Day 4 — Thursday Jun 26, 2025¶
The closing day is short — one keynote, one oral session, lunch, departure — but it's where several through-lines of the meeting land. Jason Williams (CSHL) gives the morning training-and-equity keynote on home turf; Scott Cain chairs the eight-talk Oral Session 5, which is a deliberate mix of the Bioconductor (plyxp, mia/miaverse, mitology) and Galaxy (FAIR-EASE, Galaxy-E, credential handling, database reliability) sides under a single roof. The post-conference CoFest then runs separately on Friday and Saturday at the Sandra and Edward Meyer building.
Morning¶
Jason Williams (Cold Spring Harbor Laboratory) closed the keynote arc with Conquest of Abundance: Genomics in a Time of Plenty — a training / equity / access talk rather than a tool launch, complementing the Day 3 community session under Mike Love's chairing. Williams runs CSHL's training operation, so this is essentially the host-institution closing remarks for a meeting CSHL hosted.
Oral Session 5 (10:30–12:00, chaired by Scott Cain) ran eight talks across both ecosystems. plyxp (Justin Landis, Michael Love) opened — reimagining dplyr syntax for SummarizedExperiment objects — the canonical "tidyverse-for-Bioc" artifact of the meeting, paired with Mangiola's Tidyomics talk on Day 3. Tuomas Borman / Leo Lahti followed with the oral version of Orchestrating Microbiome Analysis with Bioconductor — the mia / miaverse update, pairing the workshop the day before with a 12-minute talk that emphasizes new functionality. Stephen Salerno presented Inference with predicted data — the methodological complement to his Day 2 workshop on AI-predicted-outcomes inference (likely the IPD R package, though the package name is not in the title). John Davis on simple and secure credential handling in Galaxy. Marie Jossé / Jérôme Detoc / Erwan Bodéré on FAIR-EASE — two years of bridging Earth-system science to Galaxy. mitology (Stefania Pirrotta, Massimo Bonora, Enrica Calura) — dissecting mitochondrial activity from transcriptome data — completes the Pirrotta double-bill (signifinder on Day 2). Coline Royaux / Marie Jossé on Galaxy-E, the ecology-oriented Galaxy initiative (a 2025 update). John Davis returned to close — Little errors at big scale — on data efficiency, consistency, and reliability in the Galaxy database.
Afternoon¶
12:00–1:00 lunch and departure. No afternoon program.
The post-conference CoFest ran Friday Jun 27 – Saturday Jun 28 at the Sandra and Edward Meyer building (separate registration). The headline deliverable was GSVA→Galaxy — the Bioconductor GSVA package wrapped as a Galaxy tool with an open PR — produced by Fabio Cumbo, Jayadev Joshi, Bryan Raubenolt, and Daniel Blankenberg, with on-site contributions from Maria Doyle, Gretta Yagudayeva, Charlotte Soneson, and Marcel Ramos Pérez (and remote support from Robert Castelo). This is the artifact that connects the Day 2 bioc-to-galaxy auto-wrapping pipeline talk and the Day 3 Blankenberg workshop into a concrete shipped wrapper.
What to chase¶
- The Salerno inference with predicted data talk and his Day 2 workshop together — confirm whether the underlying R package is
ipd, an IPD-derivative, or a new artifact; this is a methods axis that AACR / RECOMB methods circuits also touch and worth a cross-vault link. - The two John Davis talks (credential handling + database reliability) bookend the session and are infrastructure work that doesn't get its own tool page, but together they describe the operational state of the Galaxy backend in mid-2025.
- The CoFest output beyond GSVA→Galaxy — the Bioconductor blog recap mentions a future maintainer field in Galaxy tool XML and embedded Shiny apps as in-progress directions; track whether either ships before EuroBioC 2025 in September.