I’ve spent the better part of this weekend putting OpenAI’s latest offerings through their paces - both the newly released open-weight models and GPT-5 itself. Armed with a selection of coding challenges, mathematical problems, and the sort of esoteric research queries that usually separate the wheat from the chaff, I’ve been conducting what amounts to a weekend-long torture test of these systems.

Here’s a new slide that wasn’t in my talk last summer. Mike and I are working on our respective talks for DinoCon 2025 — a timely concern, since Mike presents next Saturday and I’m on next Sunday. My talk will be an adapted and upgraded version of the keynote talk I gave at the Tate Geological Museum’s Annual Summer Conference last summer.

I recently wrote a piece about leaving academia for biotech. I left academia for industry in 2019. I spent four years at a consulting firm before joining Colossal Biosciences. This week I’m returning to the University of Virginia School of Data Science as a tenured associate professor and dean of research. The transition from academia to industry can be tricky, but it’s also increasingly common.

A lot is happening. If you have been following this project more closesly, you may have already seen some interesting updates, but I will post it here too. First, a quick recap. In March I started a new Blue Obelisk project to collect CCZero IUPAC names from primary literature (paper still pending). It turned out we can automate that, while legally not violating any laws or licenses.

A review of sorts, of questionable objectivity. Forty-eight minutes, so grab some popcorn and settle in. Or run screaming. Up to you!

Back in 2022, I was hyped about Retrieval-Augmented Generation (RAG).The novelty of seeing a search engine spit out a direct answer — with citations! — in tools like Elicit and Perplexity felt like the future. I even predicted that this “answers-with-citations” model could become the prominent paradigm for academic search. Three years later, that prediction has partly come true.

This week’s recap highlights nanoMDBG for metagenome assembly from nanopore reads, the SCassist AI-based workflow for single-cell analysis, discovery and characterization of GxE and GxG effects in a vertebrate model, the PIGEON framework for estimating gene-environment interaction for polygenic traits, and long-read alignment with multi-level parallelism.

Join me for an advanced reader copy of Synthetic Eden and be one of the first in the world to read my full debut novel

Birthdays, BOSC, Beatles and Bioinformatics with a Merseybeat Conference season is upon us, and the GigaScience team have just returned from a magical mystery tour to Liverpool. Regular readers will know GigaScience launched at the ISMB (International Conference on Intelligent Systems for Molecular Biology) in 2012, and every year we attend and celebrate our birthday at the meeting.

After much reflection, the time has come for me to retire, effective at the end of this year. This marks the end of a deeply fulfilling chapter in my life — one filled with purpose, collaboration, and a shared commitment to open knowledge and community-driven progress in open source, open access publishing. I’ve been fortunate to work with so many brilliant people over the years, and I’m extremely proud of what we’ve achieved together.

Wie wird aus einem geförderten Pilotprojekt eine dauerhaft tragfähige Infrastruktur? Diese zentrale Frage stellten sich viele der Teilnehmenden des Hands-on-Labs „Vom Drittmittelprojekt über die Community zur etablierten Struktur – Erfahrungsaustausch und Erarbeitung von Empfehlungen“ (Arning et al. 2025) auf dem 9. Bibliothekskongress / der 113. Bibliocon in Bremen am 26.06.2025.