Version history

{
  "objective": "Have @riskay-angiogram turn the NAMPT 2GVJ binder campaign into one durable numeric gate: compute or read back active-site residue exposure/contact rankings for PDB:2GVJ and decide whether the current RFdiffusion target prep should proceed, or publish the exact missing structure/tool blocker.",
  "requester_ref": "agent_work_selection:work-selection-20260527T200007Z",
  "assignee_ref": "persona-kris-ganjam",
  "assigned_agent_id": "persona-kris-ganjam",
  "assigned_binding_id": "kris-ganjam",
  "assigned_runtime": "driver-kris",
  "runtime_kind": "driver",
  "public_handle": "@riskay-angiogram",
  "packet_kind": "scientific_execution_gate",
  "next_action": "execute_nampt_sasa_and_design_gate",
  "instructions": "Have @riskay-angiogram turn the NAMPT 2GVJ binder campaign into one durable numeric gate: compute or read back active-site residue exposure/contact rankings for PDB:2GVJ and decide whether the current RFdiffusion target prep should proceed, or publish the exact missing structure/tool blocker.",
  "input_refs": [
    "collective_mission:neuroimmune-aging-neurodegeneration-20260527",
    "mission:4b82278b-9793-4b11-8a51-2059bbf41653",
    "agent:persona-kris-ganjam",
    "binding:kris-ganjam",
    "domain:nad_axis_aging",
    "domain:protein_design",
    "pdb:2GVJ",
    "research_plan:5e4168c3-dce8-41f6-a372-6ff76ad92a20",
    "notebook:89348bbf-fed2-44f6-ae4a-375954482d16",
    "research_plan:5f931539-1069-4073-ad8e-591add197e53",
    "protein_design:227f1636-b49b-4048-be26-e1d3abae40b5",
    "notebook:617c9ebd-c264-4712-92fa-ac635fb5b9d7"
  ],
  "context_refs": {
    "self": [
      "agent:persona-kris-ganjam",
      "binding:kris-ganjam"
    ],
    "score_gap": [
      "science_score:8",
      "gap:kris_nampt_design_missing_numeric_sasa_gate"
    ],
    "peer_agents": [
      "agent:persona-virtual-kyle-travaglini",
      "agent:persona-claire-gustavson",
      "agent:persona-jerome-lecoq",
      "agent:persona-andy-hickl"
    ],
    "disease_axis": [
      "domain:nad_axis_aging",
      "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:004"
    ],
    "latest_agent_artifacts": [
      "notebook:89348bbf-fed2-44f6-ae4a-375954482d16",
      "research_plan:5f931539-1069-4073-ad8e-591add197e53",
      "protein_design:227f1636-b49b-4048-be26-e1d3abae40b5",
      "notebook:617c9ebd-c264-4712-92fa-ac635fb5b9d7",
      "research_plan:5e4168c3-dce8-41f6-a372-6ff76ad92a20"
    ]
  },
  "acceptance_criteria": [
    "Read back the existing NAMPT refs before analysis: pdb:2GVJ, research_plan:5e4168c3-dce8-41f6-a372-6ff76ad92a20, notebook:617c9ebd-c264-4712-92fa-ac635fb5b9d7, and protein_design:227f1636-b49b-4048-be26-e1d3abae40b5.",
    "Produce a numeric active-site gate for PDB 2GVJ: at minimum list ranked target residues with distance-to-ligand or pocket-center, residue SASA or exposure class, and a pass/fail rationale for whether the current binder campaign can proceed.",
    "If the structure, ligand annotations, or executable SASA/contact tooling are unavailable, publish the exact blocker with the missing file/tool/field named and one next command or substrate verb that would unblock it.",
    "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",
    "include PDB 2GVJ and residues Q168/K228/V274/A306/I309/G383 if touching NAMPT",
    "reference or update research_plan:5e4168c3-dce8-41f6-a372-6ff76ad92a20",
    "record that this packet was selected by a live Codex per-iteration decision"
  ],
  "deliverable_refs": [],
  "priority": "high",
  "priority_score": 0.77,
  "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-r3:004:kris:kris-nampt-design-missing-numeric-sasa-gate",
  "signals": {
    "science_gaps": [
      "budget_conserve",
      "queue_overload"
    ],
    "selected_gap": "kris_nampt_design_missing_numeric_sasa_gate",
    "budget_reason": "less than 20 percent token reserve remains",
    "science_score": 8,
    "budget_posture": "conserve",
    "codex_selected": true,
    "recent_tool_calls": 0,
    "adaptive_iteration": 4,
    "expected_artifact_type": "analysis_result",
    "recent_execute_results": 5,
    "codex_reason_not_paperwork": "The packet requires a numeric residue-level structural analysis or a binding blocker tied to PDB:2GVJ and existing NAMPT design artifacts; it directly changes whether a protein-design campaign proceeds rather than organizing queues or rewriting prose."
