Structural biology (XFEL crystallography, cryoEM, electron crystallography) data processing methods developer. I use my degree in chemistry to write software to use physics to understand biology. As of 2024, based in Hamburg.
70% coffee by volume. Iâm really into electronics and 3d printing right now. I have a very fluffy and affectionate cat. Big fan of bicycles and trains, better public infrastructure generally, and investment in collective wellbeing generally. Food motivated; very easily bribed with coffee and pastries. Always learning.
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science
XFEL crystallography, cryoEM, electron diffraction, exascale computing, data processing methods development, structural biology methods development
interests
coffee, languages, electronics, 3d printing, patterns and symmetry, neurophilosophy and neuro-everything-else, basic science, math, reading, sewing, cooking, eating, aikido, bicycles, public transit, trains, accessibility, neurodiversity, cats
languages (computer, in order of fluency)
python, bash, C++, MPI/mpi4py, OpenMP, Kokkos, sed, awk, csh, regex, LaTeX, at one point I knew scheme (lisp)
languages (human, in order of fluency)
English (native), Spanish, Japanese, Italian, German (learning), Dutch (learning), ASL (learning)
I guess instance migration is a good time for an #Introduction post. Hello lovely people, I'm here both as a scientific researcher and as a human being, and you can expect a range of genres of posts and interactions from me.
On the work side, I'm a computational scientist at Lawrence Berkeley National Laboratory in the field of biological X-ray crystallography, specifically at free electron lasers. It's a glorious interdisciplinary mess, and the description I give to non-scientists is that i use my degree in chemistry to write software to do math that models the physics of experiments that we're running to learn about biology.
For fellow structural biologists: I work on crystallography data reduction software for the steps between photons hitting the detector and a merged set of structure factors. I also support XFEL experiments, both on site and remotely, and assist in post-experiment data processing as needed. My PhD focused on using simultaneous XFEL crystallography and XES spectroscopy to probe the water splitting reaction in oxygenic photosynthesis. I did a postdoc in computational methods development for cryoEM, and I'm now back to XFEL crystallography but still in methods development.
For fellow software developers: all of our work is open source and mostly under the cctbx project/repo. It's mostly python with a bunch of C++ under the hood (including some low-level stuff redundant with scipy and numpy because those weren't around yet!), plus a user-facing wxPython GUI. More recently we've done a ton of work with GPU acceleration (using Kokkos, for NVIDIA, Intel and AMD architectures) and scaling up at three different national labs' supercomputing centers in anticipation of next-gen experimental capabilities. I derive too much joy from writing bash-sed-awk monstrosities on the occasions we need them to fix an urgent problem during an experiment, and I guess I'm most proud of the fact that I somewhat understand git.
As far as hobbies, the longest-standing one is probably #coffee, followed closely by #language (s) / #languageLearning and a love of #patterns and #symmetry in various contexts. I have too many different ways of making coffee (they have overrun my coffee cupboard), but my favorite remains the classic latte, and by now I can make a better latte than I can buy. I'm trying to refresh my #Japanese and learn #Dutch and #German simultaneously/comparatively, which of course is terrible for speed of learning, but fascinating. So far I've found #ASL the most challenging but also deeply satisfying -- I only have one semester under my belt but hope to take a lot more. I studied and continue to study all the #math and #science I possibly can. Right now I seem to be pretty engrossed in #electronics, #CAD, #3DPrinting, and just generally #DIY-ing/fixing/repairing things. Other active interests include #sewing, #reading, #cooking, #bike commuting, and #publicTransit. My journeys in #aikido and #pottery are on hold but I definitely want to pick them back up when I'm not already overcommitted. I'm casually interested in #neurophilosophy, #neuropsychology, #neurodivergence and #neuroscience. I've taken one course in neurophilosophy and can read literature in the rest, with effort.
On a personal note, I'm trans and nonbinary and very open about it -- I transitioned back when I had to explain what that meant. I've retired from some forms of community engagement and support but I'm very happy to answer any questions I can about the US legal and medical landscapes, available resources, policy and terminology best practices, or whatever you know you shouldn't ask [person in your life].
Finally, I spend a lot of time with my cat Rory (pictured), who is perfect and the most affectionate creature I have ever met. I promise to share photos of him from time to time.
Over the past few days I learned more than a single human mind should be forced to comprehend about USB (form factors, protocols, and the relationships between them) and my conclusion is:
well...... I added the new partitions I needed, but now when I try to recover from my backup, it sees nothing (another computer sees everything properly, so I can still get the files), and when I try to reinstall the OS from scratch, it can't contact the recovery server. Hm.
Debian also really wants internet. It's asking me many times if I'm sure I want to continue without. (It can recognize the existence of the network I should be on, but it can't connect.) This is worrying.
well...... I added the new partitions I needed, but now when I try to recover from my backup, it sees nothing (another computer sees everything properly, so I can still get the files), and when I try to reinstall the OS from scratch, it can't contact the recovery server. Hm.
One of the hills I will die on: Everything is politics.
Whatever you're drawing a line and saying it isn't politics, I beg to differ. Politics have always been life and death for swaths of the population, and quality of life for many more. School funding, healthcare, immigration and asylum, there are people downstream of every single political decision. Politics can be arguing over what to name a particular street, but it is also, and has always been, who lives or dies. For the ways it probably is for you too, think funding hospitals, determining when it's legal to deny care, road safety, airline regulations, food safey, banned choke holds... heck, it's also the ecological regulations that prevent pollution that causes climate change that causes the kinds of massive floods, storms, etc. that decimate communities. Politics is precisely the big-picture, local and global planning that shapes so much of our lives.
It's overwhelming and paralyzing to care about everything at once, and it doesn't help to do that to yourself, so there's nothing wrong with filtering out a lot of it. This is just a commentary on the line of thought that any given event isn't politics anymore once it affects people. On the contrary, that is exactly what makes it politics.
I have dismissed this notification thousands of times manually, maybe tens of thousands.
If you want to replicate, the app is called Notifilter, works on Android, toggle notif permissions on for the app itself, check the box for include system tools when setting up the filter, enter "samsung account" for the app name (it auto expands to com.osp.app.signin) and put the exact title text of the notif as the regex (the leading and trailing slashes were added by the app).
I'm trying out Internxt for cloud file storage and I'm finding I hate the X logo enough to look for alternatives. (I assume they used it before X-nÊe-Twitter did but the association is unavoidable now.) I already moved everything from Google Drive to Internxt. I'd partially migrated to Proton before but ended up backing out. Is this my life now? Lugging my digital belongings from one plce to another once a year or so?
Update: have figured out how to substitute the app icon for the main and helper apps, but still not the drive folder icon or menu bar icon. Websearching anything about the menu bar icons inevitably turns up how to rearrange icons, not how to substitute different ones. Anybody know?
Further in the weeds: I can locate one Icon? file for the drive folder on mac that I can replace but it doesn't actually update. Also it's zero bytes but not a link, so I think this isn't the right place to change it but I'm not sure what is. I already substituted anywhere the icon showed up in Contents/Resources. Can't find any place where the menu bar version might be stored.
I'm trying out Internxt for cloud file storage and I'm finding I hate the X logo enough to look for alternatives. (I assume they used it before X-nÊe-Twitter did but the association is unavoidable now.) I already moved everything from Google Drive to Internxt. I'd partially migrated to Proton before but ended up backing out. Is this my life now? Lugging my digital belongings from one plce to another once a year or so?
Iris Young (he/they/she) (PhD)