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Bioconductor Workshop Platform

Hosted infrastructure for authoring and running Bioconductor workshops — Galaxy-based infrastructure providing containerized, Bioconductor-pre-installed workshop environments. Workshop authors ship Quarto/Rmarkdown content paired with a Docker image so attendees get a one-click reproducible session.

  • Maintainer: Alexandru Mahmoud (Bioconductor core team)
  • Platform: workshop.bioconductor.org
  • Related package: BiocBook (Jacques Serizay) — the Quarto-book authoring framework that pairs with the platform
  • Status at EuroBioC2025: infrastructure / runtime platform

Workshop at EuroBioC2025

  • Presenter: Alexandru Mahmoud (Bioconductor core)
  • Day / session: Day 2 (Thu Sep 18, 2025) — afternoon hands-on workshop (parallel with OSTA, mia, msqrob2, iSEE)
  • Workshop title: "Bioconductor Workshop Platform authoring"
  • Format: hands-on tutorial walking authors through building a workshop image and deploying it to the hosted platform
  • Workshop materials: to verify — typically linked from workshop.bioconductor.org
  • Video: workshops not recorded; the Bioconductor YouTube playlist covers plenaries only
  • Abstract / schedule: eurobioc2025 schedule

What it does

The Workshop Platform is a Galaxy-style on-demand container hosting service: an attendee opens a URL, gets a fresh Bioconductor-preinstalled R/RStudio session in a browser, and runs the workshop's Quarto/Rmarkdown materials without any local install. Authors build a Docker image with their package + dependencies, register the workshop, and the platform handles spin-up, isolation, and tear-down. It is the runtime that hosts BiocBook-authored content during BioC, EuroBioC, and GBCC hands-on sessions.

How it works

Core idea. A Galaxy-derived backend orchestrates per-attendee Docker containers behind a Keycloak-authenticated web frontend. Each workshop is packaged as a Docker image preloaded with the relevant Bioconductor release + workshop-specific dependencies; the platform spins up one container per attendee on demand and proxies an in-browser RStudio session to it.

Inputs / outputs. Author input: a Docker image (typically built on a bioconductor/bioconductor_docker base, layered with the workshop's package and Quarto/Rmarkdown materials) plus a workshop registration record. Attendee input: a workshop URL + Bioconductor account (Keycloak SSO). Output: a fresh, isolated RStudio session in the browser with the workshop content checked out and ready to run; teardown is automatic after the session ends.

Key innovation. Pairing with BiocBook (Jacques Serizay's Quarto-book authoring framework) closes the loop: BiocBook generates the workshop content as a Quarto book tied to an R package, the package bundles its Docker image build instructions, and the Workshop Platform hosts the resulting image. Authors get a one-pipeline path from package → book → hosted workshop without managing servers or per-event JupyterHub deployments.

Parameters worth knowing. Choice of Bioconductor release base image (release vs devel). Per-container resource limits (CPU/RAM/timeout — exact values not in the public landing page). Whether the workshop is registered as public or gated. Materials format (Quarto book via BiocBook is the recommended path; raw Rmarkdown also works).

Canonical example. Not specified in vignette — there is no single canonical example; the platform routinely hosts the EuroBioC2025, BioC2025, and GBCC2025 hands-on sessions (OSTA, mia, msqrob2, iSEE all use it). The Workshop Platform authoring session at EuroBioC2025 itself was the meta-example, walking authors through building a Docker image and registering it.

Where it fits in the corpus

  • AACR 2026: no direct dossier; relevant as runtime infrastructure for any AACR adjacent workshop content
  • BiocBook — pairs with the platform as the authoring half (BiocBook → Workshop Platform pipeline)
  • iSEE (entry) — iSEE workshops are typical Workshop Platform tenants
  • OSTA (entry) — OSTA chapters can be served via the platform for hands-on sessions
  • Day 3 closing keynote (Jacques Serizay) — likely covered the BiocBook half of this pipeline
  • GBCC 2025: queued — used for GBCC hands-on tutorials too

Notes

Distinct from BiocBook: BiocBook is the authoring tool (Quarto-based book scaffolding tied to a package); Workshop Platform is the runtime (Galaxy-style on-demand container hosting). Together they form the pipeline used by EuroBioC, BioC, and GBCC for hands-on tutorials.