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Physiome aed - Physics Example 1 Electrical Circuit Lab

About lab

Physiome aed - Physics Example 1 Electrical Circuit Lab

Scientific Source

  • Source type: PhysioMe CellML
  • Upstream ID: physiome:aed
  • Original URL: https://models.physiomeproject.org/workspace/aed
  • Bundled artifact: data/FAIRDO_BG_example_3.1.1.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_model_state_e_r (Model State E R (source E_R)) maps to source symbol E_R; units: joule; evidence: source symbol is too ambiguous for a stronger public label.
  • initial_model_state_q_c (Model State Q C (source q_C)) maps to source symbol q_C; units: coulomb; evidence: source symbol is too ambiguous for a stronger public label.
  • 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.
  • model_state_e_r (Model State E R (source E_R)) maps to source symbol E_R; units: joule; evidence: source symbol is too ambiguous for a stronger public label.
  • model_state_q_c (Model State Q C (source q_C)) maps to source symbol q_C; units: coulomb; evidence: source symbol is too ambiguous for a stronger public label.
  • model_state_v_l (Model State V L (source v_L)) maps to source symbol v_L; units: C_per_s; evidence: source symbol is too ambiguous for a stronger public label.
  • main_c (Main C) maps to source symbol C; units: C2_per_J; evidence: source symbol, component, or units provide a direct public name.
  • main_l (Main L) maps to source symbol L; units: Js2_per_C2; evidence: source symbol, component, or units provide a direct public name.
  • main_r (Main R) maps to source symbol R; units: Js_per_C2; 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: Selected source-variable trajectories; final observable ranking; source/runtime evidence table; scientific 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-physiome-aed-physics-example-1-electrical-circuit-lab-physiology-run-answer

02-selected-physiology-trajectories

03-selected-final-observable-values

04-source-and-runtime-evidence

Caveat

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

Source-faithful physiology lab for The Physics of Physiology - Example 1: An electrical circuit. Public controls and outputs are mapped to real source symbols for source-model physiology.

Runtime

Duration0.01
Comms Step0.01
Settle Steps1

Runs

Total0
Completed0
Failed0

Metadata

Packagephysiome-aed-physics-example-1-electrical-circuit-lab
Created2026-05-23
Updated2026-05-23
physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_model_state_e_r",
        "label": "Initial Model State E R (source E_R)",
        "maps_to": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.initial_model_state_e_r",
        "description": "Initial value for Model State E R (source E_R). Maps to source symbol `E_R`. Units: joule. Naming evidence: source symbol is too ambiguous for a stronger public label.",
        "accepted_units": [
          "joule"
        ]
      },
      {
        "name": "initial_model_state_q_c",
        "label": "Initial Model State Q C (source q_C)",
        "maps_to": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.initial_model_state_q_c",
        "description": "Initial value for Model State Q C (source q_C). Maps to source symbol `q_C`. Units: coulomb. Naming evidence: source symbol is too ambiguous for a stronger public label.",
        "accepted_units": [
          "coulomb"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.variable_labels"
      },
      {
        "name": "model_state_e_r",
        "label": "Model State E R (source E_R)",
        "maps_to": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.model_state_e_r",
        "description": "Model State E R (source E_R). Maps to source symbol `E_R`. Units: joule. Naming evidence: source symbol is too ambiguous for a stronger public label."
      },
      {
        "name": "model_state_q_c",
        "label": "Model State Q C (source q_C)",
        "maps_to": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.model_state_q_c",
        "description": "Model State Q C (source q_C). Maps to source symbol `q_C`. Units: coulomb. Naming evidence: source symbol is too ambiguous for a stronger public label."
      },
      {
        "name": "model_state_v_l",
        "label": "Model State V L (source v_L)",
        "maps_to": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.model_state_v_l",
        "description": "Model State V L (source v_L). Maps to source symbol `v_L`. Units: C_per_s. Naming evidence: source symbol is too ambiguous for a stronger public label."
      },
      {
        "name": "main_c",
        "label": "Main C",
        "maps_to": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.main_c",
        "description": "Main C. Maps to source symbol `C`. Units: C2_per_J. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "main_l",
        "label": "Main L",
        "maps_to": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.main_l",
        "description": "Main L. Maps to source symbol `L`. Units: Js2_per_C2. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "main_r",
        "label": "Main R",
        "maps_to": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.main_r",
        "description": "Main R. Maps to source symbol `R`. Units: Js_per_C2. Naming evidence: source symbol, component, or units provide a direct public name."
      }
    ]
  },
  "title": "Physiome aed - Physics Example 1 Electrical Circuit Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model",
      "alias": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model",
      "parameters": {
        "model_path": "data/FAIRDO_BG_example_3.1.1.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model_state"
      ],
      "from": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model_summary"
      ],
      "from": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model_trajectory"
      ],
      "from": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model_variable_labels"
      ],
      "from": "physiology_cellml_the_physics_of_physiology_example_1_an_electrica_aed_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for The Physics of Physiology - Example 1: An electrical circuit. Public controls and outputs are mapped to real source symbols for source-model physiology.",
  "schema_version": "2.0"
}

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