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 symbolh; 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 symbolRS_p; units:dimensionless; evidence: source metadata namesRS_pasnumber of phosphorylated receptor molecules.- 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.ip3_receptor_inactivation_gate_h(IP3 Receptor Inactivation Gate H (source h)) maps to source symbolh; units:dimensionless; evidence: calcium/IP3 context supports a conservative receptor-inactivation gate label.ip3_concentration(IP3 Concentration) maps to source symbolIP_3; units:micromolar; evidence: source metadata namesIP_3asIP3 concentration.number_of_receptor_molecules(Number Of Receptor Molecules) maps to source symbolRS; units:dimensionless; evidence: source metadata namesRSasnumber of receptor molecules.alpha(Alpha) maps to source symbolalpha; units:per_second; evidence: source symbol, component, or units provide a direct public name.volume(Volume) maps to source symbolv; units:litre; evidence: source symbol, component, or units provide a direct public name.g_gtp_g(G Gtp G) maps to source symbolG; 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




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
Runs
Metadata
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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