Iyer2004 - Computational Human Left Ventricular Epicardial Iyermazhariwin Lab

About lab

Iyer2004 - Computational Human Left Ventricular Epicardial Iyermazhariwin Lab

Scientific Source

Source type: PhysioMe CellML
Upstream ID: physiome:iyer_mazhari_winslow_2004
Original URL: https://models.physiomeproject.org/workspace/iyer_mazhari_winslow_2004
Bundled artifact: data/iyer_mazhari_winslow_2004.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: mV; evidence: source symbol, component, or units provide a direct public name.
initial_intracellular_calcium (Intracellular Calcium) maps to source symbol Cai; units: mM; 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: mV; evidence: source symbol, component, or units provide a direct public name.
intracellular_calcium (Intracellular Calcium) maps to source symbol Cai; units: mM; evidence: source symbol, component, or units provide a direct public name.
intracellular_sodium (Intracellular Sodium) maps to source symbol Nai; units: mM; evidence: source symbol, component, or units provide a direct public name.
intracellular_potassium (Intracellular Potassium) maps to source symbol Ki; units: mM; evidence: source symbol, component, or units provide a direct public name.
extracellular_calcium (Extracellular Calcium) maps to source symbol Cao; units: mM; evidence: source symbol, component, or units provide a direct public name.
extracellular_sodium (Extracellular Sodium) maps to source symbol Nao; units: mM; 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-iyer2004-computational-human-left-ventricular-epicardial-iyermazhariwin-lab-phys

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 Iyer, Mazhari, Winslow, 2004. 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

Packageiyer2004-computational-human-left-ventricular-epicardial-iyermaz

Created2026-05-23

Updated2026-05-23

physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_membrane_voltage",
        "label": "Initial Membrane Voltage",
        "maps_to": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.initial_membrane_voltage",
        "description": "Initial value for Membrane Voltage. Maps to source symbol `V`. Units: mV. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "mV"
        ]
      },
      {
        "name": "initial_intracellular_calcium",
        "label": "Initial Intracellular Calcium",
        "maps_to": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.initial_intracellular_calcium",
        "description": "Initial value for Intracellular Calcium. Maps to source symbol `Cai`. Units: mM. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "mM"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.variable_labels"
      },
      {
        "name": "membrane_voltage",
        "label": "Membrane Voltage",
        "maps_to": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.membrane_voltage",
        "description": "Membrane Voltage. Maps to source symbol `V`. Units: mV. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "intracellular_calcium",
        "label": "Intracellular Calcium",
        "maps_to": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.intracellular_calcium",
        "description": "Intracellular Calcium. Maps to source symbol `Cai`. Units: mM. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "intracellular_sodium",
        "label": "Intracellular Sodium",
        "maps_to": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.intracellular_sodium",
        "description": "Intracellular Sodium. Maps to source symbol `Nai`. Units: mM. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "intracellular_potassium",
        "label": "Intracellular Potassium",
        "maps_to": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.intracellular_potassium",
        "description": "Intracellular Potassium. Maps to source symbol `Ki`. Units: mM. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "extracellular_calcium",
        "label": "Extracellular Calcium",
        "maps_to": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.extracellular_calcium",
        "description": "Extracellular Calcium. Maps to source symbol `Cao`. Units: mM. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "extracellular_sodium",
        "label": "Extracellular Sodium",
        "maps_to": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.extracellular_sodium",
        "description": "Extracellular Sodium. Maps to source symbol `Nao`. Units: mM. Naming evidence: source symbol, component, or units provide a direct public name."
      }
    ]
  },
  "title": "Iyer2004 - Computational Human Left Ventricular Epicardial Iyermazhariwin Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model",
      "alias": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model",
      "parameters": {
        "model_path": "data/iyer_mazhari_winslow_2004.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model_state"
      ],
      "from": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model_summary"
      ],
      "from": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model_trajectory"
      ],
      "from": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model_variable_labels"
      ],
      "from": "physiology_cellml_iyer_mazhari_winslow_2004_iyermazhariwinslow2004_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Iyer, Mazhari, Winslow, 2004. Public controls and outputs are mapped to real source symbols for electrophysiology.",
  "schema_version": "2.0"
}

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