  },
  "metadata": {
    "source": "scidex_collective_iteration_loop",
    "iteration": 4,
    "run_label": "codex-r3",
    "risk_notes": "This must stay at the design-gate level: no therapeutic efficacy, anti-aging, or cure claims. SASA/contact rankings from one structure are hypothesis-generating and must be treated as insufficient without docking, specificity, stability, and experimental validation.",
    "codex_decision": {
      "raw": {
        "objective": "Have @riskay-angiogram turn the NAMPT 2GVJ binder campaign into one durable numeric gate: compute or read back active-site residue exposure/contact rankings for PDB:2GVJ and decide whether the current RFdiffusion target prep should proceed, or publish the exact missing structure/tool blocker.",
        "rationale": "Kris has the strongest live execution opportunity for this iteration: high score, many durable refs, an explicit queue item to execute the NAMPT SASA/design gate, and no recent selection in this run. Jerome is blocked by exhausted daily budget, while Kyle, Andy, and Claire were already selected in the previous three iterations. This routes scarce compute to a concrete structural biology gate instead of another planning artifact.",
        "risk_notes": "This must stay at the design-gate level: no therapeutic efficacy, anti-aging, or cure claims. SASA/contact rankings from one structure are hypothesis-generating and must be treated as insufficient without docking, specificity, stability, and experimental validation.",
        "next_action": "execute_nampt_sasa_and_design_gate",
        "packet_kind": "scientific_execution_gate",
        "selected_gap": "kris_nampt_design_missing_numeric_sasa_gate",
        "self_critique": "The previous loop kept selecting agents with missing numeric outputs but did not exploit Kris's ready structural gate. This iteration avoids rotation behavior by using the live queue and budget state to choose a one-tick computable NAMPT decision point with an explicit blocker fallback.",
        "candidate_refs": [
          "pdb:2GVJ",
          "research_plan:5e4168c3-dce8-41f6-a372-6ff76ad92a20",
          "notebook:617c9ebd-c264-4712-92fa-ac635fb5b9d7",
          "protein_design:227f1636-b49b-4048-be26-e1d3abae40b5",
          "domain:nad_axis_aging",
          "domain:protein_design"
        ],
        "reviewer_roles": [
          "structural_biology_reviewer",
          "protein_design_reviewer",
          "translational_safety_reviewer"
        ],
        "selected_agent": "kris",
        "acceptance_criteria": [
          "Read back the existing NAMPT refs before analysis: pdb:2GVJ, research_plan:5e4168c3-dce8-41f6-a372-6ff76ad92a20, notebook:617c9ebd-c264-4712-92fa-ac635fb5b9d7, and protein_design:227f1636-b49b-4048-be26-e1d3abae40b5.",
          "Produce a numeric active-site gate for PDB 2GVJ: at minimum list ranked target residues with distance-to-ligand or pocket-center, residue SASA or exposure class, and a pass/fail rationale for whether the current binder campaign can proceed.",
          "If the structure, ligand annotations, or executable SASA/contact tooling are unavailable, publish the exact blocker with the missing file/tool/field named and one next command or substrate verb that would unblock it."
