now

Here I have listed some things that I have going on right now that I also care to have floating out there on the web.

2024-12-22

Since February I have worked on a wonderful research project at the molecular dynamics group. During this project, I worked together with Jan Stevens and Bart Bruininks to build a suite of tools for setting up very large and complex molecular dynamics simulations, called bentopy. Now that the project has concluded, I look back very fondly on my time in this wonderful lab and I am very exciting to continue collaborating with these great people.

Also worth mentioning— and I will phrase this as a joke: I developed a sense of agency. Agency is a wild thing to have, you should try it.

2023-12-28

Over December I’ve worked a lot on tid and what has become a little ecosystem of related tools and libraries. I’ve become friends with Maya while collaborating on these tools.

Over our many fun discussions about the projects, we noticed how we consider these part of a wider fabric. And from the need to organize the ideas and tasks that spring from our collaboration, we set up the broader weft project.

2023-12-04

Last week, I found a wonderful second-hand ThinkPad T490s through marktplaats. I set it up with Arch, hikari, tid and all of my other favorite pieces of software. Just the way I like it. No hassle.

Excited to outline my current setup in a lot of detail, if I come around to that. I have been very happy with it on my desktop for a while now, and it is perhaps even more wonderful on this laptop. On a high level, I see that as a step toward expressing the framework through which I look at my personal computation right now. In the sense of first expressing the material situation and experience of the world in that context as a prerequisite to a formulation of a ‘romanticism about computers (good)’ that I has been waiting to crystallize within me.

(For those who know, I will just grant you the reference to “Something something I am standing on a rock, I am here.”)

I am working on a document where I reflect on my computational situation. The gist is that over a couple of kernel updates, my Chromebook with Arch devolved into a shitty Chromebook with Ubuntu Mate which was even slower than necessary. Following a series of unpleasant computational experiences where I was limited analyzing the data of an experiment by the two-core 4 GB ram 32 GB sd internal drive-situation of my Chromebook, I decided to have a cursory look at the second-hand market for something that suits my needs better. And I struck gold pretty much immediately. So glad. Perhaps I will post the more thorough reflection to my labbook at some point. But I have a bit of a vent out there as well, if you are curious about some of the background.

2023-10-21

computers

Whenever I do computers, I do a lot of rust. This has been the case for a long time now, and I still really love it.

Over the past two weekends, I have worked on my terminal xvg graph viewer called phrace.

Another weekend project of mine is a slideshow program, that I have given the working title of leif. It takes a file in my own markup language and turns them into slides. Font rendering in pixel fonts, image dithering, layout engine that drives me crazy. All the good stuff.

I’ve gotten very interested in going through the source code of some of the software I use in research. Especially the Gromacs source seems interesting to me. Did I say I currently have a thing for molecular dynamics?

In fact, for the past summer I have hit my head on my desk from time to time in a number of disparate attempts at writing an xtc compressed trajectory file format reader. This is dumb and misguided, since I only work on the project when I am utterly tired, and the intricate bit compression scheme requires more concentration than I can realistically muster.

Whenever I find myself working on stuff like this, I post about my progress on mastodon. Sometimes I also stream my work on these projects.

academics

Last summer, I got my BSc degree in Biology, with a major in Molecular Life Sciences. Currently I am working towards my Master’s degree in Biomolecular Sciences.

weekends—the shape of the year

I have been very good in doing weekends, so far in this (academic) year. That is really cool and important.