVID-19 pandemic on bioRxiv preprints
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 – […]
Shiny Cage: visualising clathrin triskelia in a lattice
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 […]
Os Mutantes: an implausible naming system for SARS-CoV-2 mutants
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 […]
You Better Run: recovering from injury
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. Measuring recovery […]
Keep A Knockin: new paper using knock-in technology
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. […]
Target: monitoring a running goal in R
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 […]
Crackerblocks: computing solutions for IQ Block game
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 box says there are more than 40 solutions! So how many are there? I wrote a solver to crack the IQ Block game. […]
I’ve Gotta Get A Message To You: automated emails from Raspberry Pi zero
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, […]