Skip to content

Jacques Serizay — "Enhancing genomic research with community-driven flexible software"

Affiliation: Institut Pasteur, Paris — Spatial Regulation of Genomes unit Day / session: Day 3 (Fri Sep 19, 2025) — closing keynote Talk title: "Enhancing genomic research with community-driven flexible software" Slides: Zenodo 10.5281/zenodo.17191256 Video: Bioconductor YouTube — plenaries playlist (keynotes recorded) Abstract / schedule: eurobioc2025 schedule

Thesis

Flexible, community-driven software is the multiplier on genomic research — but "flexible" has a specific operational meaning: composable packages, low-friction authoring of teaching material, reproducible compute substrates, and a clear path from a research script to a vignette to a book to a reusable workflow. As the BiocBook author, Serizay is positioned to argue that the authoring layer — Quarto-shaped, Bioconductor-native — is the part of the ecosystem most directly responsible for whether community contributions compound or fragment.

Speaker context

Jacques Serizay runs (or co-runs) work at Institut Pasteur on chromatin organization and regulatory genomics, with an unusually heavy software output for a wet-lab-adjacent group: he is the author of BiocBook, the Quarto-based authoring framework that produces Bioconductor-shaped books (used for OSTA and several other recent titles), and a contributor to the tidyomics / chromatin-tools landscape. The closing-keynote slot for a software-author rather than a methods-author is a deliberate framing choice — it puts the infrastructure of how we share methods on equal footing with the methods themselves.

Connections to the corpus

  • Workshop Platform — the runtime / Docker layer that pairs naturally with BiocBook-authored books; the closing keynote is essentially about this pair
  • OSTA — a BiocBook-shaped book; the canonical concrete example of "community-driven flexible software" producing teaching infrastructure
  • AACR axis: bioinfo-tools — specifically the authoring / reproducibility sub-axis, which is under-represented in the AACR vault and over-represented at EuroBioC
  • Cross-link to the Carey opening keynote — the bookends frame the conference as ecosystem-stewardship

Open questions

  • Concrete BiocBook roadmap — new templates, integration with the Workshop Platform, support for executable code-along formats — vs. a more philosophical "why community software matters" talk?
  • Does Serizay tie this back to his own Pasteur research (chromatin / regulatory genomics) as a motivating use case, or stay at the meta level the whole time?
  • Any policy-level argument — funding, recognition for software authors, citation practices for packages — or strictly tooling? Closing keynotes sometimes use the soapbox for one and not the other.