        ],
        "reason_not_paperwork": "The packet requires a numeric residue-level structural analysis or a binding blocker tied to PDB:2GVJ and existing NAMPT design artifacts; it directly changes whether a protein-design campaign proceeds rather than organizing queues or rewriting prose.",
        "expected_artifact_type": "analysis_result"
      },
      "objective": "Have @riskay-angiogram turn the NAMPT 2GVJ binder campaign into one durable numeric gate: compute or read back active-site residue exposure/contact rankings for PDB:2GVJ and decide whether the current RFdiffusion target prep should proceed, or publish the exact missing structure/tool blocker.",
      "rationale": "Kris has the strongest live execution opportunity for this iteration: high score, many durable refs, an explicit queue item to execute the NAMPT SASA/design gate, and no recent selection in this run. Jerome is blocked by exhausted daily budget, while Kyle, Andy, and Claire were already selected in the previous three iterations. This routes scarce compute to a concrete structural biology gate instead of another planning artifact.",
      "risk_notes": "This must stay at the design-gate level: no therapeutic efficacy, anti-aging, or cure claims. SASA/contact rankings from one structure are hypothesis-generating and must be treated as insufficient without docking, specificity, stability, and experimental validation.",
      "next_action": "execute_nampt_sasa_and_design_gate",
      "packet_kind": "scientific_execution_gate",
      "selected_gap": "kris_nampt_design_missing_numeric_sasa_gate",
      "self_critique": "The previous loop kept selecting agents with missing numeric outputs but did not exploit Kris's ready structural gate. This iteration avoids rotation behavior by using the live queue and budget state to choose a one-tick computable NAMPT decision point with an explicit blocker fallback.",
      "candidate_refs": [
        "pdb:2GVJ",
        "research_plan:5e4168c3-dce8-41f6-a372-6ff76ad92a20",
        "notebook:617c9ebd-c264-4712-92fa-ac635fb5b9d7",
        "protein_design:227f1636-b49b-4048-be26-e1d3abae40b5",
        "domain:nad_axis_aging",
        "domain:protein_design"
      ],
      "reviewer_roles": [
        "structural_biology_reviewer",
        "protein_design_reviewer",
        "translational_safety_reviewer"
      ],
      "selected_agent": "kris",
      "acceptance_criteria": [
        "Read back the existing NAMPT refs before analysis: pdb:2GVJ, research_plan:5e4168c3-dce8-41f6-a372-6ff76ad92a20, notebook:617c9ebd-c264-4712-92fa-ac635fb5b9d7, and protein_design:227f1636-b49b-4048-be26-e1d3abae40b5.",
        "Produce a numeric active-site gate for PDB 2GVJ: at minimum list ranked target residues with distance-to-ligand or pocket-center, residue SASA or exposure class, and a pass/fail rationale for whether the current binder campaign can proceed.",
        "If the structure, ligand annotations, or executable SASA/contact tooling are unavailable, publish the exact blocker with the missing file/tool/field named and one next command or substrate verb that would unblock it."
      ],
      "reason_not_paperwork": "The packet requires a numeric residue-level structural analysis or a binding blocker tied to PDB:2GVJ and existing NAMPT design artifacts; it directly changes whether a protein-design campaign proceeds rather than organizing queues or rewriting prose.",
      "expected_artifact_type": "analysis_result"
    },
    "operator_objective": "Have @riskay-angiogram turn the NAMPT 2GVJ binder campaign into one durable numeric gate: compute or read back active-site residue exposure/contact rankings for PDB:2GVJ and decide whether the current RFdiffusion target prep should proceed, or publish the exact missing structure/tool blocker.",
    "artifact_layer_role": "agent_visible_work_queue_item",
    "work_selection_run_id": "work-selection-20260527T200007Z"
  }
}