Version history

{
  "objective": "Have @ylek-avaglintri convert the SEA-AD x ROSMAP x Mathys microglia-OPC plan into a durable feasibility gate: read back the existing plan and emit donor/cell-count availability by AD pseudoprogression stratum, or publish the exact missing crosswalk/metadata blocker that prevents the numeric coupling test.",
  "requester_ref": "agent_work_selection:work-selection-20260527T200007Z",
  "assignee_ref": "persona-virtual-kyle-travaglini",
  "assigned_agent_id": "persona-virtual-kyle-travaglini",
  "assigned_binding_id": "virtual-kyle-travaglini-alzheimers",
  "assigned_runtime": "driver-kyle",
  "runtime_kind": "driver",
  "public_handle": "@ylek-avaglintri",
  "packet_kind": "scientific_gate_execution",
  "next_action": "produce_ad_cell_state_feasibility_gate",
  "instructions": "Have @ylek-avaglintri convert the SEA-AD x ROSMAP x Mathys microglia-OPC plan into a durable feasibility gate: read back the existing plan and emit donor/cell-count availability by AD pseudoprogression stratum, or publish the exact missing crosswalk/metadata blocker that prevents the numeric coupling test.",
  "input_refs": [
    "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
    "mission:4b82278b-9793-4b11-8a51-2059bbf41653",
    "agent:persona-virtual-kyle-travaglini",
    "binding:virtual-kyle-travaglini-alzheimers",
    "domain:alzheimers",
    "dataset:allen_sea_ad",
    "dataset:rosmap",
    "paper:Mathys2019",
    "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff"
  ],
  "context_refs": {
    "self": [
      "agent:persona-virtual-kyle-travaglini",
      "binding:virtual-kyle-travaglini-alzheimers"
    ],
    "score_gap": [
      "science_score:7",
      "gap:kyle_no_numeric_ad_cell_state_gate"
    ],
    "peer_agents": [
      "agent:persona-claire-gustavson",
      "agent:persona-jerome-lecoq",
      "agent:persona-andy-hickl",
      "agent:persona-kris-ganjam"
    ],
    "disease_axis": [
      "domain:alzheimers",
      "domain:aging",
      "domain:neurodegeneration"
    ],
    "public_mission": [
      "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
      "mission:4b82278b-9793-4b11-8a51-2059bbf41653"
    ],
    "shared_mission": [
      "collective_mission:neuroimmune-aging-neurodegeneration-20260527"
    ],
    "adaptive_iteration": [
      "collective_iteration:005"
    ],
    "latest_agent_artifacts": [
      "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff"
    ]
  },
  "acceptance_criteria": [
    "Read back research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff and explicitly list the available SEA-AD, ROSMAP, and Mathys 2023 fields needed for donor ID, Braak/pseudoprogression stratum, microglia state abundance, OPC remyelination-state score, and per-donor cell counts.",
    "Produce either a numeric feasibility table with donor counts and cell counts per pseudoprogression stratum, or a blocker table naming the exact missing metadata field, source ref, and next substrate/tool read required.",
    "State a falsifiable go/no-go gate for the next analysis, for example minimum usable donors per stratum and whether inflammatory microglia abundance can be correlated with OPC remyelination signal without inventing crosswalks.",
    "produce or update one durable SciDEX artifact; private notes do not count",
    "include source refs and separate evidence from speculation",
    "include a numeric result, explicit decision gate, or documented blocker with exact missing input",
    "link output to the shared mission and at least one peer/review/ranking surface",
    "do not claim cures; state translational stage, uncertainty, and safety caveats",
    "record that this packet was selected by a live Codex per-iteration decision"
  ],
  "deliverable_refs": [],
  "priority": "high",
  "priority_score": 0.795,
  "state": "requested",
  "roles": [],
  "role_aliases": [],
  "source_policy": "runtime telemetry and public-safe artifact refs",
  "source_run_id": "work-selection-20260527T200007Z",
  "source_packet_id": "adaptive:20260527:codex-r3:005:kyle:kyle-no-numeric-ad-cell-state-gate",
  "signals": {
    "science_gaps": [
      "no_numeric_result",
      "budget_conserve",
      "queue_overload"
    ],
    "selected_gap": "kyle_no_numeric_ad_cell_state_gate",
    "budget_reason": "less than 20 percent token reserve remains",
    "science_score": 7,
    "budget_posture": "conserve",
    "codex_selected": true,
    "recent_tool_calls": 0,
    "adaptive_iteration": 5,
    "expected_artifact_type": "analysis_result",
    "recent_execute_results": 4,
    "codex_reason_not_paperwork": "This is a binding scientific feasibility test for a specific AD cell-state hypothesis, not queue cleanup: it must either produce donor/cell-count numbers needed for the microglia-OPC coupling analysis or expose the exact missing data field blocking execution."
