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Charlotte Soneson — "From classes to community — How Bioconductor has advanced my research"

Affiliation: Friedrich Miescher Institute for Biomedical Research (FMI), Basel Day / session: Day 3 (Wed Jun 25, 2025) — Keynote 2, Grace Auditorium (9:00–10:00) Talk title: "From classes to community — How Bioconductor has advanced my research" Slides (Zenodo DOI): to verify after publish — Bioconductor speakers typically deposit within ~2 weeks of the meeting Video: GBCC2025 playlist Abstract / schedule: GBCC2025 program

Thesis

A career-arc keynote, not a tool launch. The "classes to community" framing reads as an argument that Bioconductor's S4 data classes (SummarizedExperiment, SingleCellExperiment, and the spatial / tidy descendants) are not just engineering convenience — they are the substrate on which a community of methods authors can compose work without re-litigating data shape every time. Soneson is well placed to make the argument concretely, drawing on a decade-plus of method development that has compounded precisely because everyone agreed on the container.

Speaker context

Soneson is one of Bioconductor's most prolific maintainers and reviewers. Her published / maintained software spans single-cell quantification benchmarking, differential expression methodology (with edgeR-adjacent contributions), iSEE (the interactive SummarizedExperiment explorer, with Federico Marini and Aaron Lun), and most recently footprintR for footprinting / single-molecule data. She is also a member of the GBCC CoFest team that wrapped GSVA into Galaxy. The Day-3 keynote slot is a deliberate signal: invite the maintainer-of-many-things to articulate why the ecosystem shape, not any single package, is what advances research.

Connections to the corpus

  • footprintR ↗ EuroBioC2025 — Soneson presented footprintR at EuroBioC2025; the GBCC keynote sits earlier in the calendar but in the same arc
  • iSEE ↗ EuroBioC2025 — Soneson is a co-author; iSEE is a canonical "S4-class-as-substrate" example
  • GSVA → Galaxy — Soneson is on the GBCC CoFest team that produced this wrapper; the keynote and the CoFest artifact share authorship
  • Cross-link to Vince Carey's EuroBioC2025 opening keynote — both are "ecosystem, not packages" arguments, paired naturally as the 2025 Bioconductor keynote diptych
  • AACR axis: bioinfo-tools — ecosystem-level rather than single-tool

Open questions

  • How much of the talk is autobiographical (specific projects: iSEE, footprintR, benchmarking work) vs. abstract argument about classes and community? Career-arc keynotes can go either way.
  • Does Soneson take a position on the Python/scverse boundary — i.e., does "community" stop at R/Bioconductor, or does it extend to interop with AnnData / SpatialData? Relevant given the GSVA→Galaxy CoFest crosses an even larger boundary.
  • Any concrete asks — funding, recognition, citation practice for software authors — or strictly retrospective? The slot accommodates either.