{"record_kind": "run_header", "run_id": "pearl-manuscript-s7-20260916", "seq": 1, "trace_sequence": 1, "timestamp": "2026-09-16T10:24:12+00:00", "logged_at": "2026-09-16T10:24:12.350000+00:00", "source_agent": null, "scenario_id": "S7", "provenance": "manuscript-aligned-case-log-v1", "not_wet_lab": false, "world_contract": "manuscript-case-S7", "config": {"communication_mode": "typed_events", "ir_schema_version": 4}, "user_command": "Autonomously characterize the HRP–TMB assay: identify its linear working range and estimate Km and kcat from time-resolved measurements.", "sources": [{"well": "A1", "label": "Enzyme stock (HRP), 3 nM nominal", "volume_ul": 2000, "concentration_nM": 3.0, "concentration_ng_ml": 132.0, "mw_g_per_mol": 44000.0}, {"well": "A2", "label": "Chromogenic substrate stock (TMB), 5.0 mM", "volume_ul": 5000, "concentration_mM": 5.0}, {"well": "A3", "label": "PBS, 1×", "volume_ul": 15000}], "constraints": ["The instruction does not prescribe well layout, an acid stop, or a dilution factor.", "Nominal enzyme stock is 3 nM and 2000 uL.", "96-well plate. Each reaction is read in the same well."], "instrument": {"wavelength_nm": 652, "epsilon_per_M_cm": 39000.0, "path_cm": 0.56, "path_basis": "Applied path is 0.28 cm times the well volume divided by 100 uL. At 200 uL that path is 0.56 cm.", "hrp_mw_g_per_mol": 44000.0, "initial_rate_elapsed_s": [3.0, 6.0, 9.0], "max_substrate_conversion": 0.15, "min_initial_rate_points": 3}}
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{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 6, "trace_sequence": 6, "timestamp": "2026-09-16T10:25:03+00:00", "logged_at": "2026-09-16T10:25:03.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-first-B1-tmb", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s7-first-B1-tmb", "plan_id": "plan-s7-first", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-first-B1-tmb", "action_params": {"source": "A2", "dest": "B1", "volume_ul": 1.0, "reagent": "tmb"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B1", "volume_ul": 1.0, "reagent": "tmb"}}, "result_observation_ids": ["obs-plan-s7-first-B1-tmb"], "state_delta": {"execution_disposition": "dispatched"}}
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{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 8, "trace_sequence": 8, "timestamp": "2026-09-16T10:25:18+00:00", "logged_at": "2026-09-16T10:25:18.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-first-B2-hrp", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s7-first-B2-hrp", "plan_id": "plan-s7-first", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-first-B2-hrp", "action_params": {"source": "A1", "dest": "B2", "volume_ul": 15.151515151515152, "reagent": "hrp"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B2", "volume_ul": 15.151515151515152, "reagent": "hrp"}}, "result_observation_ids": ["obs-plan-s7-first-B2-hrp"], "state_delta": {"execution_disposition": "dispatched"}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 9, "trace_sequence": 9, "timestamp": "2026-09-16T10:25:26+00:00", "logged_at": "2026-09-16T10:25:26.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-first-B2-buffer", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s7-first-B2-buffer", "plan_id": "plan-s7-first", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-first-B2-buffer", "action_params": {"source": "A3", "dest": "B2", "volume_ul": 180.84848484848484, "reagent": "buffer"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B2", "volume_ul": 180.84848484848484, "reagent": "buffer"}}, "result_observation_ids": ["obs-plan-s7-first-B2-buffer"], "state_delta": {"execution_disposition": "dispatched"}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 10, "trace_sequence": 10, "timestamp": "2026-09-16T10:25:32+00:00", "logged_at": "2026-09-16T10:25:32.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-first-B2-tmb", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s7-first-B2-tmb", "plan_id": "plan-s7-first", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-first-B2-tmb", "action_params": {"source": "A2", "dest": "B2", "volume_ul": 4.0, "reagent": "tmb"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B2", "volume_ul": 4.0, "reagent": "tmb"}}, "result_observation_ids": ["obs-plan-s7-first-B2-tmb"], "state_delta": {"execution_disposition": "dispatched"}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 11, "trace_sequence": 11, "timestamp": "2026-09-16T10:25:34+00:00", "logged_at": "2026-09-16T10:25:34.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-first-B2-mix", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "plan-s7-first-B2-mix", "plan_id": "plan-s7-first", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-first-B2-mix", "action_params": {"well": "B2"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B2", "enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 4.0, "buffer_volume_ul": 180.