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I’m posting this the morning after generating a graph, and it’s already out-of-date.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.

Part of a series on the development of Early Career Researchers in the lab. The idea for the CV clinic came from the lab themselves. We had previously had a session on creating a research profile and a large part of that session was spent looking at CVs. We scrutinised some anonymised CVs and suggested improvements to them. From this, the idea came to put everyone’s CVs through the same treatment!

Part of a series on the development of Early Career Researchers in the lab. We spent a session discussing how to create a research profile. This led to a second session on CVs. Here is an outline of what we covered. CVs We talked about different CV formats first of all. We focussed on academic CVs mainly, but we discussed the differences between academic and CVs for jobs outside academia.

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 testing out a strategy to develop the skills of people in the lab. It’s an experiment.

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. I refreshed my paper list this year to consist of solely papers published (or posted on bioRxiv) in 2019. The previous list is here.