With the fervour of someone with an n = 1 positive experience, I thought I’d write about what I learned from a recent writing retreat. My University organises one-day events to encourage writing. They’re on-campus, in the neutral territory of the Library, so perhaps calling them “writing retreats” is a little far-fetched. Nonetheless, the idea […]
Author: Stephen Royle
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 […]
Exodus: moving to Mastodon
I jumped ship from Twitter following the Musk takeover in 2022. Seeking an alternative, I joined Mastodon and didn’t look back. Since then, I’ve enjoyed many wonderful interactions and conversations; and I feel a bit sad at what Twitter turned into. Now, with many more people realising that Twitter/X is not appropriate for scientific discussions, […]
King of the Mountain: using R to bag a Strava KOM
One of the best features of Strava is the battle to be King (or Queen) of the Mountain. Originally, in cycling, segments were typically climbs or difficult sections of road, and the simple idea, is who can complete the segment in the quickest time. Hence they would be KOM/QOM, King or Queen of the Mountain. […]
Slacker II: archiving information from a Slack workspace
I wrote previously about how to archive a Slack workspace. Well, now Slack announced a new policy, effective from August 26th, 2024. Under the new policy, messages and files older than one year in workspaces on the free tier will be deleted. This is in addition to the 90 day limit for viewing content in […]
Prehistoric: when do authors preprint their papers?
Previously, I took advantage of a dataset that linked preprints to their published counterparts to look at the fraction of papers in a journal that are preprinted. This linkage can be used to answer other interesting questions. Such as: when do authors preprint their papers relative to submission? And does this differ by journal? There’s […]
Smaller: methods to reduce the size of a PDF file
Hot on the heals of the post on how to downsize microscopy movie files, let’s look at ways to shrink the size of a PDF file. There’s several ways to tackle this – suggestions came from this thread on Mastodon. Scenario: you have created a preprint/manuscript/proposal in PDF format. It looks great and is 18.4 […]
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 […]