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "enzyme_concentration_M": 2.2727272727272728e-10, "rate_A652_per_min": 0.6160452238117213, "rate_uM_per_s": 0.4701199815413013, "hrp_source": "A1", "hrp_source_labware": "reservoir", "dilution_factor": 1, "neat_enzyme_ul": 15.151515151515152, "rate_uM_per_s_mean": 0.4701199815413013, "rate_residual_uM_per_s": 0.0, "replicate_sign": 0, "series": "mm", "used_for_fit": false, "initial_rate_eligible": false}}, "result_observation_ids": ["obs-plan-s7-first-B2-mix"], "state_delta": {"execution_disposition": "dispatched"}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 12, "trace_sequence": 12, "timestamp": "2026-09-16T10:25:48+00:00", "logged_at": "2026-09-16T10:25:48.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-first-B3-hrp", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s7-first-B3-hrp", "plan_id": "plan-s7-first", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-first-B3-hrp", "action_params": {"source": "A1", "dest": "B3", "volume_ul": 15.151515151515152, "reagent": "hrp"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B3", "volume_ul": 15.151515151515152, "reagent": "hrp"}}, "result_observation_ids": ["obs-plan-s7-first-B3-hrp"], "state_delta": {"execution_disposition": "dispatched"}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 13, "trace_sequence": 13, "timestamp": "2026-09-16T10:25:55+00:00", "logged_at": "2026-09-16T10:25:55.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-first-B3-buffer", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s7-first-B3-buffer", "plan_id": "plan-s7-first", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-first-B3-buffer", "action_params": {"source": "A3", "dest": "B3", "volume_ul": 168.84848484848484, "reagent": "buffer"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B3", "volume_ul": 168.84848484848484, "reagent": "buffer"}}, "result_observation_ids": ["obs-plan-s7-first-B3-buffer"], "state_delta": {"execution_disposition": "dispatched"}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 14, "trace_sequence": 14, "timestamp": "2026-09-16T10:26:02+00:00", "logged_at": "2026-09-16T10:26:02.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-first-B3-tmb", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s7-first-B3-tmb", "plan_id": "plan-s7-first", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-first-B3-tmb", "action_params": {"source": "A2", "dest": "B3", "volume_ul": 16.0, "reagent": "tmb"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B3", "volume_ul": 16.0, "reagent": "tmb"}}, "result_observation_ids": ["obs-plan-s7-first-B3-tmb"], "state_delta": {"execution_disposition": "dispatched"}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 15, "trace_sequence": 15, "timestamp": "2026-09-16T10:26:03+00:00", "logged_at": "2026-09-16T10:26:03.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-first-B3-mix", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "plan-s7-first-B3-mix", "plan_id": "plan-s7-first", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-first-B3-mix", "action_params": {"well": "B3"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B3", "enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 16.0, "buffer_volume_ul": 168.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "enzyme_concentration_M": 2.2727272727272728e-10, "rate_A652_per_min": 0.9767477592829704, "rate_uM_per_s": 0.745381379184196, "hrp_source": "A1", "hrp_source_labware": "reservoir", "dilution_factor": 1, "neat_enzyme_ul": 15.151515151515152, "rate_uM_per_s_mean": 0.745381379184196, "rate_residual_uM_per_s": 0.0, "replicate_sign": 0, "series": "mm", "used_for_fit": false, "initial_rate_eligible": false}}, "result_observation_ids": ["obs-plan-s7-first-B3-mix"], "state_delta": {"execution_disposition": "dispatched"}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 16, "trace_sequence": 16, "timestamp": "2026-09-16T10:26:15+00:00", "logged_at": "2026-09-16T10:26:15.350000+00:00", "source_agent": null, "event_id": "obs-s7-first-composition", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s7-first-composition", "wells": {"plate:B1": {"enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 1.0, "buffer_volume_ul": 183.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 25.0, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "enzyme_concentration_M": 2.2727272727272728e-10, "rate_A652_per_min": 0.2486903874813711, "rate_uM_per_s": 0.18978204172876303, "hrp_source": "A1", "hrp_source_labware": "reservoir", "dilution_factor": 1, "neat_enzyme_ul": 15.151515151515152, "rate_uM_per_s_mean": 0.18978204172876303, "rate_residual_uM_per_s": 0.0, "replicate_sign": 0, "series": "mm", "used_for_fit": false, "initial_rate_eligible": false}, "plate:B2": {"enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 4.0, "buffer_volume_ul": 180.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "enzyme_concentration_M": 2.2727272727272728e-10, "rate_A652_per_min": 0.6160452238117213, "rate_uM_per_s": 0.4701199815413013, "hrp_source": "A1", "hrp_source_labware": "reservoir", "dilution_factor": 1, "neat_enzyme_ul": 15.151515151515152, "rate_uM_per_s_mean": 0.4701199815413013, "rate_residual_uM_per_s": 0.0, "replicate_sign": 0, "series": "mm", "used_for_fit": false, "initial_rate_eligible": false}, "plate:B3": {"enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 16.0, "buffer_volume_ul": 168.