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Bindschadler2001 - Bifurcation Analysis Two Coupled Calcium Oscillators Lab

About lab

Bindschadler2001 - Bifurcation Analysis Two Coupled Calcium Oscillators Lab

Scientific Source

  • Source type: PhysioMe CellML
  • Upstream ID: physiome:bindschadler_sneyd_2001
  • Original URL: https://models.physiomeproject.org/workspace/bindschadler_sneyd_2001
  • Bundled artifact: data/bindschadler_sneyd_2001.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_receptor_concentration_in_cell_1 (Receptor Concentration In Cell 1) maps to source symbol h1; units: dimensionless; evidence: source metadata names h1 as receptor concentration in cell 1.
  • initial_concentration_c1 (Concentration C1 (source c1)) maps to source symbol c1; units: micro_molar; evidence: amount concentration units identify a concentration state.
  • 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.
  • phi1_c1 (Phi1 C1) maps to source symbol phi1_c1; units: second_order_rate; evidence: source symbol, component, or units provide a direct public name.
  • phi1_c2 (Phi1 C2) maps to source symbol phi1_c2; units: second_order_rate; evidence: source symbol, component, or units provide a direct public name.
  • phi2_c1 (Phi2 C1) maps to source symbol phi2_c1; units: per_second; evidence: source symbol, component, or units provide a direct public name.
  • phi2_c2 (Phi2 C2) maps to source symbol phi2_c2; units: per_second; evidence: source symbol, component, or units provide a direct public name.
  • phi3_c1 (Phi3 C1) maps to source symbol phi3_c1; units: per_second; evidence: source symbol, component, or units provide a direct public name.
  • phi3_c2 (Phi3 C2) maps to source symbol phi3_c2; units: per_second; 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: Calcium-state trajectories; peak calcium response; calcium-store/source evidence table.

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-bindschadler2001-bifurcation-analysis-two-coupled-calcium-oscillators-lab-physio

02-selected-physiology-trajectories

03-selected-final-observable-values

04-source-and-runtime-evidence

Caveat

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

Source-faithful physiology lab for Bindschadler, Sneyd, 2001. Public controls and outputs are mapped to real source symbols for calcium handling.

Runtime

Duration0.01
Comms Step0.01
Settle Steps1

Runs

Total0
Completed0
Failed0

Metadata

Packagebindschadler2001-bifurcation-analysis-two-coupled-calcium-oscill
Created2026-05-23
Updated2026-05-23
physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_receptor_concentration_in_cell_1",
        "label": "Initial Receptor Concentration In Cell 1",
        "maps_to": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.initial_receptor_concentration_in_cell_1",
        "description": "Initial value for Receptor Concentration In Cell 1. Maps to source symbol `h1`. Units: dimensionless. Naming evidence: source metadata names `h1` as `receptor concentration in cell 1`.",
        "accepted_units": [
          "dimensionless"
        ]
      },
      {
        "name": "initial_concentration_c1",
        "label": "Initial Concentration C1 (source c1)",
        "maps_to": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.initial_concentration_c1",
        "description": "Initial value for Concentration C1 (source c1). Maps to source symbol `c1`. Units: micro_molar. Naming evidence: amount concentration units identify a concentration state.",
        "accepted_units": [
          "micro_molar"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.variable_labels"
      },
      {
        "name": "phi1_c1",
        "label": "Phi1 C1",
        "maps_to": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.phi1_c1",
        "description": "Phi1 C1. Maps to source symbol `phi1_c1`. Units: second_order_rate. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "phi1_c2",
        "label": "Phi1 C2",
        "maps_to": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.phi1_c2",
        "description": "Phi1 C2. Maps to source symbol `phi1_c2`. Units: second_order_rate. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "phi2_c1",
        "label": "Phi2 C1",
        "maps_to": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.phi2_c1",
        "description": "Phi2 C1. Maps to source symbol `phi2_c1`. Units: per_second. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "phi2_c2",
        "label": "Phi2 C2",
        "maps_to": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.phi2_c2",
        "description": "Phi2 C2. Maps to source symbol `phi2_c2`. Units: per_second. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "phi3_c1",
        "label": "Phi3 C1",
        "maps_to": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.phi3_c1",
        "description": "Phi3 C1. Maps to source symbol `phi3_c1`. Units: per_second. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "phi3_c2",
        "label": "Phi3 C2",
        "maps_to": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.phi3_c2",
        "description": "Phi3 C2. Maps to source symbol `phi3_c2`. Units: per_second. Naming evidence: source symbol, component, or units provide a direct public name."
      }
    ]
  },
  "title": "Bindschadler2001 - Bifurcation Analysis Two Coupled Calcium Oscillators Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model",
      "alias": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model",
      "parameters": {
        "model_path": "data/bindschadler_sneyd_2001.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model_state"
      ],
      "from": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model_summary"
      ],
      "from": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model_trajectory"
      ],
      "from": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model_variable_labels"
      ],
      "from": "physiology_cellml_bindschadler_sneyd_2001_bindschadlersneyd2001_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Bindschadler, Sneyd, 2001. Public controls and outputs are mapped to real source symbols for calcium handling.",
  "schema_version": "2.0"
}

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