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GBCC 2025

Galaxy and Bioconductor Community Conference 2025 — Cold Spring Harbor Laboratory, NY · June 23–26, 2025.

Status: Scaffold — program ingested; per-tool entries queued. The full session-by-session program (5 oral sessions, 11 lightning talks, 10 hands-on workshops, 50+ posters) has been extracted into _program-extracted.md; bulk tool-page generation is the next pass.

Why this is in the vault

GBCC2025 is the first-ever joint conference between Galaxy and Bioconductor — bridging the two flagship open-source bioinformatics communities (Galaxy = workflow / web-platform / training; Bioconductor = R packages for statistical genomics). For the AACR tools matrix this is uniquely valuable: it's the one place each year where workflow tools and analysis packages get presented under the same roof, with explicit "package wrapped into Galaxy" sessions making the integration story load-bearing.

GBCC2025 is the sister event to EuroBioC2025 (Barcelona, Sep 17–19, 2025) — together they form the two annual community meetings in Bioconductor's calendar. EuroBioC is the European leg with a tighter R/package focus; GBCC is the joint US event where Galaxy workflow tools and Bioconductor packages share the same program. Roughly 30% of GBCC2025 oral talks introduce a named Bioconductor or Galaxy tool; another 20% introduce cross-platform integration scaffolding (e.g., GalaxyMCP, Bioconductor-R-Shiny on Galaxy, automatic R package wrapping).

What we have to work with

Source Coverage Notes
Schedule (at-a-glance) full 4-day grid gbcc2025 program/glance
Scientific program every oral talk: title, speaker, affiliation, session, chair gbcc2025 scientific_program
Meeting report community recap with lightning-talk + workshop summaries Galaxy June 2025 newsletter
CSHL meeting page conference-level metadata, organizers meetings.cshl.edu (galaxy)
Repo Hugo source for site; speaker/abstract YAML github.com/Bioconductor/gbcc2025
Abstract book full abstracts (PDF) URL referenced as meetings.cshl.edu/posters/galaxy25/gbcc25_AbstractBook.pdf — 404 at fetch time; flagged for retry
CoFest recap which Bioconductor tools wrapped into Galaxy at the post-conf hackathon Bringing Bioconductor to Galaxy (Bioconductor blog)
Plenary recordings keynotes + selected talks "GBCC2025 YouTube Playlist" referenced in the meeting report — playlist URL not surfaced in current crawl
Slides varies Bioconductor speakers typically deposit to Zenodo Bioconductor community; Galaxy speakers vary

Program shape

  • Day 1 (Mon Jun 23) — Registration → dinner → Opening Ceremony → "GBCC2025 LIVE!" evening session.
  • Day 2 (Tue Jun 24) — Keynote 1: Sergei L. Kosakovsky Pond (Temple) "Interactive Genomic Analytics with responsive notebooks, in-the-browser computation, and AI-assisted development" → Oral Session 1 (9 talks; Galaxy infrastructure / AI agents / R-Bioc-into-Galaxy integration; chair Sehyun Oh) → 5 concurrent workshops (Galaxy workflows; AI-predicted-outcomes inference; Galaxy backend; autonomous workflows for materials labs; spatial-omics) → Oral Sessions 2A (12 talks; Galaxy workflows + ML + multi-omics; chair Jenny Drnevich) and 2B (12 talks; Bioconductor packages — RAIDS, signifinder, SEMplR, HiFi-MAG, etc.; chair Vincent Carey) → wine-and-cheese networking → poster session 1.
  • Day 3 (Wed Jun 25) — Keynote 2: Charlotte Soneson (Friedrich Miescher Institute) "From classes to community — How Bioconductor has advanced my research" → Lightning Talks (11 short talks: Tidyomics, atena, iscream, SummarizedExperiment-tidy interfaces, kinome analysis, FAIR-EASE, Galaxy-E ecology, etc.) → Birds of a Feather sessions → Oral Session 3 (6 talks; imaging × multi-omics, Visium HD, sosta, genome-assembly curation; chair Lambda Moses) → 5 concurrent workshops (Bioc-tools-in-Galaxy; microbiome with Bioc; immunopeptidogenomics; AnVIL secure cloud; IGB Galaxy alignment) → Oral Session 4 (6 talks; community / training / global access; chair Mike Love) → second BoF block → banquet → DJ Party + Galaxy 20th Anniversary celebration.
  • Day 4 (Thu Jun 26) — Keynote 3: Jason Williams (CSHL) "Conquest of Abundance: Genomics in a Time of Plenty" → Oral Session 5 (8 talks; plyxp, microbiome orchestration, predicted-data inference, mitology, Galaxy ecology, infrastructure; chair Scott Cain) → lunch + departure.
  • Post-conference (Jun 27–28) — CoFest at the Sandra and Edward Meyer building (separate registration) — Galaxy + Bioconductor hackathon. Featured artifact: GSVA wrapped as a Galaxy tool; on-site team Doyle, Yagudayeva, Soneson, Ramos Pérez.

