Publications by quantixed
Til I Die: Seeking new music
I’ve been following the tweets from an account called Albums You Must Hear @Albums2Hear. Each tweet is an album recommended by the account owner. I’m a sucker for lists of Albums That I Must Hear Before I Die since I’m always interested in new (or not so new) music recommendations. I wanted to assemble a list of the albums that I don’t ha...
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All Around The World: Maps and Flags in R
Our lab is international. People born all over the world have come to work in my group. I’m proud of this fact, especially in the current political climate. I’ve previously used the GoogleMaps API to display a heat map on our lab webpage. It shows where in the world people in the lab come from. This was OK, but I wanted to get an R based solu...
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Garmonbozia: Using R to look at Garmin CSV data
Garmin Connect has a number of plots built in, but to take a deeper dive into all your fitness data, you need to export a CSV and fire up R. This post is a quick guide to some possibilities for running data. There’s a few things that I wanted to look at. For example, how does my speed change through the year? How does that compare to previous...
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Turn A Square: generative aRt
A while back I visited Artistes & Robots in Paris. Part of the exhibition was on the origins of computer-based art. Nowadays this is referred to as generative art, where computers generate artwork according to rules specified by the programmer. I wanted to emulate some of the early generative artwork I saw there, using R. Some examples of early ...
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Communication Breakdown
There is an entertaining rumour going around about the journal Nature Communications. When I heard it for the fourth or fifth time, I decided to check out whether there is any truth in it. The rumour goes something like this: the impact factor of Nature Communications is driven by physical sciences papers. Sometimes it is put another way: cell bi...
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Notes from a panel II: Value of successful BBSRC grants
This post follows on from the last post on BBSRC Responsive Mode funding. Another frequent question from applicants is: “How much can I ask for?” One answer is: the same amount as successful grants. This information is freely available and can be downloaded from the UKRI website. All awarded grants can be searched (even those that have comple...
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Get Better: early career researcher development
How can we contribute to the development of early career researchers in a lab environment? I’m talking about how people in the lab acquire “soft skills” or “get better” in ways that are parallel to doing research. This sort of training can get overlooked in the chase for new results and the excitement of doing biomedical research. I’m...
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Get Better: R for absolute beginners
As part of the series on development of early career researchers in the lab, we spent three sessions over three weeks learning the basics of R. In my book “The Digital Cell”, I advocate R as the main number-crunching software but the R literacy in my lab is actually quite mixed. In order to know how to pitch the training, I conducted a quick ...
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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 – one of the people who d...
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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 what journals declare as the time from when a p...
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