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "enzyme_concentration_M": 2.2727272727272728e-10, "rate_A652_per_min": 0.9767477592829704, "rate_uM_per_s": 0.745381379184196, "hrp_source": "A1", "hrp_source_labware": "reservoir", "dilution_factor": 1, "neat_enzyme_ul": 15.151515151515152, "rate_uM_per_s_mean": 0.745381379184196, "rate_residual_uM_per_s": 0.0, "replicate_sign": 0, "series": "mm", "used_for_fit": false, "initial_rate_eligible": false}}, "note": "First wells, before any read, at 10 ng/mL HRP."}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 17, "trace_sequence": 17, "timestamp": "2026-09-16T10:26:27+00:00", "logged_at": "2026-09-16T10:26:27.350000+00:00", "source_agent": "human", "event_id": "s7-pause", "event_type": "external_perturbation", "message": "A person paused the run after the reactions were started. The early reads were not taken.", "rationale": "A person paused the run after the reactions were started. The early reads were not taken.", "payload": {"announced": false, "early_reads_acquired": false}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 18, "trace_sequence": 18, "timestamp": "2026-09-16T10:46:27+00:00", "logged_at": "2026-09-16T10:46:27.350000+00:00", "source_agent": null, "event_id": "obs-s7-late", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s7-late", "wells": {"plate:B1": {"enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 1.0, "buffer_volume_ul": 183.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 25.0, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "enzyme_concentration_M": 2.2727272727272728e-10, "rate_A652_per_min": 0.2486903874813711, "rate_uM_per_s": 0.189782041728763, "hrp_source": "A1", "hrp_source_labware": "reservoir", "dilution_factor": 1, "neat_enzyme_ul": 15.151515151515152, "rate_uM_per_s_mean": 0.18978204172876303, "rate_residual_uM_per_s": 0.0, "replicate_sign": 0, "series": "mm", "used_for_fit": false, "initial_rate_eligible": false, "A652": 3.5, "elapsed_s": 1284.0, "reaction_started_at": "2026-09-16T10:25:03+00:00", "acquired_at": "2026-09-16T10:46:27+00:00", "acid_stopped": false, "predicted_A652_uncapped": 5.321974292101341, "saturated": true, "early_points_missing": true}, "plate:B2": {"enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 4.0, "buffer_volume_ul": 180.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "enzyme_concentration_M": 2.2727272727272728e-10, "rate_A652_per_min": 0.6160452238117213, "rate_uM_per_s": 0.4701199815413013, "hrp_source": "A1", "hrp_source_labware": "reservoir", "dilution_factor": 1, "neat_enzyme_ul": 15.151515151515152, "rate_uM_per_s_mean": 0.4701199815413013, "rate_residual_uM_per_s": 0.0, "replicate_sign": 0, "series": "mm", "used_for_fit": false, "initial_rate_eligible": false, "A652": 3.5, "elapsed_s": 1255.0, "reaction_started_at": "2026-09-16T10:25:32+00:00", "acquired_at": "2026-09-16T10:46:27+00:00", "acid_stopped": false, "predicted_A652_uncapped": 12.885612598061838, "saturated": true, "early_points_missing": true}, "plate:B3": {"enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 16.0, "buffer_volume_ul": 168.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "enzyme_concentration_M": 2.2727272727272728e-10, "rate_A652_per_min": 0.9767477592829704, "rate_uM_per_s": 0.7453813791841959, "hrp_source": "A1", "hrp_source_labware": "reservoir", "dilution_factor": 1, "neat_enzyme_ul": 15.151515151515152, "rate_uM_per_s_mean": 0.745381379184196, "rate_residual_uM_per_s": 0.0, "replicate_sign": 0, "series": "mm", "used_for_fit": false, "initial_rate_eligible": false, "A652": 3.5, "elapsed_s": 1225.0, "reaction_started_at": "2026-09-16T10:26:02+00:00", "acquired_at": "2026-09-16T10:46:27+00:00", "acid_stopped": false, "predicted_A652_uncapped": 19.941933418693978, "saturated": true, "early_points_missing": true}}, "note": "These wells are saturated, so the initial rate could not be estimated. The 3, 6, and 9 s points are missing, and this course is not used for the fit."}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 19, "trace_sequence": 19, "timestamp": "2026-09-16T10:46:39+00:00", "logged_at": "2026-09-16T10:46:39.350000+00:00", "source_agent": "planner", "event_id": "msg-0019", "event_type": "recovery_decision", "rationale": "The pause let the reactions run past the early window. I will not fit that course. I prepare fresh wells and read each one at 3, 6, and 9 s after TMB is dispensed.", "message": "The pause let the reactions run past the early window. I will not fit that course. I prepare fresh wells and read each one at 3, 6, and 9 s after TMB is dispensed."