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 symbolv; units:dimensionless; evidence: source symbol, component, or units provide a direct public name.initial_membrane_u(Membrane U) maps to source symbolu; units:dimensionless; evidence: source symbol, component, or units provide a direct public name.- The simulator still uses an internal
integration_stepparameter from the model manifest; it is not exposed as a biological lab input.
Selected outputs:
state,summary,trajectory, andvariable_labelsremain available for traceability.membrane_voltage(Membrane Voltage) maps to source symbolv; units:dimensionless; evidence: source symbol, component, or units provide a direct public name.membrane_voltage_vm(Membrane Voltage Vm) maps to source symbolVm; units:mV; evidence: source symbol, component, or units provide a direct public name.membrane_u(Membrane U) maps to source symbolu; 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 symbolw; units:dimensionless; evidence: source symbol, component, or units provide a direct public name.membrane_capacitance(Membrane Capacitance) maps to source symbolCm; 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 symbolV_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




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
Runs
Metadata
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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