Outline

One-Sentence Version

Galaxy Notebooks turn a documented Galaxy history into a reproducible communication artifact: narrative, outputs, provenance graph, and extracted workflow report stay connected.

Reader

Bioinformatics readers who know Galaxy histories and workflows but do not yet see documentation as part of the reproducibility surface.

Proposed Structure

1. Problem: histories preserve execution but not communicative intent.
2. Design: history-attached notebooks reuse Galaxy Pages, revisions, sharing, and API.
3. Authoring modes: human solo, human plus in-app agent, external agent via API.
4. Narrative-to-workflow: notebook references identify meaningful outputs; graph walk recovers provenance.
5. Graph confirmation: users review the extracted structure visually, not from a flat job list.
6. Report continuity: the notebook seeds the extracted workflow report.
7. Evidence: implementation scope, tests, and three worked vignettes demonstrating notebook-driven extraction.

Do Not Let This Become

• A generic “AI chat in Galaxy” paper.
• A Pages refactor paper.
• A workflow extraction paper that forgets the notebook narrative.