}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 20, "trace_sequence": 20, "timestamp": "2026-09-16T10:46:51+00:00", "logged_at": "2026-09-16T10:46:51.350000+00:00", "source_agent": "planner", "event_id": "plan-plan-s7-fresh", "event_type": "plan", "plan_id": "plan-s7-fresh", "revision_id": "rev_0", "rationale": "Fresh wells at the same 3 nM stock and 10 ng/mL final HRP, with an HRP working-range titration. The 0.5 ng/mL point comes from a diluted aliquot in H12 so that transfer is at least 1 uL. Read each well at 3, 6, and 9 s after TMB is dispensed. A blank matches each substrate concentration.", "canonical_operations": [{"action_id": "plan-s7-fresh-H12-hrp", "tool_name": "transfer", "source": "reservoir:A1", "dest": "plate:H12", "volume_ul": 20.0, "reagent": "hrp"}, {"action_id": "plan-s7-fresh-H12-buffer", "tool_name": "transfer", "source": "reservoir:A3", "dest": "plate:H12", "volume_ul": 20.0, "reagent": "buffer"}, {"action_id": "plan-s7-fresh-H12-mix", "tool_name": "mix_well", "well": "H12"}, {"action_id": "plan-s7-fresh-A1-hrp", "tool_name": "transfer", "source": "plate:H12", "dest": "plate:A1", "volume_ul": 1.5151515151515151, "reagent": "hrp"}, {"action_id": "plan-s7-fresh-A1-buffer", "tool_name": "transfer", "source": "reservoir:A3", "dest": "plate:A1", "volume_ul": 190.4848484848485, "reagent": "buffer"}, {"action_id": "plan-s7-fresh-A1-tmb", "tool_name": "transfer", "source": "reservoir:A2", "dest": "plate:A1", "volume_ul": 8.0, "reagent": "tmb"}, {"action_id": "plan-s7-fresh-A1-mix", "tool_name": "mix_well", "well": 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{"action_id": "plan-s7-fresh-A5-tmb", "tool_name": "transfer", "source": "reservoir:A2", "dest": "plate:A5", "volume_ul": 8.0, "reagent": "tmb"}, {"action_id": "plan-s7-fresh-A5-mix", "tool_name": "mix_well", "well": "A5"}, {"action_id": "plan-s7-fresh-A6-hrp", "tool_name": "transfer", "source": "reservoir:A1", "dest": "plate:A6", "volume_ul": 30.303030303030305, "reagent": "hrp"}, {"action_id": "plan-s7-fresh-A6-buffer", "tool_name": "transfer", "source": "reservoir:A3", "dest": "plate:A6", "volume_ul": 161.6969696969697, "reagent": "buffer"}, {"action_id": "plan-s7-fresh-A6-tmb", "tool_name": "transfer", "source": "reservoir:A2", "dest": "plate:A6", "volume_ul": 8.0, "reagent": "tmb"}, {"action_id": "plan-s7-fresh-A6-mix", "tool_name": "mix_well", "well": "A6"}, {"action_id": "plan-s7-fresh-A7-hrp", "tool_name": "transfer", "source": "reservoir:A1", "dest": "plate:A7", "volume_ul": 60.60606060606061, "reagent": "hrp"}, {"action_id": "plan-s7-fresh-A7-buffer", "tool_name": "transfer", 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{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 156, "trace_sequence": 156, "timestamp": "2026-09-16T10:58:09+00:00", "logged_at": "2026-09-16T10:58:09.350000+00:00", "source_agent": null, "event_id": "obs-s7-fresh-E1-t9", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s7-fresh-E1-t9", "wells": {"plate:E1": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 1.0, "buffer_volume_ul": 199.0, "total_volume_ul": 200.0, "substrate_uM": 25.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 25.0, "A652": 0.0, "elapsed_s": 9.0, "reaction_started_at": "2026-09-16T10:58:00+00:00", "acquired_at": "2026-09-16T10:58:09+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Fresh well, read at 3, 6, and 9 s after TMB was dispensed. No acid stop."}}
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{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 160, "trace_sequence": 160, "timestamp": "2026-09-16T10:58:27+00:00", "logged_at": "2026-09-16T10:58:27.350000+00:00", "source_agent": null, "event_id": "obs-s7-fresh-E2-t3", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s7-fresh-E2-t3", "wells": {"plate:E2": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 2.0, "buffer_volume_ul": 198.0, "total_volume_ul": 200.0, "substrate_uM": 50.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 50.0, "A652": 0.0, "elapsed_s": 3.0, "reaction_started_at": "2026-09-16T10:58:24+00:00", "acquired_at": "2026-09-16T10:58:27+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Fresh well, read at 3, 6, and 9 s after TMB was dispensed. No acid stop."}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 161, "trace_sequence": 161, "timestamp": "2026-09-16T10:58:30+00:00", "logged_at": "2026-09-16T10:58:30.350000+00:00", "source_agent": null, "event_id": "obs-s7-fresh-E2-t6", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s7-fresh-E2-t6", "wells": {"plate:E2": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 2.0, "buffer_volume_ul": 198.0, "total_volume_ul": 200.0, "substrate_uM": 50.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 50.0, "A652": 0.0, "elapsed_s": 6.0, "reaction_started_at": "2026-09-16T10:58:24+00:00", "acquired_at": "2026-09-16T10:58:30+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Fresh well, read at 3, 6, and 9 s after TMB was dispensed. No acid stop."}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 162, "trace_sequence": 162, "timestamp": "2026-09-16T10:58:33+00:00", "logged_at": "2026-09-16T10:58:33.350000+00:00", "source_agent": null, "event_id": "obs-s7-fresh-E2-t9", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s7-fresh-E2-t9", "wells": {"plate:E2": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 2.0, "buffer_volume_ul": 198.0, "total_volume_ul": 200.0, "substrate_uM": 50.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 50.0, "A652": 0.0, "elapsed_s": 9.0, "reaction_started_at": "2026-09-16T10:58:24+00:00", "acquired_at": "2026-09-16T10:58:33+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Fresh well, read at 3, 6, and 9 s after TMB was dispensed. No acid stop."}}
