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Lemon2003 - Calcium Inositol 1 4 5 Trisphosphate Dynamics Following Lab

About lab

Lemon2003 - Calcium Inositol 1 4 5 Trisphosphate Dynamics Following Lab

Scientific Source

  • Source type: PhysioMe CellML
  • Upstream ID: physiome:lemon_gibson_bennett_2003
  • Original URL: https://models.physiomeproject.org/workspace/lemon_gibson_bennett_2003
  • Bundled artifact: data/lemon_2003.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_ip3_receptor_inactivation_gate_h (IP3 Receptor Inactivation Gate H (source h)) maps to source symbol h; units: dimensionless; evidence: calcium/IP3 context supports a conservative receptor-inactivation gate label.
  • initial_number_of_phosphorylated_receptor_molecules (Number Of Phosphorylated Receptor Molecules) maps to source symbol RS_p; units: dimensionless; evidence: source metadata names RS_p as number of phosphorylated receptor molecules.
  • 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.
  • ip3_receptor_inactivation_gate_h (IP3 Receptor Inactivation Gate H (source h)) maps to source symbol h; units: dimensionless; evidence: calcium/IP3 context supports a conservative receptor-inactivation gate label.
  • ip3_concentration (IP3 Concentration) maps to source symbol IP_3; units: micromolar; evidence: source metadata names IP_3 as IP3 concentration.
  • number_of_receptor_molecules (Number Of Receptor Molecules) maps to source symbol RS; units: dimensionless; evidence: source metadata names RS as number of receptor molecules.
  • alpha (Alpha) maps to source symbol alpha; units: per_second; evidence: source symbol, component, or units provide a direct public name.
  • volume (Volume) maps to source symbol v; units: litre; evidence: source symbol, component, or units provide a direct public name.
  • g_gtp_g (G Gtp G) maps to source symbol G; units: dimensionless; 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-lemon2003-calcium-inositol-1-4-5-trisphosphate-dynamics-following-lab-physiology

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 Lemon, Gibson, Bennett, 2003. 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

Packagelemon2003-calcium-inositol-1-4-5-trisphosphate-dynamics-e6b7c968
Created2026-05-23
Updated2026-06-13
physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_ip3_receptor_inactivation_gate_h",
        "label": "Initial IP3 Receptor Inactivation Gate H (source h)",
        "maps_to": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.initial_ip3_receptor_inactivation_gate_h",
        "description": "Initial value for IP3 Receptor Inactivation Gate H (source h). Maps to source symbol `h`. Units: dimensionless. Naming evidence: calcium/IP3 context supports a conservative receptor-inactivation gate label.",
        "accepted_units": [
          "dimensionless"
        ]
      },
      {
        "name": "initial_number_of_phosphorylated_receptor_molecules",
        "label": "Initial Number Of Phosphorylated Receptor Molecules",
        "maps_to": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.initial_number_of_phosphorylated_receptor_molecules",
        "description": "Initial value for Number Of Phosphorylated Receptor Molecules. Maps to source symbol `RS_p`. Units: dimensionless. Naming evidence: source metadata names `RS_p` as `number of phosphorylated receptor molecules`.",
        "accepted_units": [
          "dimensionless"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.variable_labels"
      },
      {
        "name": "ip3_receptor_inactivation_gate_h",
        "label": "IP3 Receptor Inactivation Gate H (source h)",
        "maps_to": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.ip3_receptor_inactivation_gate_h",
        "description": "IP3 Receptor Inactivation Gate H (source h). Maps to source symbol `h`. Units: dimensionless. Naming evidence: calcium/IP3 context supports a conservative receptor-inactivation gate label."
      },
      {
        "name": "ip3_concentration",
        "label": "IP3 Concentration",
        "maps_to": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.ip3_concentration",
        "description": "IP3 Concentration. Maps to source symbol `IP_3`. Units: micromolar. Naming evidence: source metadata names `IP_3` as `IP3 concentration`."
      },
      {
        "name": "number_of_receptor_molecules",
        "label": "Number Of Receptor Molecules",
        "maps_to": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.number_of_receptor_molecules",
        "description": "Number Of Receptor Molecules. Maps to source symbol `RS`. Units: dimensionless. Naming evidence: source metadata names `RS` as `number of receptor molecules`."
      },
      {
        "name": "alpha",
        "label": "Alpha",
        "maps_to": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.alpha",
        "description": "Alpha. Maps to source symbol `alpha`. Units: per_second. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "volume",
        "label": "Volume",
        "maps_to": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.volume",
        "description": "Volume. Maps to source symbol `v`. Units: litre. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "g_gtp_g",
        "label": "G Gtp G",
        "maps_to": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.g_gtp_g",
        "description": "G Gtp G. Maps to source symbol `G`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      }
    ]
  },
  "title": "Lemon2003 - Calcium Inositol 1 4 5 Trisphosphate Dynamics Following Lab",
  "models": [
    {
      "path": "models/core",
      "alias": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model",
      "parameters": {
        "model_path": "data/lemon_2003.cellml",
        "integration_step": 0.01
      }
    },
    {
      "path": "models/visualisation",
      "alias": "visualisation"
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model_state"
      ],
      "from": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model_summary"
      ],
      "from": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model_trajectory"
      ],
      "from": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model_variable_labels"
      ],
      "from": "physiology_cellml_lemon_gibson_bennett_2003_lemongibsonbennett2003_model.variable_labels"
    }
  ],
  "package": "lemon2003-calcium-inositol-1-4-5-trisphosphate-dynamics-e6b7c968",
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "version": "1.0.0",
  "description": "Source-faithful physiology lab for Lemon, Gibson, Bennett, 2003. Public controls and outputs are mapped to real source symbols for calcium handling.",
  "schema_version": "2.0"
}

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