Bio/cheminformatician, software developer, open scientist. πΊπΈ living in Bonn π©πͺπͺπΊ (he/him)
Current projects: @NFDI4Chem and @dalia
π bridged from β https://scholar.social/@cthoyt, follow @ap.brid.gy to interact

@cthoyt.scholar.social.ap.brid.gy
Bio/cheminformatician, software developer, open scientist. πΊπΈ living in Bonn π©πͺπͺπΊ (he/him)
Current projects: @NFDI4Chem and @dalia
π bridged from β https://scholar.social/@cthoyt, follow @ap.brid.gy to interact
Iβve read today a contributor to an open source project says, in substance: "If generated code is accepted in the project, I will stop contributing because I donβt want to spend time trying to understand the code in order to contribute just to see it changed the next generated commit" [β¦]
When I talk about the impact of language-model-based and "agentic" coding on open-source communities, and on human to human interaction, I am more often than not talking about: - How I cannot trust there is a human on the other end who wants to learn or be part of my community - How it is an [β¦]
@andrewnez then I challenge you to write a program to make revving your car's engine into music :)
@andrewnez are you musical? do you want to try and record some of these covers? happy to supply guitar, bass, or saxophone
alternate perspective, if you're from a background with high respect and position: your title isn't part of your label, that's modeled with a relationship to the kind of degree you got, when, and by whom it was conferred
one minor way I try and promote early career researchers in academia is to always remove titles (e.g., Dr. and Prof.) from senior researchers in written text
-> currently building the @NFDI bibliometric knowledge graphs for NFDI Section International Engagaement
@egonw @bioregistry does the linkml handle render for you alright? fosstodon is blocked on scholar.social
just submitted an abstract to present @bioregistry at the @[email protected] 2026 Virtual LinkML Community Symposium
the proposed talk is about the `bioregistry validate linkml` command, which can help LinkML modelers to choose standard prefixes for their CURIEs and URIs
it'll expand on [β¦]
@biohackrxiv sounds great, will read soon! building a more sustainable foundation than pandoc would be a key step towards this. My experience contributing to pandoc/inara/the JOSS platform left a lot to be desired
there's an unfortunate conflict between open science (I can participate in discussion and contribute to code on a centralized platform like GitHub) and sovereign science (I can't easily contribute or meet people on internal platforms like institutional GitLab instances) anyway, my EBI GitLab [β¦]
@niklaskorz feels like something that would get listed on @bonnjetzt
[Fires of December spoilers]
do you think that the sixth word is related to the dawnshard(s?) that Hoid held?
@egonw lol
blogged today about ChEBI, data properties in OWL ontologies, computational chemistry, atomic numbers, and basis sets
https://cthoyt.com/2026/09/04/chebi-atomic-numbers.html
all part of @NFDI4Chem, now onto a weekend full of dancing π
a semantic web-heavy paper that declares a prefix map in its appendix! very cool!
https://www.sciencedirect.com/science/article/pii/S2666546824000429
i'm signing off pull requests with this from now on:
π« No generative artificial intelligence was used to produce the code and text for this contribution; only human intelligence
anyone have ideas on how to make this text better?
#opensource #openscience #python #github #git #software [β¦]
like any sane person, I auto-formatted the code before. and they added in a spurious space while editing the variable names. stay safe out there
i submitted a beautiful, hand-crafted PR with good variable names, which got merged, then the maintainers updated it in a follow-up to change the variable names to be cryptic. crazy times we live in
RE: https://mastodon.social/@andrewnez/117172702770260949
lincoln, nebraska got me