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{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 166, "trace_sequence": 166, "timestamp": "2026-09-16T10:58:52+00:00", "logged_at": "2026-09-16T10:58:52.350000+00:00", "source_agent": null, "event_id": "obs-s7-fresh-E3-t3", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s7-fresh-E3-t3", "wells": {"plate:E3": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 4.0, "buffer_volume_ul": 196.0, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 100.0, "A652": 0.0, "elapsed_s": 3.0, "reaction_started_at": "2026-09-16T10:58:49+00:00", "acquired_at": "2026-09-16T10:58:52+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Fresh well, read at 3, 6, and 9 s after TMB was dispensed. No acid stop."}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 167, "trace_sequence": 167, "timestamp": "2026-09-16T10:58:55+00:00", "logged_at": "2026-09-16T10:58:55.350000+00:00", "source_agent": null, "event_id": "obs-s7-fresh-E3-t6", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s7-fresh-E3-t6", "wells": {"plate:E3": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 4.0, "buffer_volume_ul": 196.0, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 100.0, "A652": 0.0, "elapsed_s": 6.0, "reaction_started_at": "2026-09-16T10:58:49+00:00", "acquired_at": "2026-09-16T10:58:55+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Fresh well, read at 3, 6, and 9 s after TMB was dispensed. No acid stop."}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 168, "trace_sequence": 168, "timestamp": "2026-09-16T10:58:58+00:00", "logged_at": "2026-09-16T10:58:58.350000+00:00", "source_agent": null, "event_id": "obs-s7-fresh-E3-t9", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s7-fresh-E3-t9", "wells": {"plate:E3": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 4.0, "buffer_volume_ul": 196.0, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 100.0, "A652": 0.0, "elapsed_s": 9.0, "reaction_started_at": "2026-09-16T10:58:49+00:00", "acquired_at": "2026-09-16T10:58:58+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Fresh well, read at 3, 6, and 9 s after TMB was dispensed. No acid stop."}}
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{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 170, "trace_sequence": 170, "timestamp": "2026-09-16T10:59:16+00:00", "logged_at": "2026-09-16T10:59:16.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-fresh-E4-tmb", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s7-fresh-E4-tmb", "plan_id": "plan-s7-fresh", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-fresh-E4-tmb", "action_params": {"source": "A2", "dest": "E4", "volume_ul": 8.0, "reagent": "tmb"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E4", "volume_ul": 8.0, "reagent": "tmb"}}, "result_observation_ids": ["obs-plan-s7-fresh-E4-tmb"], "state_delta": {"execution_disposition": "dispatched"}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 171, "trace_sequence": 171, "timestamp": "2026-09-16T10:59:18+00:00", "logged_at": "2026-09-16T10:59:18.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-fresh-E4-mix", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "plan-s7-fresh-E4-mix", "plan_id": "plan-s7-fresh", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-fresh-E4-mix", "action_params": {"well": "E4"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E4", "enzyme_volume_ul": 0.0, "tmb_volume_ul": 8.0, "buffer_volume_ul": 192.0, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 200.0}}, "result_observation_ids": ["obs-plan-s7-fresh-E4-mix"], "state_delta": {"execution_disposition": "dispatched"}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 172, "trace_sequence": 172, "timestamp": "2026-09-16T10:59:19+00:00", "logged_at": "2026-09-16T10:59:19.350000+00:00", "source_agent": null, "event_id": "obs-s7-fresh-E4-t3", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s7-fresh-E4-t3", "wells": {"plate:E4": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 8.0, "buffer_volume_ul": 192.0, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 200.0, "A652": 0.0, "elapsed_s": 3.0, "reaction_started_at": "2026-09-16T10:59:16+00:00", "acquired_at": "2026-09-16T10:59:19+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Fresh well, read at 3, 6, and 9 s after TMB was dispensed. No acid stop."}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 173, "trace_sequence": 173, "timestamp": "2026-09-16T10:59:22+00:00", "logged_at": "2026-09-16T10:59:22.350000+00:00", "source_agent": null, "event_id": "obs-s7-fresh-E4-t6", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s7-fresh-E4-t6", "wells": {"plate:E4": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 8.0, "buffer_volume_ul": 192.0, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 200.0, "A652": 0.0, "elapsed_s": 6.0, "reaction_started_at": "2026-09-16T10:59:16+00:00", "acquired_at": "2026-09-16T10:59:22+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Fresh well, read at 3, 6, and 9 s after TMB was dispensed. No acid stop."