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GBCC2025 — Program Extracted (working notes)

Internal-use working file. Source for the bulk tool-page generation pass. Not for end-reader consumption — formatting is utilitarian. Sources: gbcc2025.bioconductor.org/program/scientific_program/, gbcc2025.bioconductor.org/program/glance/, Galaxy June 2025 newsletter meeting report, Bioconductor "Bringing Bioconductor to Galaxy" CoFest recap.

Tag legend: - [BIOC] — clearly a Bioconductor R package (has or will have a Bioconductor page) - [GALAXY] — Galaxy tool / workflow / platform feature (XML wrapper or platform-side software) - [INTEGRATION] — cross-platform scaffolding (Bioc-in-Galaxy, MCP protocols, auto-wrapping) - [METHOD] — methods talk; package not clearly named in title (recheck against full abstract) - [COMMUNITY] — community / training / global-access talk; no tool anchor - [?] — unclear from title alone; needs abstract-book lookup

Sparse-coverage flags: - gbcc25_AbstractBook.pdf (CSHL-hosted) returned 404 at fetch time → full abstracts not yet ingested; tool/package mentions hidden in abstract bodies are missed - GBCC2025 YouTube playlist URL referenced in the meeting report but not surfaced in our crawl → video-link column will stay TBD until the playlist is found - Slide DOIs (Zenodo) typically posted 2–4 weeks post-conference; recheck after Aug 2025

Day 1 — Mon Jun 23, 2025 (arrival)

  • 5–7 PM Dinner
  • 7–8 PM Opening Ceremony [no talks indexed]
  • 8–9 PM "GBCC2025 LIVE!" — special evening session

Day 2 — Tue Jun 24, 2025

Keynote 1 (9:00–10:00, Grace Auditorium)

  • Sergei L. Kosakovsky Pond (Temple University) — "Interactive Genomic Analytics with responsive notebooks, in-the-browser computation, and AI-assisted development" — [METHOD] (Pond is the HyPhy developer; HyPhy is implicit ecosystem context, not necessarily a launch artifact)

Oral Session 1 (10:30–12:00, Grace Auditorium; chair Sehyun Oh)

  1. Junhao Qiu, Jeremy Goecks — "Galaxy All-in-One Agent: A Unified Natural Language Interface for Cross-Galaxy Data Analysis" — Tool: GAIA — [GALAXY] [INTEGRATION]
  2. Dannon Baker, Junhao Qiu, Jeremy Goecks, Mike Schatz — "Introducing GalaxyMCP: Integrating AI Assistants with Galaxy Through the Model Context Protocol" — Tool: GalaxyMCP — [GALAXY] [INTEGRATION]
  3. Jayadev Joshi, Fabio Cumbo, Daniel Blankenberg — "Automated integration of R/Bioconductor tools into Galaxy" — [INTEGRATION] (no single package name — auto-wrapping pipeline)
  4. Marius van den Beek — "User-Defined, Safe, and Rapidly Deployable Galaxy Tools with Embedded Type-Safe Editing" — [GALAXY] (YAML tool authoring system)
  5. Aysam Guerler, Ahmed Awan, Alireza Heidari, Bjoern Gruening, et al. — "Bringing Data to Life: Galaxy's New Visualization Framework" — [GALAXY]
  6. Leandro Liborio, Subindev Devadasan, et al. — "Managing materials science workflows with Galaxy at STFC" — [GALAXY] [COMMUNITY] (domain transfer; case study)
  7. Vincent J Carey — "Language-agnostic strategies for genomic data representation in Bioconductor" — [BIOC] [METHOD] (no specific package; framework talk)
  8. Leonid Kostrykin, Beatriz Serrano-Solano, Riccardo Massei, Karl Rohr — "Streamlining the User Experience for Reproducible Image Analysis in Galaxy" — [GALAXY]
  9. Stephen L Mosher, Michael C Schatz, Jonathan Lawson, Robert Carroll — "Enabling Genomic Research at Scale with NHGRI AnVIL: A Cloud Platform for Genomic Data Analysis" — Tool: AnVIL — [GALAXY] [INTEGRATION] (cloud platform)

