We are pleased to announce that BOSC and the newly-renamed Bio-Ontologies and Knowledge Representation (BOKR) will join forces for a day at ISMB/ECCB 2025!
Fausta Gantús, DR © Fotografía digital (exposición normal) 2019 Redes sociales de la artista X Esta es una reproducción digital, con fines de divulgación, de una obra original proporcionada por su autora o propietaria. Todos los derechos están reservados por la artista.
I gave a workshop on preregistration to honours students last Friday and mentioned that preregistration provides evidence that you created your hypothesis in advance of seeing the data. The students naturally asked how to prove that the data were collected after the preregistration. I pointed out that one can’t even prove that the data are real. At least, nobody has put together an accepted method for this.
Where the first workshop day had several talks about new and old features of the Chemistry Development Kit (CDK), the second day was a hackathon day. We hacked and we talked.
What is a complex problem and what do we need to tackle it? Problems can be simple or complex. Simple problems have a clear first step, a known answer, and steps you can follow to get the answer. Complex problems do not have a single right answer. They have many possible answers or no answer at all. What makes complex problems really hard is that they can change over time. They have lots of different pieces that connect in unexpected ways.
Joachim Schöpfel, Niels-Oliver Walkowski and I are excited to announce the Open Divide Lecture Series (2025–2026), a year-long exploration of the challenges, contradictions, and evolving landscape of Open Access and scholarly publishing.
Librarians have ceded our control of collections and collection-building in the digital realm to a few commercial vendors. Among other things, this has professional ethical implications. We must host our own digital resources or be subject to censorship and extortion.
The DataCite metadata schema provides many options for describing relations between research objects. This talk, from the Winter 2025 ESIP meeting, describes how the most common relationTyprs are used, opportunities for more detail in DataCite metadata, and measures of repository connectivity with bright-spots.
A copyedited, annotated transcript of my interview with Martin Eve.
Anyone reading this newsletter has surely used the frontier models like ChatGPT, Claude, and Gemini. I’ve written a few posts about using local models but haven’t really talked much about the tools I use to directly interact with these models. Those previous posts interact with local models using tools like ellmer in R or my own biorecap package which interacts with a locally running Ollama server.
I first saw the mirror fern in a valley that shouldn’t have existed. I had been leading a planetary survey team on Ross 249-b, an exoplanet flagged as a high-probability candidate for habitability but never explored beyond remote sensing.