Architecture Reference — Diagram 04

Wet-Lab Round Trip

HARDWARE IN THE LOOP · BLOCK D
PROTOCOL → SAFETY → INSTRUMENT → RESULT
Assay Planning Agent in sandbox (Block B) ProtocolSubmission Protocol Compiler abstract → instrument scripts capability validation Safety & Constraint Engine BSL · reagent · combo policy outside agent trust boundary reject + reason → agent revises Lab State Manager inventory · queue chain of custody Instrument Abstraction Layer submit · status · fetch · cancel the only contract agents see reject + reason → agent revises approved → reserve slot Virtual Lab Simulator simulated instruments · seeded noise zero-change swap with real hardware Physical Instruments robots · plate readers · sequencers cloud labs Telemetry → Provenance normalized AssayResult QC flags + run lineage raw output RED DASHED = REJECTION PATH (AGENT REVISES) · SOLID = EXECUTION PATH · ALIGNMENT: MCP + ANTHROPIC MODEL HARDWARE STANDARD
Agents / instruments Lab services Safety boundary IAL / provenance

Agents only ever see the IAL contract; the Safety & Constraint Engine sits outside any agent's trust boundary — rejections carry reasons so the agent can revise, but no agent path marks a protocol safe. Development runs end-to-end against the Virtual Lab Simulator; swapping to real hardware is one adapter change. IAL aligns with MCP semantics and tracks Anthropic's Model Hardware Standard.