During the pandemic, many virtual seminar programmes have popped up. One series, “Motors in Quarantine“, has been very successful. It’s organised by my colleagues Anne Straube, Alex Zwetsloot and Huong Vu. Anne wanted to know if attendees of the seminar series were a fair representation of the field. We know the geographical location of the seminar attendees, but the challenge was to find a way to examine research activity at a country level.

The coronavirus crisis has meant that scientific meetings and seminars have moved online. This change has led to me wondering: why don’t scientists give talks the way that musicians do gigs? The idea is: after posting a preprint or publishing a paper, a scientist advertises that they will livestream a seminar to explain the work. Attendance is free.

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 (EF)? Essentially, EF is the average distance that you are propelled forward per heart beat. The higher the number, the more efficient you are at running.

I’m a long-term fan of Weezer. Such was the brilliance of their first two albums that I have stuck with them through thick and thin. And dear me, there has been some very thin music. Nonetheless I own every album – thirteen of them. Among them are six albums entitled “Weezer”. These records are colloquially referred to by the colour of the album. In chronological order: blue, green, red, white, teal and black.

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 paper is received to when it was published. The code is below and can be found here.

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 does the screening. Preprints wait in a queue to be screened.

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 it is growing daily.

A short tech-tip this week. How can you find a line of code somewhere on your computer? I often find that I need to write a line of code and I can’t remember the exact syntax. To add to the frustration, I can remember writing a similar line before, but can’t remember in which file it was (or for what project, or even when it might’ve been). How can I quickly track that line down? Today I needed to write a LoadWave command in Igor.

As part of the series on development of early career researchers in the lab, we spent a session (with homework) to learn how to write a document in LaTeX. Like the R session, we spent an hour or so in a room with laptops writing a document and then homework was set, to be completed for the following week. There’s a mix of TeX abilities in the lab.

As a scientist and a music lover, I see parallels in the process of doing science and in making music. They’re both creative endeavours after all. The lab’s latest paper is like an album release. The authors of the paper are like the players in the band. See, the analogy works quite well.

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 poll in our lab Slack workspace to find out what R skills people in the lab already had.