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Protocol-to-Agent Builder

Turn any protocol — wet-lab SOP, microscopy workflow, computational pipeline — into a grounded, queryable assistant that can answer practical execution questions and produce checklists.

  • Lead: ,
  • Theme: Research tooling & AI agents
  • Repo:

Team

Why this project

Protocols at Scripps live as PDFs, methods sections, SOPs, and slide decks — formats that aren’t structured for an agent to reason over. Lifting them into a structured, queryable form is broadly useful across the institute and directly aligned with the hackathon’s AI-tooling premise.

What a team could build in one day

A prototype that:

  • Ingests protocols from PDFs, text, spreadsheets, or web pages.
  • Extracts steps, materials, timings, parameters, hazards, and dependencies.
  • Normalizes them into a structured representation.
  • Exposes the result through chat, checklist, or workflow-card views.
  • Answers grounded questions with links back to the source passages.

Minimum viable demo: one real protocol ingested end to end, with a user asking practical execution questions and getting source-grounded answers.

How Claude and AWS help

  • Claude is central — extraction, normalization, grounding, and question answering all use it.
  • AWS hosts storage, retrieval, embeddings, and the lightweight app infrastructure to make the assistant usable during the event.

Stretch directions

  • Compare two versions of a protocol and surface the diff.
  • Generate reagent / shopping lists.
  • Produce execution checklists or calendarized task sequences.
  • Support multiple protocol types with shared templates.