NIAID-BRCs AI Codeathon 2.0 · September 16–18, 2026 · Argonne National Laboratory
Turning a researcher’s free-form analysis request into a validated, runnable Galaxy workflow — by reusing, adapting, or building one.
Project page: https://niaid-brc-codeathons.github.io/projects/interview-driven-workflows/
This is a draft pitch, not a plan.
What follows is a one-slide proposal from the organizing team. It exists to seed a team, not to constrain one. Scope, methods, target organism, and success criteria are all still open — expect them to change substantially. Turning this into a real plan is the team’s first job, and it lands in the project charter due August 28, 2026.
Convert a researcher’s free-form analysis request into a validated, runnable Galaxy workflow — either by reusing, adapting, or building one.
Build an MCP-native interview agent that first searches the IWC registry to decide use / adapt / build, grounds analysis choices in BRC Analytics data and tools, and resolves missing information through follow-up questions. Use Galaxy Foundry to translate intent into validated workflow steps.
Demonstrate both creation of a new workflow and conversational adaptation of an existing published workflow.
Workflow validation and Planemo test success; correctness of tool/version/parameter selection; regression testing for adapted workflows; and expert scoring of analysis choice, provenance, and clarification quality.
A longer write-up is available at https://gist.github.com/dannon/ceb8685f9c958f5a20ad6e4b0eb630ca.
This repository is the team’s working space for the codeathon — code, notebooks, data pointers, and notes. Replace this README with the real thing once the charter is written. Team members get access through the NIAID-BRC-Codeathons organization; accept the invitation if you have not already.
Three end-to-end runs of the Galaxy Workflow Foundry pipelines, each with a run dashboard, the generated workflow, tests, validation reports, and a phase-by-phase write-up. The site version of this page is at https://niaid-brc-codeathons.github.io/interview-driven-workflows/.
| Case study | Pipeline | Outcome | Dashboard | Write-up |
|---|---|---|---|---|
| Ebola virus host RNA-seq | INTERVIEW → GALAXY | 12/12 phases, Planemo tests passing | dashboard | CASE_STUDY.md · bundle |
| Candida auris SCF1 adhesin RNA-seq | PAPER → GALAXY | 10/12 phases, static gates green, execution not yet passing | dashboard | CASE_STUDY.md · bundle |
| Candida auris reproduction (Sonnet) | PAPER → GALAXY | 12/12 phases, UDT authoring, deployed to usegalaxy.org | dashboard | foundry-run-review.md · bundle |
Test fixtures are not committed. Each bundle’s test-data-refs.json records the pinned source URLs, checksums, and subsetting recipe needed to regenerate them; dashboard links into test-data/ will not resolve on the published site.