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 […]
Category: publishing
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 – […]
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. […]
Culture Move: new preprint on cell migration
We have a new preprint out. This is a short post to describe our findings and highlight some of the software I developed for analysing cell migration and cell shape data. Intracellular nanovesicles mediate integrin trafficking during cell migration bioRxiv doi: 10.1101/2020.08.19.257287 It is mainly the work of Gabrielle Larocque with help from Penny La-Borde […]
Same Time Next Year: crunching PubMed data
I am giving a talk next week and wanted to update some plots from an old analysis that previously featured on quantixed. The question is: how long does it take for a paper get published? The answer is complex (as previously discussed on quantixed), but we can at least find out using data from PubMed […]
Screenager: screening times at bioRxiv
When a preprint is uploaded to bioRxiv, it undergoes screening before it appears online. How long does it take for Affiliates to screen preprints at bioRxiv? tl;dr I used R to look at bioRxiv screening times. Even though bioRxiv has expanded massively, screening happens quickly (in about 24 h). I am a bioRxiv Affiliate – […]
Take Off: preprints on COVID-19
I’m posting this the morning after generating a graph, and it’s already out-of-date. During the worldwide COVID-19 outbreak, preprint servers such as bioRxiv and medRxiv have again shown that they are the most effective way of communicating science rapidly. A collection of all papers on COVID-19 deposited on these two servers is available here, and […]
Methods papers for MD997 – 2020 edition
I run a Masters module called MD997. Over six weeks, students have to write a grant proposal and then assess their peers’ proposals at a mock grant panel. Each student bases their proposal on a paper. They present that paper to the class and then they write their proposal using the paper as a springboard. […]
Not What You Want II
This is a follow up to a previous post. Despite what the title says, it is what we wanted. Our paper on dongles has just been published in Journal of Cell Science. The previous post on quantixed, explained all about the paper and the background to it. The journal featured our paper as a research […]