Version history

{
  "objective": "Continue Jesse Gray synthetic-biology cell-control trajectory jesse-gray-20260525T042012: execute the MERFISH-based ARC-SARE/FOS hybrid enhancer validation challenge, incorporating domain and rigor review feedback (CREB site count, SST subtype breakdown, scran normalization). Artifact graph: landscape=cd0dcb48-b157-4475-a584-da1f2d1643c9, knowledge_gap=6bb44f01-a63a-4758-871c-85684972ceab, hypothesis=06bd01a3-0a80-4c32-94a3-5a6805384b6f, challenge=4275e95a-a5e7-4ccd-8292-d289964f966a. showcase_query_id=cell-control-construct-loop",
  "requester_ref": "agent:persona-jesse-gray",
  "packet_kind": "science_discovery",
  "next_action": "execute_merfish_hybrid_enhancer_challenge",
  "instructions": "1. Validate that hybrid ARC-SARE/FOS construct design includes ≥3 CREB sites as per domain review revision. 2. Run MERFISH profiling of hybrid vs. monolithic ARC SARE and FOS reporters (sparse optogenetic activation, ≥200 cells/condition). 3. Compute scran log-normalized Spearman ρ for endogenous ARC/FOS correlation (target: ρ ≥ 0.3). 4. Run LNP vs. AAV delivery comparison (target: ρ ≥ 0.5). 5. Report SST-Martinotti vs. SST-NGF subtype breakdown. 6. Update hypothesis confidence score after challenge result.",
  "input_refs": [
    "cd0dcb48-b157-4475-a584-da1f2d1643c9",
    "6bb44f01-a63a-4758-871c-85684972ceab",
    "06bd01a3-0a80-4c32-94a3-5a6805384b6f",
    "4275e95a-a5e7-4ccd-8292-d289964f966a",
    "620a22d0-5933-49c0-aae2-473502561595",
    "c792598c-2c45-4deb-abb5-0142975bfc63",
    "a60cb82b-c827-4077-81f5-f715bd5d124a"
  ],
  "context_refs": {},
  "acceptance_criteria": [
    "domain_reviewer and rigor_reviewer verdicts recorded on hypothesis",
    "at least 1 revision applied after review",
    "challenge execution attempted or blocked with documented reason",
    "hypothesis confidence score updated",
    "MERFISH readout covers ≥500 gene panel anchored to ABC Atlas"
  ],
  "deliverable_refs": [],
  "priority": "high",
  "state": "requested",
  "roles": [
    "domain_reviewer",
    "rigor_reviewer"
  ],
  "role_aliases": [],
  "source_policy": "public-safe",
  "source_run_id": "jesse-gray-20260525T042012",
  "signals": {},
  "metadata": {}
}