GBCC 2025 — Tools¶
GBCC2025 ran 3 keynotes + 53 oral talks across 5 sessions + 11 lightning talks + 10 hands-on workshops + 50+ posters. A substantial fraction of the oral and lightning talks introduce or update a named Bioconductor package, a Galaxy tool, or a cross-platform integration artifact — that's what this directory captures. Each entry below corresponds to one tool presented at GBCC2025 (Bioconductor package, Galaxy tool, or integration scaffolding).
Status: Active — bulk extraction complete (24 tool entries across Bioconductor packages, Galaxy tools, and cross-platform integration). Talks-with-packages source list at ../program-notes.md. Slide DOIs (Zenodo) and YouTube playlist links TBD pending Bioconductor community deposits.
Per-tool entry template¶
Each tool gets its own page (tools/<package-slug>.md) following this structure:
# <PackageName>
**One-line description** — what the package does in plain language.
- **Maintainer:** <name> (<institution>)
- **Ecosystem:** Bioconductor / Galaxy / cross-platform
- **Bioconductor:** [package page] *(if applicable)*
- **Galaxy ToolShed:** [tool page] *(if applicable)*
- **Source:** [GitHub link]
- **Vignette / docs:** [link]
- **Status at GBCC2025:** new release / major update / methods talk / case study / workshop / integration demo
## Talk at GBCC2025
- **Speaker:** ...
- **Day / session:** Day X — Oral Session N / Lightning / Workshop
- **Slides:** [Zenodo DOI]
- **Video:** [GBCC2025 YouTube playlist link if recorded]
- **Abstract / talk page:** [scientific-program link or CSHL abstract-book page]
## What it does
2–3 sentences: the problem it solves, key methodological idea, what it consumes/produces.
## Where it fits in the corpus
- AACR 2026: [link if mentioned]
- ISMB 2026: [link if mentioned]
- RECOMB 2026: [link if mentioned]
- Nextflow Summit 2026: [link if mentioned]
- EuroBioC 2025: [link if also presented at sister event]
## Notes
Free-form impressions, benchmarks claimed, comparisons to alternatives. For Galaxy-wrapped Bioconductor tools: link the wrapper PR or the `tools-iuc` shed entry.
Tool index¶
24 entries from oral sessions, lightning talks, workshops, and the post-conference CoFest deliverable, ordered by day/session. Three keynotes deferred to the keynotes/ subdirectory and day digests.
Skipped (not in this table): community / training / non-tool talks (Doyle on Bioconductor in Africa; Gauthier on UseGalaxy Canada; Santana on sertão research; Kucher on AnVIL training); methods talks without a clearly named package anchor (Hansen on allele-specific methylation; Nanda on viral-infection signaling networks; Lakshman on orthology-at-scale; Eagles on Visium HD; Moses on LUAD spatial; Campillo on differential transcript usage — flagged for follow-up after the abstract book is retrieved).
| Package / Tool | Ecosystem | Domain | Speaker | Day / Session | Slides | Video | Mentioned elsewhere |
|---|---|---|---|---|---|---|---|
| GAIA | Galaxy | AI agent / NLI | Qiu, Goecks | Day 2 / Oral 1 | TBD | TBD | GalaxyMCP |
| GalaxyMCP | Galaxy | AI / MCP | Baker, Qiu, Goecks, Schatz | Day 2 / Oral 1 | TBD | TBD | GAIA |
| AnVIL | Galaxy + cloud | cloud platform | Mosher, Schatz et al. | Day 2 / Oral 1 + Day 3 workshop | TBD | TBD | bioc-to-galaxy |
| torch | CRAN / R | DL / epigenetic clock | Jamie Park | Day 2 / Oral 2A | TBD | TBD | — |
| Galaxy-ML2 | Galaxy | ML tool suite | Lyra Junior, Qiu | Day 2 / Oral 2A | TBD | TBD | — |
| NOVA | Galaxy | neutron scattering | Gregory R Watson | Day 2 / Oral 2A | TBD | TBD | — |
| TPV Broker | Galaxy | scheduler | De Geest, Srikakulam et al. | Day 2 / Oral 2A | TBD | TBD | — |
| gINTomics | Bioconductor | multi-omics integration | Velle, Romualdi | Day 2 / Oral 2A | TBD | TBD | MOSClip ↗ EuroBioC |
| RAIDS | Bioconductor | ancestry inference | Belleau, Deschênes et al. | Day 2 / Oral 2B | TBD | TBD | — |
| signifinder | Bioconductor | cancer signatures | Stefania Pirrotta | Day 2 / Oral 2B | TBD | TBD | mitology |
| SEMPLR | Bioconductor | TF-binding variants | Kenney, Boyle, Phanstiel | Day 2 / Oral 2B | TBD | TBD | — |
| Meta-iPep | Galaxy | metaimmunopeptidomics | Do, Mehta | Day 2 / Oral 2B | TBD | TBD | — |
| HiFi-MAG | Galaxy | long-read metagenomics | Collins, Schatz | Day 2 / Oral 2B | TBD | TBD | mia |
| bsseq | Bioconductor | ASM methylation (ONT) | Kasper D Hansen | Day 2 / Oral 2B | TBD | TBD | — |