Workshops (1:00–2:30, concurrent)

  • Marius van den Beek — "Exploring Galaxy Workflows" — [GALAXY] workshop
  • Stephen Salerno — "Inference Challenges and Corrections for AI-Predicted Outcomes" — [METHOD] workshop (post-prediction inference)
  • John Davis, Ahmed Awan — "Galaxy Backend Architecture and Software Development" — [GALAXY] workshop
  • Greg Watson — "Deploying Autonomous Galaxy Workflows for Materials Laboratories" — [GALAXY] workshop
  • Ellis Patrick — "Making Space Count - Strategies for Analysing Spatial Omics Data" — [BIOC] workshop (Patrick's spatial-omics ecosystem)

Oral Session 2A (3:00–5:00, Bush Hall; chair Jenny Drnevich)

  1. Ahmed H Awan, Dannon Baker, et al. — "From Upload to Execution: A Unified Galaxy Workflow Run Interface" — [GALAXY]
  2. John Chilton, Marius van den Beek, Ahmed Awan — "More Usable and More Powerful Galaxy Dataset Collections" — [GALAXY]
  3. Junhao Qiu, Jeremy Goecks — "AI-augmented data analyses in Galaxy" — [GALAXY] [INTEGRATION] (likely GAIA-adjacent; recheck)
  4. Bryan Raubenolt, Akhil Mohan, et al. — "Benchmarking Quantum Machine Learning Models in Galaxy" — [GALAXY] [METHOD]
  5. Jamie Park — "Leveraging Deep Learning with torch in R for Next-Generation Epigenetic Clock Development" — Tool: torch (R) — [BIOC] [METHOD] (epigenetic clock case study)
  6. Paulo Cilas Morais Lyra Junior, Junhao Qiu, et al. — "The Galaxy-ML2 tool suite: Using Galaxy to promote best practices in machine learning for biomedical data science" — Tool: Galaxy-ML2 — [GALAXY]
  7. Gregory R Watson — "NOVA: Leveraging Galaxy for Neutrons Scattering Data Analysis and Visualization" — Tool: NOVA — [GALAXY] (cross-domain)
  8. Fabio Cumbo, Jayadev Joshi, Daniel Blankenberg — "Towards the automatic integration of tools in Galaxy: the anvi'o suite and a new AI-driven automation pipeline" — Tool: anvi'o (auto-wrapped) — [INTEGRATION]
  9. Paul De Geest, Sanjay Srikakulam, et al. — "Dynamic meta-scheduling in Galaxy with TPV Broker for smarter workload distribution" — Tool: TPV Broker — [GALAXY]
  10. Marisa J Loach, Daniel M Johnson, Wendi Bacon — "One Million Heart Cells: Integrating Public Data on Galaxy to Explore How Cardiomyocytes Change in Atrial Fibrillation" — [GALAXY] [COMMUNITY] (case study; single-cell + Galaxy)
  11. Angelo Velle, Francesco Patanè, Chiara Romualdi — "gINTomics, a powerful Bioconductor package for multiomics data integration and visualization" — Package: gINTomics — [BIOC]
  12. Pavankumar Videm, Paul Zierep, et al. — "Bioconductor-R-Shiny Applications on Galaxy" — [INTEGRATION] (Shiny-on-Galaxy)

Oral Session 2B (3:00–5:00, Grace Auditorium; chair Vincent Carey)