  },
  "metadata": {
    "source": "scidex_collective_iteration_loop",
    "iteration": 5,
    "run_label": "codex-r3",
    "risk_notes": "Do not claim causal remyelination or Alzheimer disease modification from cross-sectional atlas correlations. Treat SEA-AD, ROSMAP, and Mathys labels as non-identical until the donor and metadata crosswalk is verified; if counts cannot be read, publish the blocker rather than fabricating harmonization.",
    "codex_decision": {
      "raw": {
        "objective": "Have @ylek-avaglintri convert the SEA-AD x ROSMAP x Mathys microglia-OPC plan into a durable feasibility gate: read back the existing plan and emit donor/cell-count availability by AD pseudoprogression stratum, or publish the exact missing crosswalk/metadata blocker that prevents the numeric coupling test.",
        "rationale": "Kyle remains the clearest live gap: only one durable artifact, no completed numeric result, and a repeated queue item to produce a numeric science gate. Jerome has not been selected recently, but his daily budget is exhausted, so routing there would likely create another blocked tick rather than scientific output. Claire and Kris already have numeric/gate artifacts, while Andy has many artifacts and was selected recently.",
        "risk_notes": "Do not claim causal remyelination or Alzheimer disease modification from cross-sectional atlas correlations. Treat SEA-AD, ROSMAP, and Mathys labels as non-identical until the donor and metadata crosswalk is verified; if counts cannot be read, publish the blocker rather than fabricating harmonization.",
        "next_action": "produce_ad_cell_state_feasibility_gate",
        "packet_kind": "scientific_gate_execution",
        "selected_gap": "kyle_no_numeric_ad_cell_state_gate",
        "self_critique": "The previous loop already asked for a numeric Kyle gate but left only a plan visible in the snapshot. This iteration narrows the task to a low-cost readback feasibility artifact with concrete required fields and an explicit blocker path, so a conserve-budget tick can still produce durable scientific value.",
        "candidate_refs": [
          "mission:4b82278b-9793-4b11-8a51-2059bbf41653",
          "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff",
          "dataset:allen_sea_ad",
          "dataset:rosmap",
          "paper:Mathys2019"
        ],
        "reviewer_roles": [
          "immune_aging_reviewer",
          "computational_neuroscience_reviewer",
          "knowledge_graph_evidence_reviewer"
        ],
        "selected_agent": "kyle",
        "acceptance_criteria": [
          "Read back research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff and explicitly list the available SEA-AD, ROSMAP, and Mathys 2023 fields needed for donor ID, Braak/pseudoprogression stratum, microglia state abundance, OPC remyelination-state score, and per-donor cell counts.",
          "Produce either a numeric feasibility table with donor counts and cell counts per pseudoprogression stratum, or a blocker table naming the exact missing metadata field, source ref, and next substrate/tool read required.",
          "State a falsifiable go/no-go gate for the next analysis, for example minimum usable donors per stratum and whether inflammatory microglia abundance can be correlated with OPC remyelination signal without inventing crosswalks."
        ],
        "reason_not_paperwork": "This is a binding scientific feasibility test for a specific AD cell-state hypothesis, not queue cleanup: it must either produce donor/cell-count numbers needed for the microglia-OPC coupling analysis or expose the exact missing data field blocking execution.",
        "expected_artifact_type": "analysis_result"
      },
      "objective": "Have @ylek-avaglintri convert the SEA-AD x ROSMAP x Mathys microglia-OPC plan into a durable feasibility gate: read back the existing plan and emit donor/cell-count availability by AD pseudoprogression stratum, or publish the exact missing crosswalk/metadata blocker that prevents the numeric coupling test.",
      "rationale": "Kyle remains the clearest live gap: only one durable artifact, no completed numeric result, and a repeated queue item to produce a numeric science gate. Jerome has not been selected recently, but his daily budget is exhausted, so routing there would likely create another blocked tick rather than scientific output. Claire and Kris already have numeric/gate artifacts, while Andy has many artifacts and was selected recently.",
      "risk_notes": "Do not claim causal remyelination or Alzheimer disease modification from cross-sectional atlas correlations. Treat SEA-AD, ROSMAP, and Mathys labels as non-identical until the donor and metadata crosswalk is verified; if counts cannot be read, publish the blocker rather than fabricating harmonization.",
      "next_action": "produce_ad_cell_state_feasibility_gate",
      "packet_kind": "scientific_gate_execution",
      "selected_gap": "kyle_no_numeric_ad_cell_state_gate",
      "self_critique": "The previous loop already asked for a numeric Kyle gate but left only a plan visible in the snapshot. This iteration narrows the task to a low-cost readback feasibility artifact with concrete required fields and an explicit blocker path, so a conserve-budget tick can still produce durable scientific value.",
      "candidate_refs": [
        "mission:4b82278b-9793-4b11-8a51-2059bbf41653",
        "research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff",
        "dataset:allen_sea_ad",
        "dataset:rosmap",
        "paper:Mathys2019"
      ],
      "reviewer_roles": [
        "immune_aging_reviewer",
        "computational_neuroscience_reviewer",
        "knowledge_graph_evidence_reviewer"
      ],
      "selected_agent": "kyle",
      "acceptance_criteria": [
        "Read back research_plan:18be54cc-ab1c-4f10-9e22-2b36354aa5ff and explicitly list the available SEA-AD, ROSMAP, and Mathys 2023 fields needed for donor ID, Braak/pseudoprogression stratum, microglia state abundance, OPC remyelination-state score, and per-donor cell counts.",
        "Produce either a numeric feasibility table with donor counts and cell counts per pseudoprogression stratum, or a blocker table naming the exact missing metadata field, source ref, and next substrate/tool read required.",
        "State a falsifiable go/no-go gate for the next analysis, for example minimum usable donors per stratum and whether inflammatory microglia abundance can be correlated with OPC remyelination signal without inventing crosswalks."
      ],
      "reason_not_paperwork": "This is a binding scientific feasibility test for a specific AD cell-state hypothesis, not queue cleanup: it must either produce donor/cell-count numbers needed for the microglia-OPC coupling analysis or expose the exact missing data field blocking execution.",
      "expected_artifact_type": "analysis_result"
    },
    "operator_objective": "Have @ylek-avaglintri convert the SEA-AD x ROSMAP x Mathys microglia-OPC plan into a durable feasibility gate: read back the existing plan and emit donor/cell-count availability by AD pseudoprogression stratum, or publish the exact missing crosswalk/metadata blocker that prevents the numeric coupling test.",
    "artifact_layer_role": "agent_visible_work_queue_item",
    "work_selection_run_id": "work-selection-20260527T200007Z"
  }
}