| SynExtend | Bioconductor | orthology / ExoLabel | Lakshman, Wright | Day 2 / Oral 2B | TBD | TBD | — |
| SeqArray | Bioconductor | rare-variant annotation | Xiuwen Zheng | Day 2 / Oral 2B | TBD | TBD | — |
| Voyager | Bioconductor | spatial multiscale (LUAD) | Lambda Moses | Day 2 / Oral 2B | TBD | TBD | SpatialData ↗ EuroBioC |
| splicelogic | Bioconductor | differential transcript usage | Campillo, Love | Day 2 / Oral 2B | TBD | TBD | plyxp |
| atena | Bioconductor | transposable elements | Robert Castelo | Day 3 / Lightning | TBD | TBD | GSVA→Galaxy |
| iscream | Bioconductor | BED queries (Rcpp) | James Eapen | Day 3 / Lightning | TBD | TBD | — |
| KRSA | Bioconductor | kinome analysis | Ali Imami | Day 3 / Lightning | TBD | TBD | — |
| sosta | Bioconductor | spatial omics | Gunz, Robinson | Day 3 / Oral 3 | TBD | TBD | spatialFDA ↗ EuroBioC, SpatialData ↗ EuroBioC |
| IWC | Galaxy | workflow registry | Marius van den Beek | Day 3 / Oral 3 | TBD | TBD | — |
| spatialLIBD | Bioconductor | Visium HD | Nicholas Eagles | Day 3 / Oral 3 | TBD | TBD | Voyager, SpatialData ↗ EuroBioC |
| mia | Bioconductor | microbiome | Tuomas Borman | Day 3 workshop + Day 4 / Oral 5 | TBD | TBD | mia ↗ EuroBioC, miaTime ↗ EuroBioC |
| Tidyomics | Bioconductor | tidyverse for omics | Stefano Mangiola | Day 3 / Lightning + Oral 4 | TBD | TBD | plyxp |
| bioc-to-galaxy | Integration | auto-wrap pipeline | Joshi, Cumbo, Blankenberg | Day 2 + Day 3 workshop | TBD | TBD | GSVA→Galaxy, mia |
| plyxp | Bioconductor | dplyr for SummarizedExperiment | Landis, Love | Day 4 / Oral 5 | TBD | TBD | Tidyomics, DeeDeeExperiment ↗ EuroBioC |
| mitology | Bioconductor | mitochondrial activity | Pirrotta, Bonora, Calura | Day 4 / Oral 5 | TBD | TBD | signifinder |
| FAIR-EASE | Galaxy | Earth-system | Jossé, Detoc, Bodéré | Day 4 / Oral 5 | TBD | TBD | — |
| ipd | CRAN / R | post-prediction inference | Stephen Salerno | Day 2 workshop + Day 4 / Oral 5 | TBD | TBD | — |
| GSVA→Galaxy | Integration | wrapper deliverable | Cumbo, Joshi, Raubenolt, Blankenberg | CoFest (Jun 27-28) | — | — | bioc-to-galaxy, atena |
Why this format¶
- Cross-vault links matter — same as EuroBioC2025: tool released here, used in cancer-research talk X, benchmarked in methods paper Y, all one click apart
- Slides + video + vignette + Bioconductor-or-Galaxy page in one place
- Ecosystem field is GBCC-specific — separates R packages from Galaxy tools from cross-platform scaffolding without forcing them into separate directories
- Status field distinguishes a v1.0 announcement from a 4-year-old package's annual update from a methods talk from an integration demo
- Mentioned-elsewhere points the reader at the EuroBioC2025 vault when the same package was presented at both events (Soneson, Mangiola, Castelo, Pirrotta, Borman, and others appear in both lineups)
Open questions for the pilot¶
- Granularity — ✅ inherited from EuroBioC2025: one page per tool
- AACR dossier mirroring — ✅ inherited: full entry in both vaults, cross-linked
- Sample tools to draft first — open: candidate set is GAIA + GalaxyMCP (Galaxy AI scaffolding pair, exercises the ecosystem-field variant) and RAIDS / signifinder / sosta (canonical Bioconductor methods talks). plyxp is also a strong template-validation pick because it's a tidyverse-for-SummarizedExperiment package — exactly the cross-cutting kind of tool we want to make sure renders well
- Edge case: non-Bioconductor tools — open: GBCC's edge case is GAIA / GalaxyMCP / NOVA — Galaxy-side tools with no Bioconductor page at all. Proposed: same template, swap "Bioconductor" line for "Galaxy ToolShed" and use a "Galaxy" ecosystem badge
- Galaxy workflows vs. Bioconductor packages — same template, or split? — open: a Galaxy tool/workflow has different surface (XML wrapper, ToolShed entry, training material) than a Bioconductor package (DESCRIPTION, vignette, BiocCheck). The template above tries to unify them with the "Ecosystem" field plus optional Bioconductor/Galaxy-ToolShed lines. Decision deferred until 3 sample entries (1 Bioconductor, 1 Galaxy-only, 1 integration scaffold) are drafted by hand. If the unified shape is awkward, fall back to two templates and add a third for "integration scaffolding" (Bioc-in-Galaxy wrappers, GalaxyMCP-style protocols, automatic-wrapping pipelines).