  1. Pascal Belleau, Xintong Li, Astrid Deschênes, et al. — "Robust ancestry inference from challenging human molecular data with RAIDS" — Package: RAIDS — [BIOC]
  2. Katherine T Do, Subina Mehta, et al. — "Meta-iPep: A metaimmunopeptidomics pipeline implemented within Galaxy platform to characterize HLA-bound microbial peptides for immunotherapy" — Tool: Meta-iPep — [GALAXY] (pipeline)
  3. Kasper D Hansen — "Analyzing allele-specific methylation using Oxford Nanopore long-read DNA sequencing" — [BIOC] [METHOD] (no clear package name in title; check abstract — Hansen maintains several methylation packages)
  4. Stefania Pirrotta, Laura Masatti, et al. — "Public gene expression cancer signatures across bulk, single-cell and spatial transcriptomics data with signifinder Bioconductor package" — Package: signifinder — [BIOC]
  5. Pariksheet Nanda, Jason E Shoemaker — "Host cell signaling during viral infection network perturbation analysis" — [METHOD] (no clear package — recheck abstract)
  6. Grace E Kenney, Rintsen N Sherpa, Alan P Boyle, Douglas H Phanstiel — "SEMplR: An R package for predicting the effects of genetic variation on transcription factor binding" — Package: SEMplR — [BIOC]
  7. Xiuwen Zheng, Raven Chen — "Enhancing rare variant analysis in biobanks: whole-genome annotation using GDS files" — [BIOC] (Zheng maintains the GDS / SeqArray ecosystem; check abstract for specific package)
  8. Aidan H Lakshman, Erik S Wright — "Orthology Detection at the Scale of Modern Genomics" — [BIOC] [METHOD] (Wright maintains DECIPHER + SynExtend; check abstract)
  9. Lambda Moses, Bianca Dumitrascu — "Multiscale analysis of lung adenocarcinoma spatial transcriptomics data" — [BIOC] [METHOD] (Moses is Voyager / SpatialFeatureExperiment maintainer; check abstract)
  10. Pascal Belleau, Astrid Deschênes, et al. — "Deciphering CLEC12A Negative Regulation of Neutrophil Activation by Network and Functional Enrichment Analyses" — [METHOD] (case study)
  11. Tyler Collins, Alex Ostrovsky, Michael Schatz — "Broadening Metagenomic Horizons in Galaxy: Introducing the HiFi-MAG Pipeline, New Profilers, and Insights from BioDIGS" — Tool: HiFi-MAG Pipeline — [GALAXY]
  12. Beatriz Campillo, Michael Love — "Visualizing and analyzing differential transcript usage" — [BIOC] [METHOD] (Love maintains DESeq2/tximeta/fishpond; check abstract for specific package — likely fishpond or new tool)

Evening

  • 5–6 PM wine-and-cheese networking
  • 6–7 PM dinner
  • 7:30–9:30 PM Poster Session 1 — [POSTERS] 25+ posters (out of 50+ total); not enumerated here

Day 3 — Wed Jun 25, 2025

Keynote 2 (9:00–10:00, Grace Auditorium)

  • Charlotte Soneson (Friedrich Miescher Institute) — "From classes to community — How Bioconductor has advanced my research" — [BIOC] (career-arc keynote; Soneson is a prolific Bioc maintainer — also speaks at EuroBioC2025 footprintR talk)

Lightning Talks (10:30–11:15) — 11 speakers

Per the Galaxy newsletter recap: - Ali Imami — Kinome analysis R package — Package: (name TBD) — [BIOC] - James Eapen (Van Andel Institute) — "iscream: fast and efficient BED file queries" — Package: iscream (Rcpp + htslib) — [BIOC] - Sunita Sharma — Ciliary gene regulation — [METHOD] [?] - Stefano Mangiola (Adelaide University) — Tidyomics package — Package: Tidyomics — [BIOC] (also gives Oral Session 4 talk; lightning was likely a teaser) - Robert Castelo (Pompeu Fabra) — atena (transposable element analysis) — Package: atena — [BIOC] - Plus 6 more covering: tidy-style interfaces for SummarizedExperiment objects (Landis/Love-adjacent? plyxp gets a full Oral Session 5 slot — distinct talk?), Bioconductor microbiome tools, ML interpretation, credential security in Galaxy, FAIR-EASE Earth-system workflows, Galaxy-E ecology extensions - [?] — full lineup of all 11 names not surfaced in current crawl; flagged for follow-up via the abstract-book PDF

BoF Session 1 (11:15–12:00) — [COMMUNITY] self-organized; topics not all indexed (workflow reproducibility, ML integration mentioned as examples)

