Articles by quantixed

Over and Over: Preprint revisions on bioRxiv

April 7, 2021 | quantixed

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, ...
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Os Mutantes: an implausible naming system for SARS-CoV-2 mutants

February 27, 2021 | quantixed

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 ...
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Target: monitoring a running goal in R

February 11, 2021 | quantixed

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 ...
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Color Bars

June 23, 2020 | quantixed

Here is a fun post about using colour palettes in R. It starts with a computer game… After a few years of sporadically playing Super Mario World 2 – Yoshi’s Island on the Retropie, I made it to the final level. In the background, as Bowser approached, I noticed that those ...
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Running Free: Calculating Efficiency Factor in R

May 19, 2020 | quantixed

Joe Friel reposted an article earlier this year on Efficiency Factor in running. Efficiency Factor (EF) can be viewed in Training Peaks software and he describes how it is calculated. This post describes how I went about calculating EF in R using a single gpx file. What is Efficiency Factor (...
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Same Time Next Year: crunching PubMed data

May 8, 2020 | quantixed

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 ...
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Screenager: screening times at bioRxiv

March 30, 2020 | quantixed

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 ...
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Get Better: R for absolute beginners

February 18, 2020 | quantixed

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 ...
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Get Better: early career researcher development

January 14, 2020 | quantixed

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 ... [Read more...]

Notes from a panel II: Value of successful BBSRC grants

October 1, 2019 | quantixed

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 ...
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Communication Breakdown

June 11, 2019 | quantixed

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 ...
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Turn A Square: generative aRt

May 26, 2019 | quantixed

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 ...
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All Around The World: Maps and Flags in R

March 20, 2019 | quantixed

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 ...
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Til I Die: Seeking new music

November 30, 2018 | quantixed

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 ... [Read more...]

Multiplex: Small multiple artwork from GPX tracks

September 21, 2018 | quantixed

I’d seen the small multiple artwork of running and cycling routes from Marcus Volz’s R package Strava all over the web. Ads for “posters of your GPS tracks” pop up on Reddit and I’d notice a few #Rstats people put up their posters on Twitter. I’ve ...
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