While I was a program director at NSF, I led the SI2 (Software Infrastructure for Sustained Innovation) program that had been created by Manish Parashar and Abani Patra, then was led by Gabrielle Allen, before it was my turn to shape it and lead it for about four years, from 2012 to 2016. This program initially funded projects that developed and maintained software, as well as projects that planned and built community institutes around software.

The Front Matter blog is launching a new membership model today. In August 2021 this blog started offering optional paid membership via the Buy Me a Coffee service. Unfortunately. two things happened: a) Paypal dropped supporting Buy Me a Coffee for membership payments at the end of last year, and b) there wasn't really any uptake of this support model, even if only charging $3 (or a cup of coffee) per month.

What is renv RStudio’s renv package is a powerful dependency management toolkit for R. It allows you to create a lockfile that records the exact versions of R packages used in a given project, and provides tooling to install exactly those same versions on another machine, or at a later point in time. This is very useful to create an isolated project environment for reproducibility or production purposes.

A quick post about a puzzle called Wordle that is currently taking over the internet. It’s a mastermind-like game where the object is to guess an unknown 5-letter word. Puzzlers are encouraged to share their results after completing a puzzle. Here is an example for puzzle 192. So how do you know if your performance on today’s puzzle was any good? Why not benchmark your effort against the crowd?

Between self-supervised approaches for transfer learning, contrastive losses and representational similarity analysis, these last few years were as rich in ideas as buzzing with confusing words. Here is a little dictionary to celebrate the end of 2021. If you have time for only one entry, check out the self-supervised learning one above all!

Fresh into 2022, the Front Matter blog today is launching an important new feature: a full-text search of all blog posts. An example query would be for reference manager. As the Front Matter blog has a lot of posts about reference managers, a tag would also have worked in this particular case, but tags are much less flexible and become overwhelming when used too frequently.

I keep returning to the problem of viewing large graphs and trees, which means my hard drive has accumulated lots of failed prototypes. Inspired by some recent discussions on comparing taxonomic classifications I decided to package one of these (wildly incomplete) prototypes up so that I can document the idea and put the code somewhere safe.

My relationship with reading borders on pathological (and by “borders on” I mean “has literally been a topic of discussion in therapy”). I mean, I’ve gotten it under control somewhat —we’ll use my 2014 Goodreads Reading Challenge as a bar for a bit out of control—which means I can take a look back on my 2021 year in books without too much self-recrimination.

This recent tweet made me chuckle. It does seem that many structural biology papers have a title that begins “The structural basis of…”. I took a quick PubMed survey to look at its popularity. First a search of "structural basis"[ti] AND "journal article"[pt] gives us the number of research papers with “structural basis” in the title. This plot of the number of papers with this title each year is levelling off.

I recently got a new laptop (see Making the M1 leap if you’re curious how that journey went), and in so doing, got lots of great advice about how other developers set up their machines.