Kurata2002 - Dynamical Description Sinoatrial Node Pacemaking Improved Lab

About lab

Kurata2002 - Dynamical Description Sinoatrial Node Pacemaking Improved Lab

Scientific Source

Source type: PhysioMe CellML
Upstream ID: physiome:kurata_hisatome_imanishi_shibamoto_2002
Original URL: https://models.physiomeproject.org/workspace/kurata_hisatome_imanishi_shibamoto_2002
Bundled artifact: data/kurata_hisatome_imanishi_shibamoto_2002.cellml

The bundled CellML/SBML artifact remains the scientific source of truth. This cleanup does not rewrite equations, parameters, units, or initial values; it exposes selected source symbols with conservative user-facing names.

Public Interface

Source-backed inputs:

initial_membrane_voltage (Membrane Voltage) maps to source symbol V; units: millivolt; evidence: source symbol, component, or units provide a direct public name.
initial_calcium_d_gate (Calcium D Gate) maps to source symbol d; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
The simulator still uses an internal integration_step parameter from the model manifest; it is not exposed as a biological lab input.

Selected outputs:

state, summary, trajectory, and variable_labels remain available for traceability.
k12 (K12) maps to source symbol k12; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
k14 (K14) maps to source symbol k14; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
k1ni (K1ni) maps to source symbol K1ni; units: millimolar; evidence: source symbol, component, or units provide a direct public name.
k1no (K1no) maps to source symbol K1no; units: millimolar; evidence: source symbol, component, or units provide a direct public name.
k21 (K21) maps to source symbol k21; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
k23 (K23) maps to source symbol k23; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.

Ambiguous source symbols are intentionally given conservative names such as model_state_*, cell_population_*, or rate_constant_* rather than unsupported biological interpretations.

Visualisations

Visual scope: Membrane-voltage and gating-variable trajectories; ionic current ranking; action-potential response Q/A.

The visualisation renders a scientific Q/A table, selected source-variable trajectories, final observable values, and source/runtime evidence. The cards use runtime outputs from the core wrapper and suppress empty data.

Output Visualizations

01-kurata2002-dynamical-description-sinoatrial-node-pacemaking-improved-lab-physiol

02-selected-physiology-trajectories

03-selected-final-observable-values

04-source-and-runtime-evidence

Caveat

This validates source-faithful execution and Biosimulant wiring for electrophysiology; it does not claim clinical safety or full reproduction of every upstream figure.

Source-faithful physiology lab for Kurata, Hisatome, Imanishi, Shibamoto, 2002. Public controls and outputs are mapped to real source symbols for electrophysiology.

Runtime

Duration0.01

Comms Step0.01

Settle Steps1

Runs

Total0

Completed0

Failed0

Metadata

Packagekurata2002-dynamical-description-sinoatrial-node-pacemaking-impr

Created2026-05-23

Updated2026-05-23

physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_membrane_voltage",
        "label": "Initial Membrane Voltage",
        "maps_to": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.initial_membrane_voltage",
        "description": "Initial value for Membrane Voltage. Maps to source symbol `V`. Units: millivolt. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "millivolt"
        ]
      },
      {
        "name": "initial_calcium_d_gate",
        "label": "Initial Calcium D Gate",
        "maps_to": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.initial_calcium_d_gate",
        "description": "Initial value for Calcium D Gate. Maps to source symbol `d`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "dimensionless"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.variable_labels"
      },
      {
        "name": "k12",
        "label": "K12",
        "maps_to": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.k12",
        "description": "K12. Maps to source symbol `k12`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "k14",
        "label": "K14",
        "maps_to": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.k14",
        "description": "K14. Maps to source symbol `k14`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "k1ni",
        "label": "K1ni",
        "maps_to": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.k1ni",
        "description": "K1ni. Maps to source symbol `K1ni`. Units: millimolar. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "k1no",
        "label": "K1no",
        "maps_to": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.k1no",
        "description": "K1no. Maps to source symbol `K1no`. Units: millimolar. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "k21",
        "label": "K21",
        "maps_to": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.k21",
        "description": "K21. Maps to source symbol `k21`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "k23",
        "label": "K23",
        "maps_to": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.k23",
        "description": "K23. Maps to source symbol `k23`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      }
    ]
  },
  "title": "Kurata2002 - Dynamical Description Sinoatrial Node Pacemaking Improved Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model",
      "alias": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model",
      "parameters": {
        "model_path": "data/kurata_hisatome_imanishi_shibamoto_2002.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model_state"
      ],
      "from": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model_summary"
      ],
      "from": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model_trajectory"
      ],
      "from": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model_variable_labels"
      ],
      "from": "physiology_cellml_kurata_hisatome_imanishi_shibamoto_2002_kuratahisatomeimanishishibamoto2002_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Kurata, Hisatome, Imanishi, Shibamoto, 2002. Public controls and outputs are mapped to real source symbols for electrophysiology.",
  "schema_version": "2.0"
}

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