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Day 3 — Wednesday Jun 25, 2025

Day 3 is the most Bioconductor-flavored day of the meeting — Charlotte Soneson's career-arc keynote opens it, eleven lightning talks introduce small-but-named R packages back-to-back, and Mike Love chairs the late-afternoon community / training session. Wedged between are six imaging × multi-omics oral talks (chaired by Lambda Moses), five concurrent workshops including the Blankenberg "Bioconductor tools in Galaxy" session that anticipates the post-conference CoFest, and two birds-of-a-feather blocks. The day closes with the conference banquet and the Galaxy 20th Anniversary DJ party.

Morning

Charlotte Soneson (Friedrich Miescher Institute) opened with From classes to community — How Bioconductor has advanced my research — a career-arc keynote rather than a launch talk. Soneson is one of the most prolific Bioconductor maintainers active today and a co-author at EuroBioC 2025 (footprintR), so the talk works as a natural bridge between the two events: the same person, the same ecosystem, two recap pages three months apart.

The lightning-talk block (10:30–11:15) ran 11 short talks. Coverage in the Galaxy newsletter recap surfaces only a partial roster: Ali Imami on a kinome-analysis R package (name TBD); James Eapen (Van Andel) on iscream, a fast Rcpp+htslib BED-file query engine; Sunita Sharma on ciliary gene regulation; Stefano Mangiola (Adelaide) with a Tidyomics teaser ahead of his Oral Session 4 talk; Robert Castelo (Pompeu Fabra) on atena for transposable-element analysis. The remaining six are described in the recap by topic but not by speaker — tidy-style interfaces for SummarizedExperiment objects (probably distinct from the plyxp Day-4 talk but plausibly adjacent), Bioconductor microbiome tools, ML interpretation, credential security in Galaxy, FAIR-EASE Earth-system workflows, and Galaxy-E ecology extensions. The full lineup with names is gated on the abstract-book PDF, which was unreachable at fetch time.

A BoF block (11:15–12:00) ran self-organized topical sessions; workflow-reproducibility and ML-integration are mentioned as examples but the full BoF list isn't surfaced in the program.

Afternoon

Oral Session 3 (1:00–2:00, chaired by Lambda Moses) was the imaging × multi-omics × spatial block. Marius van den Beek opened with IWC — the Intergalactic Workflow Commission — Galaxy's standardized-workflow registry and testing pipeline. Ilaria Billato and Marcel Ramos Pérez followed with a standardized R/Bioconductor framework for integrative analysis of histopathological images alongside multi-omics data — Ramos Pérez maintains MultiAssayExperiment and curatedTCGAData, and Billato also presents at EuroBioC 2025, putting both speakers in the cross-vault overlap set. Cameron Watson, Luke Sargent, Allison Creason on Galaxy tools for histopathology foundation models continued the digital-pathology theme. Nicholas Eagles (LIBD) on Visium HD analysis from a Bioconductor-user perspective — likely SpatialExperiment-extended, though the specific package is not in the title. Samuel Gunz / Mark Robinson presented sosta — a framework for analyzing anatomical structures from spatial-omics data — a Robinson-lab artifact that connects directly to the EuroBioC spatial stack (spatialFDA ↗ EuroBioC, SpatialData ↗ EuroBioC, DESpace ↗ EuroBioC). Delphine Lariviere et al. closed with universally accessible interactive curation workflows for large genome assembly.

Five concurrent workshops ran 2:00–3:30. Daniel Blankenberg's "Streamlining Bioinformatics: Adding Bioconductor Tools in Galaxy" is the most consequential — it's the workshop-form of the bioc-to-galaxy Day 2 oral and the immediate precursor to the post-conference CoFest's GSVA→Galaxy wrapper deliverable. Tuomas Borman ran "Orchestrating Microbiome Analysis with Bioconductor" — the mia / miaverse workshop, a re-taught version of the analogous mia ↗ EuroBioC workshop. Pratik Jagtap on immunopeptidogenomics in Galaxy (companion to Meta-iPep on Day 2). Frederick Tan on AnVIL for secure controlled-access computing. Ann Loraine on Galaxy-history-based alignment comparison in IGB.

Oral Session 4 (4:00–5:00, chaired by Mike Love) was the community / training / global-access block — structurally larger than EuroBioC's equivalent, and one of the genuinely distinctive features of the joint conference. Maria Doyle on Bioconductor in Africa; Carol Gauthier / Charles Coulombe on UseGalaxy Canada; Subina Mehta on mass-spectrometry multi-omics training materials; Natalie Kucher / Mike Schatz on AnVIL training in the cloud; Carolina Santana / Pieter Spealman / Gabriel Perron on molecular ecology at the Brazilian sertão. Stefano Mangiola closed the session — Democratising the Analysis of the Human Cell Atlas with Bioconductor — promoting the Tidyomics ecosystem (tidySingleCellExperiment, tidybulk, etc.) as the access-layer for HCA-scale analysis. Mike Love chairing this session is itself notable — he's the plyxp co-author and the through-line for the "tidy interfaces to S4 data classes" thread.

A second BoF block ran 5–6 PM. The 6–8 PM banquet was followed by an 8–11 PM DJ party doubling as the Galaxy 20th Anniversary celebration — the implicit closing-night event of the meeting (Day 4 wraps at noon).

What to chase

  • The complete lightning-talk lineup with names — six of eleven speakers are not surfaced in the current crawl, including the SummarizedExperiment-tidy-interface talk that may overlap or compete with plyxp. The abstract-book PDF is the gating artifact.
  • The cross-walk between Borman's mia workshop here and the mia ↗ EuroBioC and miaTime ↗ EuroBioC talks/workshop — same lineage, two events, three months apart; track which features were shipped in between.
  • Whether the Eagles Visium-HD talk anchors on a specific package (spatialLIBD-family or new) and whether the Moses LUAD spatial talk is a Voyager / SpatialFeatureExperiment update — both are flagged as methods talks pending abstract-book retrieval.