Oral Session 3 (1:00–2:00, Grace Auditorium; chair Lambda Moses)

  1. Marius van den Beek — "The Intergalactic Workflow Commission: Standardizing, Testing, and Distributing Reproducible Galaxy Workflows" — Tool: Intergalactic Workflow Commission (IWC) — [GALAXY]
  2. Ilaria Billato, Marcel Ramos Perez, et al. — "A standardized R/Bioconductor framework for integrative analysis of histopathological images with multi-omics data" — [BIOC] [METHOD] (Ramos Perez maintains MultiAssayExperiment / curatedTCGAData; recheck abstract for specific package — Billato also presents at EuroBioC2025)
  3. Cameron Watson, Luke Sargent, Allison L Creason — "Advancing digital pathology with Galaxy: Tools for histological imaging foundation models" — [GALAXY] [METHOD]
  4. Nicholas J Eagles, Sarah E Maguire, et al. — "Computational considerations for analysis of Visium HD: A Bioconductor user's perspective" — [BIOC] [METHOD] (Eagles is from LIBD; check abstract for specific package — likely SpatialExperiment-extended)
  5. Samuel Gunz, Mark D Robinson — "sosta: a framework to analyze anatomical structures from spatial omics data" — Package: sosta — [BIOC]
  6. Delphine Lariviere, Erick Duarte, et al. — "Universally accessible interactive curation workflows for large genome assembly" — [GALAXY]

Workshops (2:00–3:30, concurrent)

  • Daniel Blankenberg — "Streamlining Bioinformatics: Adding Bioconductor Tools in Galaxy" — [INTEGRATION] workshop (links to GSVA wrapper + auto-integration)
  • Tuomas Borman — "Orchestrating Microbiome Analysis with Bioconductor" — Package: mia (and miaverse) — [BIOC] workshop (Borman also runs the analogous EuroBioC2025 workshop)
  • Pratik Jagtap — "Immunopeptidogenomics Pipeline in Galaxy for MHC-Bound Neoantigens" — [GALAXY] workshop
  • Frederick Tan — "AnVIL: Secure, scalable computing for controlled access data" — [GALAXY] [INTEGRATION] workshop
  • Ann Loraine — "Galaxy History Based Alignment Comparison in IGB" — Tool: IGB (Integrated Genome Browser) — [GALAXY] workshop

Oral Session 4 (4:00–5:00, Grace Auditorium; chair Mike Love)

  1. Maria Doyle, Umar Ahmad, et al. — "Empowering Bioinformatics in Africa through Bioconductor: Expanding Training and Community Engagement" — [COMMUNITY]
  2. Carol Gauthier, Charles Coulombe, et al. — "Building UseGalaxy Capability in Canada" — [COMMUNITY] [GALAXY]
  3. Subina Mehta, Katherine Do, et al. — "Mass Spectrometry-Centered Multi-Omics: Advancing Galaxy Training Materials for Integrated Analysis and Community Adoption" — [COMMUNITY] [GALAXY]
  4. Natalie Kucher, Michael C Schatz, et al. — "Training and education in the cloud with the NHGRI AnVIL" — [COMMUNITY] [GALAXY]
  5. Carolina O Santana, Pieter Spealman, Gabriel Perron — "Molecular ecology at the sertão - Using Galaxy to empower research in developing communities" — [COMMUNITY] [GALAXY]
  6. Stefano Mangiola — "Democratising the Analysis of the Human Cell Atlas with Bioconductor" — Package: Tidyomics ecosystem (tidySingleCellExperiment etc.) — [BIOC] (community + tool talk)

BoF Session 2 (5:00–6:00) — [COMMUNITY] self-organized

Evening

  • 6–8 PM Banquet
  • 8–11 PM DJ Party + Galaxy 20th Anniversary Celebration

Day 4 — Thu Jun 26, 2025

Keynote 3 (9:00–10:00, Grace Auditorium)

  • Jason Williams (Cold Spring Harbor Laboratory) — "Conquest of Abundance: Genomics in a Time of Plenty" — [COMMUNITY] (training equity, access — not a tool talk)

