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 symbolh1; units:dimensionless; evidence: source metadata namesh1asreceptor concentration in cell 1.initial_concentration_c1(Concentration C1 (source c1)) maps to source symbolc1; units:micro_molar; evidence: amount concentration units identify a concentration state.- 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.phi1_c1(Phi1 C1) maps to source symbolphi1_c1; units:second_order_rate; evidence: source symbol, component, or units provide a direct public name.phi1_c2(Phi1 C2) maps to source symbolphi1_c2; units:second_order_rate; evidence: source symbol, component, or units provide a direct public name.phi2_c1(Phi2 C1) maps to source symbolphi2_c1; units:per_second; evidence: source symbol, component, or units provide a direct public name.phi2_c2(Phi2 C2) maps to source symbolphi2_c2; units:per_second; evidence: source symbol, component, or units provide a direct public name.phi3_c1(Phi3 C1) maps to source symbolphi3_c1; units:per_second; evidence: source symbol, component, or units provide a direct public name.phi3_c2(Phi3 C2) maps to source symbolphi3_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




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
Runs
Metadata
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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