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Fenton2006 - Vortex Dynamics Three Dimensional Continuous Myocardium Lab

About lab

Fenton2006 - Vortex Dynamics Three Dimensional Continuous Myocardium Lab

Scientific Source

  • Source type: PhysioMe CellML
  • Upstream ID: physiome:fenton_karma_2006
  • Original URL: https://models.physiomeproject.org/workspace/fenton_karma_2006
  • Bundled artifact: data/fenton_karma_2006.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: dimensionless; evidence: source symbol, component, or units provide a direct public name.
  • initial_membrane_u (Membrane U) maps to source symbol u; 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.
  • membrane_voltage (Membrane Voltage) maps to source symbol v; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
  • membrane_voltage_vm (Membrane Voltage Vm) maps to source symbol Vm; units: mV; evidence: source symbol, component, or units provide a direct public name.
  • membrane_u (Membrane U) maps to source symbol u; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
  • slow_inward_current_w_gate_w (Slow Inward Current W Gate W) maps to source symbol w; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
  • membrane_capacitance (Membrane Capacitance) maps to source symbol Cm; units: uF_per_cm2; evidence: source symbol, component, or units provide a direct public name.
  • model_variable_v_0 (Model Variable V 0 (source V_0)) maps to source symbol V_0; units: mV; evidence: source symbol is too ambiguous for a stronger public label.

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-fenton2006-vortex-dynamics-three-dimensional-continuous-myocardium-lab-physiolog

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 Fenton, Karma, 2006. 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

Packagefenton2006-vortex-dynamics-three-dimensional-continuous-myocardi
Created2026-05-23
Updated2026-05-23
physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_membrane_voltage",
        "label": "Initial Membrane Voltage",
        "maps_to": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.initial_membrane_voltage",
        "description": "Initial value for Membrane Voltage. Maps to source symbol `v`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "dimensionless"
        ]
      },
      {
        "name": "initial_membrane_u",
        "label": "Initial Membrane U",
        "maps_to": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.initial_membrane_u",
        "description": "Initial value for Membrane U. Maps to source symbol `u`. 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_fenton_karma_2006_fentonkarma2006_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.variable_labels"
      },
      {
        "name": "membrane_voltage",
        "label": "Membrane Voltage",
        "maps_to": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.membrane_voltage",
        "description": "Membrane Voltage. Maps to source symbol `v`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "membrane_voltage_vm",
        "label": "Membrane Voltage Vm",
        "maps_to": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.membrane_voltage_vm",
        "description": "Membrane Voltage Vm. Maps to source symbol `Vm`. Units: mV. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "membrane_u",
        "label": "Membrane U",
        "maps_to": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.membrane_u",
        "description": "Membrane U. Maps to source symbol `u`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "slow_inward_current_w_gate_w",
        "label": "Slow Inward Current W Gate W",
        "maps_to": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.slow_inward_current_w_gate_w",
        "description": "Slow Inward Current W Gate W. Maps to source symbol `w`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "membrane_capacitance",
        "label": "Membrane Capacitance",
        "maps_to": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.membrane_capacitance",
        "description": "Membrane Capacitance. Maps to source symbol `Cm`. Units: uF_per_cm2. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "model_variable_v_0",
        "label": "Model Variable V 0 (source V_0)",
        "maps_to": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.model_variable_v_0",
        "description": "Model Variable V 0 (source V_0). Maps to source symbol `V_0`. Units: mV. Naming evidence: source symbol is too ambiguous for a stronger public label."
      }
    ]
  },
  "title": "Fenton2006 - Vortex Dynamics Three Dimensional Continuous Myocardium Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_fenton_karma_2006_fentonkarma2006_model",
      "alias": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model",
      "parameters": {
        "model_path": "data/fenton_karma_2006.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_fenton_karma_2006_fentonkarma2006_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_fenton_karma_2006_fentonkarma2006_model_state"
      ],
      "from": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_fenton_karma_2006_fentonkarma2006_model_summary"
      ],
      "from": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_fenton_karma_2006_fentonkarma2006_model_trajectory"
      ],
      "from": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_fenton_karma_2006_fentonkarma2006_model_variable_labels"
      ],
      "from": "physiology_cellml_fenton_karma_2006_fentonkarma2006_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Fenton, Karma, 2006. Public controls and outputs are mapped to real source symbols for electrophysiology.",
  "schema_version": "2.0"
}

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