Oral Session 5 (10:30–12:00, Grace Auditorium; chair Scott Cain)

  1. Justin T Landis, Michael I Love — "plyxp: reimagining dplyr syntax for SummarizedExperiment objects" — Package: plyxp — [BIOC]
  2. Tuomas Borman, Leo Lahti — "Orchestrating Microbiome Analysis with Bioconductor" — Package: mia / miaverse — [BIOC] (oral version of the workshop)
  3. Stephen Salerno, Jiacheng Miao, et al. — "Inference with predicted data – what do we do after we have machine learned everything?" — [METHOD] (likely IPD / ipd-R; check abstract — Salerno also runs the Day-2 workshop)
  4. John Davis, Alireza Heidari, et al. — "Simple and Secure Credential Handling for Tools in Galaxy" — [GALAXY]
  5. Marie Jossé, Jérôme Detoc, Erwan Bodéré — "Bridging Earth System Sciences with Galaxy: Two Years of FAIR-EASE" — Tool: FAIR-EASE — [GALAXY] [COMMUNITY]
  6. Stefania Pirrotta, Massimo Bonora, Enrica Calura — "Dissect mitochondrial activity by transcriptome data with mitology R package" — Package: mitology — [BIOC] (Pirrotta also presents signifinder in 2B)
  7. Coline Royaux, Marie Jossé, et al. — "Galaxy-E: Ecology oriented Galaxy initiative, a 2025 update!" — Tool: Galaxy-E — [GALAXY] [COMMUNITY]
  8. John Davis — "Little errors at big scale: towards efficiency, consistency, and reliability of data in the Galaxy database" — [GALAXY] (infrastructure)

12:00–1:00 lunch + departure

CoFest — Jun 27–28, 2025 (post-conference, separate registration)

Not part of the main 4-day program but produces concrete tool artifacts that belong in the GBCC vault: - GSVA (Gene Set Variation Analysis) — Bioconductor package wrapped as a Galaxy tool; draft PR open. Speakers: Fabio Cumbo, Jayadev Joshi, Bryan Raubenolt, Daniel Blankenberg. On-site team: Maria Doyle, Gretta Yagudayeva, Charlotte Soneson, Marcel Ramos Pérez. Remote: Robert Castelo. — [INTEGRATION] - Future direction: developer guide for wrapping Bioconductor tools; embedding Shiny apps in Galaxy; "maintainer" field in Galaxy tool XML.

Tool/package shortlist for the bulk extraction pass

Confirmed package/tool name in title (clear [BIOC] or [GALAXY] candidates for tool pages):

Bioconductor packages — strong candidates: 1. gINTomics — multi-omics integration (Velle/Romualdi, Day 2 / Oral 2A #11) 2. RAIDS — ancestry inference (Belleau, Day 2 / Oral 2B #1) 3. signifinder — cancer signatures across bulk/SC/spatial (Pirrotta, Day 2 / Oral 2B #4) 4. SEMplR — TF-binding variant effects (Kenney, Day 2 / Oral 2B #6) 5. sosta — spatial anatomical structures (Gunz/Robinson, Day 3 / Oral 3 #5) 6. plyxp — dplyr for SummarizedExperiment (Landis/Love, Day 4 / Oral 5 #1) 7. mitology — mitochondrial activity from transcriptome (Pirrotta, Day 4 / Oral 5 #6) 8. Tidyomics (and tidySingleCellExperiment family) — Mangiola, Day 3 lightning + Day 3 / Oral 4 #6 9. atena — transposable elements (Castelo, Day 3 lightning) 10. iscream — BED file queries via Rcpp+htslib (Eapen, Day 3 lightning) 11. mia / miaverse — microbiome (Borman/Lahti, Day 4 / Oral 5 #2 + Day 3 workshop) 12. torch (in R) — epigenetic clock case study (Park, Day 2 / Oral 2A #5) — note: torch is established; this is a methods-talk anchor 13. (Imami's kinome package) — [?] name TBD from abstract book

