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.

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. Segments quickly expanded to pretty much any section of a course and to include running segments, to separate them from cycling.

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 the workspace. This causes a problem with the solution I outlined previously.

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 a bit of preamble. If you just want to know the answer, click here.

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.

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 compounded by the fact that there are so many options to make movie files and not much guidance on what is the best method.

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: the vials are in specific positions in a box (10 x 10) there are 13 boxes to a cane we have 5 canes Ideally, to retrieve the correct vial from the cell store requires a map.

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.

It is time for my annual post of the papers I selected for a module that I teach (MD9A8, the module formerly known as MD997). Previous selections are grouped here or here. The list serves as a snapshot of interesting papers published in the previous 12 months or so. I hope it is useful to others who are looking for lists of papers to read, for student selections or for anything else.

I am having some fun running AlphaPulldown on a computing cluster. A requirement is to have input sequences in FASTA format. I found that I needed to get ~600 sequences. I had a list of the relevant Uniprot IDs. Surely getting the sequences for these proteins should be straightforward? Solution The Uniprot IDs can be converted – using the ID Mapping Tool on the Uniprot website – into any number of other IDs.