It’s plot recreation time! In this post, we’ll look at how we can recreate a plot in R. I thought it might be useful to provide the solution but also to detail the process I went through to get there. We have a FACS plot taken from a BD FACS Aria machine: Briefly, it’s a […]
Category: science
Stacked Up: my academic software stack
The software that we use to do our work is our academic software stack. I often see requests for advice on which software works well. Since recommendations from labs that have road-tested a few options are quite valuable, I thought I would document what we’re currently using and why. I have tried to note if […]
Exploding, Impacting: looking at bioRxiv preprint view dynamics with R
One of the joys of posting a preprint is seeing that people are viewing, downloading and (hopefully) reading your paper. On bioRxiv you can check out the statistics for your paper in the metrics tab. We posted a preprint recently and it clocked up over 1,000 views in the first day or so. This made […]
Monster Movie: making movie files from microscopy data
What’s the best way to make a movie file from microscopy data? Maybe you need to generate a movie for the supplementary info for a paper, or insert one into your electronic lab notebook, or to show in a talk. The problem is that the requirements for each of those is different. This situation is […]
Bird’s Eye View: using R to generate inventory maps for lab reagents
This is a rather niche post, but the method can likely be adapted for other use cases. In the lab we have many different cell lines stored in liquid nitrogen. The arrangement is: Ideally, to retrieve the correct vial from the cell store requires a map. We have a FileMaker Pro database of all of […]
Pre Self: what fraction of a journal’s papers are preprinted?
Answering the question of what fraction of a journal’s papers were previously available as a preprint is quite difficult to do. The tricky part is matching preprints (from a number of different servers) with the published output from a journal. The easy matches are those that are directly linked together, the remainder though can be […]
Tips from the Blog XVI: getting FASTA sequences
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 […]
No Synths! Use of AI in scientific publications
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 […]
Crosstown Traffic: new paper on vesicle transport
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. […]
Line Up: recommendations for the best human cell line
Here is a summary of the info I gleaned from asking for recommendations for the best human cell line. These were my criteria: For context, we currently use a number of human cell lines in the lab: HeLa, RPE1, HCT116, SKOV3; as well as many others in the past: HEK293, DLD-1, U2OS. I consider HeLa […]