}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 174, "trace_sequence": 174, "timestamp": "2026-09-16T10:59:25+00:00", "logged_at": "2026-09-16T10:59:25.350000+00:00", "source_agent": null, "event_id": "obs-s7-fresh-E4-t9", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s7-fresh-E4-t9", "wells": {"plate:E4": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 8.0, "buffer_volume_ul": 192.0, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 200.0, "A652": 0.0, "elapsed_s": 9.0, "reaction_started_at": "2026-09-16T10:59:16+00:00", "acquired_at": "2026-09-16T10:59:25+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Fresh well, read at 3, 6, and 9 s after TMB was dispensed. No acid stop."}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 175, "trace_sequence": 175, "timestamp": "2026-09-16T10:59:36+00:00", "logged_at": "2026-09-16T10:59:36.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-fresh-E5-buffer", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s7-fresh-E5-buffer", "plan_id": "plan-s7-fresh", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-fresh-E5-buffer", "action_params": {"source": "A3", "dest": "E5", "volume_ul": 184.0, "reagent": "buffer"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E5", "volume_ul": 184.0, "reagent": "buffer"}}, "result_observation_ids": ["obs-plan-s7-fresh-E5-buffer"], "state_delta": {"execution_disposition": "dispatched"}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 176, "trace_sequence": 176, "timestamp": "2026-09-16T10:59:43+00:00", "logged_at": "2026-09-16T10:59:43.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-fresh-E5-tmb", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s7-fresh-E5-tmb", "plan_id": "plan-s7-fresh", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-fresh-E5-tmb", "action_params": {"source": "A2", "dest": "E5", "volume_ul": 16.0, "reagent": "tmb"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E5", "volume_ul": 16.0, "reagent": "tmb"}}, "result_observation_ids": ["obs-plan-s7-fresh-E5-tmb"], "state_delta": {"execution_disposition": "dispatched"}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 177, "trace_sequence": 177, "timestamp": "2026-09-16T10:59:44+00:00", "logged_at": "2026-09-16T10:59:44.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s7-fresh-E5-mix", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "plan-s7-fresh-E5-mix", "plan_id": "plan-s7-fresh", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s7-fresh-E5-mix", "action_params": {"well": "E5"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E5", "enzyme_volume_ul": 0.0, "tmb_volume_ul": 16.0, "buffer_volume_ul": 184.0, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 400.0}}, "result_observation_ids": ["obs-plan-s7-fresh-E5-mix"], "state_delta": {"execution_disposition": "dispatched"}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 178, "trace_sequence": 178, "timestamp": "2026-09-16T10:59:46+00:00", "logged_at": "2026-09-16T10:59:46.350000+00:00", "source_agent": null, "event_id": "obs-s7-fresh-E5-t3", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s7-fresh-E5-t3", "wells": {"plate:E5": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 16.0, "buffer_volume_ul": 184.0, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 400.0, "A652": 0.0, "elapsed_s": 3.0, "reaction_started_at": "2026-09-16T10:59:43+00:00", "acquired_at": "2026-09-16T10:59:46+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Fresh well, read at 3, 6, and 9 s after TMB was dispensed. No acid stop."}}
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15.151515151515152, "rate_uM_per_s_mean": 0.4701199815413013, "rate_residual_uM_per_s": -0.0028481144887389236, "replicate_sign": -1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true}, "plate:F4": {"enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 8.0, "buffer_volume_ul": 176.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "enzyme_concentration_M": 2.2727272727272728e-10, "rate_A652_per_min": 0.8209773482894044, "rate_uM_per_s": 0.626508965422317, "hrp_source": "A1", "hrp_source_labware": "reservoir", "dilution_factor": 1, "neat_enzyme_ul": 15.151515151515152, "rate_uM_per_s_mean": 0.6236608509335781, "rate_residual_uM_per_s": 0.0028481144887389236, "replicate_sign": 1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true}, "plate:G4": {"enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 8.0, "buffer_volume_ul": 176.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "enzyme_concentration_M": 2.2727272727272728e-10, "rate_A652_per_min": 0.8135130098373174, "rate_uM_per_s": 0.6208127364448393, "hrp_source": "A1", "hrp_source_labware": "reservoir", "dilution_factor": 1, "neat_enzyme_ul": 15.151515151515152, "rate_uM_per_s_mean": 0.6236608509335781, "rate_residual_uM_per_s": -0.0028481144887389236, "replicate_sign": -1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true}, "plate:F5": {"enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 16.0, "buffer_volume_ul": 168.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "enzyme_concentration_M": 2.2727272727272728e-10, "rate_A652_per_min": 0.980479928509014, "rate_uM_per_s": 0.7482294936729349, "hrp_source": "A1", "hrp_source_labware": "reservoir", "dilution_factor": 1, "neat_enzyme_ul": 15.151515151515152, "rate_uM_per_s_mean": 0.745381379184196, "rate_residual_uM_per_s": 0.0028481144887389236, "replicate_sign": 1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true}, "plate:G5": {"enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 16.0, "buffer_volume_ul": 168.