Galaxy tools / platforms: 14. GAIA — natural-language Galaxy agent (Qiu/Goecks, Day 2 / Oral 1 #1) 15. GalaxyMCP — MCP protocol for Galaxy (Baker/Qiu/Goecks/Schatz, Day 2 / Oral 1 #2) 16. Galaxy-ML2 — ML tool suite (Lyra Junior, Day 2 / Oral 2A #6) 17. NOVA — neutron-scattering on Galaxy (Watson, Day 2 / Oral 2A #7) 18. TPV Broker — meta-scheduling (De Geest, Day 2 / Oral 2A #9) 19. HiFi-MAG Pipeline — long-read metagenomics (Collins/Schatz, Day 2 / Oral 2B #11) 20. AnVIL — cloud platform (Mosher et al., Day 2 / Oral 1 #9 — and Day 3 workshop) 21. Intergalactic Workflow Commission (IWC) — workflow standardization (van den Beek, Day 3 / Oral 3 #1) 22. Meta-iPep — metaimmunopeptidomics pipeline (Do/Mehta, Day 2 / Oral 2B #2) 23. FAIR-EASE — Earth-system workflows on Galaxy (Jossé, Day 4 / Oral 5 #5) 24. Galaxy-E — ecology-oriented Galaxy (Royaux/Jossé, Day 4 / Oral 5 #7) 25. IGB — Integrated Genome Browser (Loraine, Day 3 workshop)

Cross-platform / integration scaffolding: 26. Auto-wrapping pipeline for R/Bioc → Galaxy (Joshi/Cumbo/Blankenberg, Day 2 / Oral 1 #3) 27. anvi'o auto-wrapped suite + AI-driven automation (Cumbo/Joshi/Blankenberg, Day 2 / Oral 2A #8) 28. Bioconductor-R-Shiny-on-Galaxy (Videm/Zierep, Day 2 / Oral 2A #12) 29. GSVA Galaxy wrapper (CoFest deliverable — Cumbo/Joshi/Raubenolt/Blankenberg)

Methods talks worth a tool page once specific package is confirmed via abstract book: 30. Hansen — allele-specific methylation, ONT long-read ([?]) 31. Eagles — Visium HD analysis ([?] — Bioc package likely from LIBD's spatialLIBD ecosystem) 32. Moses — multiscale spatial-transcriptomics LUAD ([?] — likely Voyager / SpatialFeatureExperiment update) 33. Lakshman/Wright — orthology at scale ([?] — likely SynExtend update) 34. Campillo/Love — differential transcript usage ([?] — likely fishpond / DRIMSeq-adjacent or new)

Excluded from tool pages (community / training / case-study only, no clear tool anchor): - Doyle (Africa training); Gauthier (UseGalaxy Canada); Mehta (MS multi-omics training); Kucher (AnVIL training); Santana (sertão); Liborio (STFC materials science); Loach (heart-cell case study); Belleau-#10 (CLEC12A case study); Nanda (viral signaling); Williams keynote; Pond keynote (HyPhy implicit); Soneson keynote (career arc, not a launch)

Open follow-ups before bulk extraction

  1. Fetch CSHL gbcc25_AbstractBook.pdf — try alternate paths or contact organizers; needed for the 11 lightning-talk full lineup, the [?]-tagged methods talks, and the missing Bioconductor package names in case-study abstracts.
  2. Locate the GBCC2025 YouTube playlist — meeting report mentions it but URL not surfaced; needed for video links across all tool pages.
  3. Confirm Zenodo DOI deposits — Bioconductor speakers typically deposit slides 2–4 weeks post-conference; recheck after Aug 2025.
  4. Cross-walk EuroBioC2025 ↔ GBCC2025 talks by same speaker — Soneson, Mangiola, Castelo, Pirrotta, Borman, Billato, Ramos Pérez at minimum overlap. Cross-link wired both directions in the per-tool pages.
  5. Sponsors / organizers list — captured in index.md but full sponsor table (Silver: CZI, BMS; Bronze: Limagrain, GalaxyWorks, R Consortium) goes in a footer of the digest if/when written.