Counts: 3 keynotes · 53 oral talks across 5 sessions · 11 lightning talks · 10 workshops · 50+ posters · ~6 BoF slots.

Organization

conferences/gbcc-2025/
├── index.md                 # this page
├── _program-extracted.md    # working notes — every talk with package + tags
├── themes.md                # cross-day synthesis (deferred)
├── digest/                  # day-by-day recap (deferred)
│   ├── day-1.md
│   ├── day-2.md
│   ├── day-3.md
│   └── day-4.md
├── topics/                  # cross-cutting bins (deferred)
│   ├── galaxy-infra/        # AI agents, MCP, dataset collections, scheduling
│   ├── bioc-packages/       # short-talk Bioc package introductions
│   ├── spatial-imaging/     # Visium HD, sosta, histopathology FMs
│   ├── multi-omics/         # RAIDS, signifinder, gINTomics, MOSClip-adjacent
│   ├── training-community/  # Africa, Canada, sertão, AnVIL training
│   └── integration/         # the seam — Bioc-in-Galaxy, R-Shiny-on-Galaxy
├── tools/                   # PRIMARY artifact — one entry per package or Galaxy tool
│   └── index.md
└── sessions/                # full abstracts, indexed (deferred until abstract-book PDF available)
    └── index.md

The tools/ directory is, as in the EuroBioC2025 vault, the load-bearing artifact. GBCC adds two new entry shapes the EuroBioC template doesn't quite cover: Galaxy workflow tools (web-deployable, often with no R/Python "import" surface) and integration scaffolding (e.g., automatic R-package-to-Galaxy wrapping pipelines). The tools/index.md template stub flags this as Open Question 5.

What's different from EuroBioC2025

  • Two ecosystems on one program — every "Bioc package" entry has a sibling "Galaxy tool" question: was it wrapped? is the wrapper PR open? what's its tool-shed ID? The sister-vault cross-link from eurobioc-2025/tools/<pkg> to gbcc-2025/tools/<pkg> matters more here because GBCC is where the wrapping conversation actually happens.
  • Galaxy is workflow-first, conceptually adjacent to Nextflow Summit 2026 even though the engines and communities differ. Cross-link target: nextflow-2026/ — the seam to watch is "what does each platform's tool-wrapping story look like, and which papers reference which?"
  • CoFest as a separate artifact — the post-conference 2-day hackathon produces concrete "package X is now a Galaxy tool" deliverables that don't exist after EuroBioC. These belong in the GBCC vault, not the per-package pages.
  • Training and global-access talks are first-class — Session 4 (Doyle on Bioconductor in Africa; Gauthier on UseGalaxy Canada; Santana on Brazilian sertão research; Kucher on AnVIL training) is structurally larger than EuroBioC's equivalent. We track these as community-talk entries (not tool entries) but link them from the relevant tool pages where applicable.

Sources

Next step

See tools/ for the per-tool entry template and the talks-with-packages list. After that template is reviewed against the EuroBioC2025 version, the bulk pass populates ~25–30 tool pages from _program-extracted.md. Open question — whether Galaxy workflow tools share the Bioconductor template or get their own variant — is tracked there as Q5.