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "enzyme_concentration_M": 2.2727272727272728e-10, "rate_A652_per_min": 0.9730155900569271, "rate_uM_per_s": 0.7425332646954571, "hrp_source": "A1", "hrp_source_labware": "reservoir", "dilution_factor": 1, "neat_enzyme_ul": 15.151515151515152, "rate_uM_per_s_mean": 0.745381379184196, "rate_residual_uM_per_s": -0.0028481144887389236, "replicate_sign": -1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true}, "plate:E1": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 1.0, "buffer_volume_ul": 199.0, "total_volume_ul": 200.0, "substrate_uM": 25.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 25.0}, "plate:E2": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 2.0, "buffer_volume_ul": 198.0, "total_volume_ul": 200.0, "substrate_uM": 50.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 50.0}, "plate:E3": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 4.0, "buffer_volume_ul": 196.0, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 100.0}, "plate:E4": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 8.0, "buffer_volume_ul": 192.0, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 200.0}, "plate:E5": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 16.0, "buffer_volume_ul": 184.0, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 400.0}}, "note": "Fresh-well compositions, including final enzyme concentration."}}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 182, "trace_sequence": 182, "timestamp": "2026-09-16T11:00:16+00:00", "logged_at": "2026-09-16T11:00:16.350000+00:00", "source_agent": "planner", "event_id": "msg-0182", "event_type": "recovery_decision", "rationale": "Reported KM = 97 uM. kcat = Vmax/[E] = 4075 /s at 10 ng/mL (0.2273 nM) HRP. Reported kcat uses the prepared-well concentration, 10 ng/mL. Vmax is 0.9261 uM/s, converted from 1.2136 A652/min with epsilon 39000 /M/cm and path 0.56 cm. That path is 0.28 cm times the well volume divided by 100 uL, which is 0.56 cm at 200 uL. The linear HRP working range is 0.5-10 ng/mL.", "message": "Reported KM = 97 uM. kcat = Vmax/[E] = 4075 /s at 10 ng/mL (0.2273 nM) HRP. Reported kcat uses the prepared-well concentration, 10 ng/mL. Vmax is 0.9261 uM/s, converted from 1.2136 A652/min with epsilon 39000 /M/cm and path 0.56 cm. That path is 0.28 cm times the well volume divided by 100 uL, which is 0.56 cm at 200 uL. The linear HRP working range is 0.5-10 ng/mL."}
{"record_kind": "event", "run_id": "pearl-manuscript-s7-20260916", "seq": 183, "trace_sequence": 183, "timestamp": "2026-09-16T11:00:28+00:00", "logged_at": "2026-09-16T11:00:28.350000+00:00", "source_agent": "planner", "event_id": "done-S7", "event_type": "completion_decision", "plan_id": "plan-s7-fresh", "revision_id": "rev_0", "adopted": {"summary": "Fit from the fresh wells after the missed early window.", "KM_uM": 97.0, "kcat_per_s": 4075.0, "Vmax_M_per_s": 9.261363636363637e-07, "Vmax_uM_per_s": 0.9261363636363636, "Vmax_A652_per_min": 1.213609090909091, "enzyme_concentration_M": 2.2727272727272728e-10, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "basis": "kcat_per_s = Vmax_M_per_s / enzyme_concentration_M", "read_mode": "same_well", "acid_stop": false, "enzyme_stock": "3 nM nominal, 2000 uL", "working_range_analyte": "HRP", "linear_working_range_hrp_ng_ml": [0.5, 10.0], "linear_working_range_hrp_nM": [0.011363636363636364, 0.22727272727272727], "preparation_id": "prep-s7-fresh", "discarded_preparation_id": "prep-s7-first"}, "discarded": ["prep-s7-first"], "message": "Fit from the fresh wells after the missed early window."}
{"record_kind": "trial", "run_id": "pearl-manuscript-s7-20260916", "seq": 184, "trace_sequence": 184, "timestamp": "2026-09-16T11:00:40+00:00", "logged_at": "2026-09-16T11:00:40.350000+00:00", "source_agent": null, "scenario_id": "S7", "termination": "completed", "not_wet_lab": false, "adopted": {"summary": "Fit from the fresh wells after the missed early window.", "KM_uM": 97.0, "kcat_per_s": 4075.0, "Vmax_M_per_s": 9.261363636363637e-07, "Vmax_uM_per_s": 0.9261363636363636, "Vmax_A652_per_min": 1.213609090909091, "enzyme_concentration_M": 2.2727272727272728e-10, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "basis": "kcat_per_s = Vmax_M_per_s / enzyme_concentration_M", "read_mode": "same_well", "acid_stop": false, "enzyme_stock": "3 nM nominal, 2000 uL", "working_range_analyte": "HRP", "linear_working_range_hrp_ng_ml": [0.5, 10.0], "linear_working_range_hrp_nM": [0.011363636363636364, 0.22727272727272727], "preparation_id": "prep-s7-fresh", "discarded_preparation_id": "prep-s7-first"}, "discarded": ["prep-s7-first"], "commentary": "The first reactions ran longer than intended and the early measurements were missing. Fresh wells were read on schedule. Reported KM = 97 uM and kcat = Vmax/[E] = 4075 /s.", "analysis_report": {"KM_uM": 97.0, "kcat_per_s": 4075.0, "kcat_calculation": {"equation": "kcat_per_s = Vmax_M_per_s / enzyme_concentration_M", "absorbance_conversion": "Vmax_M_per_s = Vmax_A652_per_min / (epsilon_per_M_cm * path_cm * 60)", "concentration_conversion": "ng/mL = nM * hrp_mw_g_per_mol / 1000", "KM_uM": 97.0, "kcat_per_s": 4075.0, "physical_kcat_per_s": 4075.0, "replicate_delta_uM_per_s": 0.0028481144887389236, "fit_KM_uM": 96.9999999999999, "fit_Vmax_uM_per_s": 0.9261363636363632, "fit_r2": 0.999799236915292, "Vmax_M_per_s": 9.261363636363637e-07, "Vmax_uM_per_s": 0.9261363636363636, "Vmax_A652_per_min": 1.213609090909091, "epsilon_per_M_cm": 39000.0, "path_cm": 0.56, "wavelength_nm": 652, "hrp_mw_g_per_mol": 44000.0, "enzyme_stock_nM": 3.0, "enzyme_stock_volume_ul": 2000.0, "enzyme_stock_ng_ml": 132.0, "enzyme_volume_ul": 15.151515151515152, "neat_enzyme_ul": 15.151515151515152, "enzyme_source_nM": 3.0, "enzyme_source_well": "A1", "enzyme_source_labware": "reservoir", "dilution_factor": 1, "total_volume_ul": 200.0, "enzyme_concentration_M": 2.2727272727272728e-10, "enzyme_concentration_nM": 0.22727272727272727, "enzyme_concentration_ng_ml": 10.0, "physical_enzyme_concentration_M": 2.2727272727272728e-10, "physical_enzyme_concentration_nM": 0.22727272727272727, "physical_enzyme_concentration_ng_ml": 10.0, "enzyme_concentration_ng_ml_from_label": 10.0, "kcat_basis": "prepared_well", "apparent_kcat_per_s_on_label": 4075.0, "kcat_basis_note": "Reported kcat divides Vmax by the prepared-well enzyme concentration. The labelled stock and the dispense volumes produce that concentration."}, "working_range": {"analyte": "HRP", "criterion": "initial rate proportional to final HRP concentration", "fixed_substrate_uM": 200.0, "linear_ng_ml": [0.5, 10.0], "linear_nM": [0.011363636363636364, 0.22727272727272727], "assay_enzyme_ng_ml": 10.0, "assay_enzyme_nM": 0.22727272727272727, "points": [{"hrp_ng_ml": 0.5, "hrp_nM": 0.011363636363636364, "enzyme_volume_ul": 1.5151515151515151, "neat_enzyme_ul": 0.7575757575757576, "hrp_source": "H12", "hrp_source_labware": "plate", "enzyme_source_nM": 1.5, "dilution_factor": 2, "tmb_volume_ul": 8.0, "buffer_volume_ul": 190.4848484848485, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 0.04086225895316804, "rate_uM_per_s": 0.031183042546678905, "in_linear_range": true}, {"hrp_ng_ml": 1.0, "hrp_nM": 0.022727272727272728, "enzyme_volume_ul": 1.5151515151515151, "neat_enzyme_ul": 1.5151515151515151, "hrp_source": "A1", "hrp_source_labware": "reservoir", "enzyme_source_nM": 3.0, "dilution_factor": 1, "tmb_volume_ul": 8.0, "buffer_volume_ul": 190.4848484848485, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 0.08172451790633609, "rate_uM_per_s": 0.06236608509335781, "in_linear_range": true}, {"hrp_ng_ml": 2.0, "hrp_nM": 0.045454545454545456, "enzyme_volume_ul": 3.0303030303030303, "neat_enzyme_ul": 3.0303030303030303, "hrp_source": "A1", "hrp_source_labware": "reservoir", "enzyme_source_nM": 3.0, "dilution_factor": 1, "tmb_volume_ul": 8.0, "buffer_volume_ul": 188.96969696969697, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 0.16344903581267217, "rate_uM_per_s": 0.12473217018671562, "in_linear_range": true}, {"hrp_ng_ml": 5.0, "hrp_nM": 0.11363636363636363, "enzyme_volume_ul": 7.575757575757576, "neat_enzyme_ul": 7.575757575757576, "hrp_source": "A1", "hrp_source_labware": "reservoir", "enzyme_source_nM": 3.0, "dilution_factor": 1, "tmb_volume_ul": 8.0, "buffer_volume_ul": 184.42424242424244, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 0.40862258953168046, "rate_uM_per_s": 0.3118304254667891, "in_linear_range": true}, {"hrp_ng_ml": 10.0, "hrp_nM": 0.22727272727272727, "enzyme_volume_ul": 15.151515151515152, "neat_enzyme_ul": 15.151515151515152, "hrp_source": "A1", "hrp_source_labware": "reservoir", "enzyme_source_nM": 3.0, "dilution_factor": 1, "tmb_volume_ul": 8.0, "buffer_volume_ul": 176.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 0.8172451790633609, "rate_uM_per_s": 0.6236608509335781, "in_linear_range": true}, {"hrp_ng_ml": 20.0, "hrp_nM": 0.45454545454545453, "enzyme_volume_ul": 30.303030303030305, "neat_enzyme_ul": 30.303030303030305, "hrp_source": "A1", "hrp_source_labware": "reservoir", "enzyme_source_nM": 3.0, "dilution_factor": 1, "tmb_volume_ul": 8.0, "buffer_volume_ul": 161.6969696969697, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 1.4710413223140495, "rate_uM_per_s": 1.1225895316804404, "in_linear_range": false}, {"hrp_ng_ml": 40.0, "hrp_nM": 0.9090909090909091, "enzyme_volume_ul": 60.60606060606061, "neat_enzyme_ul": 60.60606060606061, "hrp_source": "A1", "hrp_source_labware": "reservoir", "enzyme_source_nM": 3.0, "dilution_factor": 1, "tmb_volume_ul": 8.0, "buffer_volume_ul": 131.39393939393938, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 2.4517355371900824, "rate_uM_per_s": 1.8709825528007342, "in_linear_range": false}, {"hrp_ng_ml": 80.0, "hrp_nM": 1.8181818181818181, "enzyme_volume_ul": 121.21212121212122, "neat_enzyme_ul": 121.21212121212122, "hrp_source": "A1", "hrp_source_labware": "reservoir", "enzyme_source_nM": 3.0, "dilution_factor": 1, "tmb_volume_ul": 8.0, "buffer_volume_ul": 70.78787878787878, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 3.6776033057851243, "rate_uM_per_s": 2.8064738292011016, "in_linear_range": false}]}}}