About lab
Physiome ca5 - Proton Pump Physics Lab
Scientific Source
- Source type:
PhysioMe CellML - Upstream ID:
physiome:ca5 - Original URL: https://models.physiomeproject.org/workspace/ca5
- Bundled artifact:
data/BG_H_pump.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_q_1(Model State Q 1 (source q_1)) maps to source symbolq_1; units:fmol; evidence: source symbol is too ambiguous for a stronger public label.initial_model_state_q_2(Model State Q 2 (source q_2)) maps to source symbolq_2; units:fmol; evidence: source symbol is too ambiguous for a stronger public label.- 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.atp_i(ATP I) maps to source symbolATP_i; units:mM; evidence: source symbol, component, or units provide a direct public name.mu_atpi(Mu Atpi) maps to source symbolmu_ATPi; units:J_per_mol; evidence: source symbol, component, or units provide a direct public name.q_init_atpi(Q Init Atpi) maps to source symbolq_init_ATPi; units:fmol; evidence: source symbol, component, or units provide a direct public name.adp_i(ADP I) maps to source symbolADP_i; units:mM; evidence: source symbol, component, or units provide a direct public name.mu_adpi(Mu Adpi) maps to source symbolmu_ADPi; units:J_per_mol; evidence: source symbol, component, or units provide a direct public name.q_init_adpi(Q Init Adpi) maps to source symbolq_init_ADPi; units:fmol; 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: Transporter state trajectories; flux/current ranking; transport-balance 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




Caveat
This validates source-faithful execution and Biosimulant wiring for transport physiology; it does not claim clinical safety or full reproduction of every upstream figure.
Source-faithful physiology lab for Proton pump - The Physics of Physiology. Public controls and outputs are mapped to real source symbols for transport physiology.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_model_state_q_1",
"label": "Initial Model State Q 1 (source q_1)",
"maps_to": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.initial_model_state_q_1",
"description": "Initial value for Model State Q 1 (source q_1). Maps to source symbol `q_1`. Units: fmol. Naming evidence: source symbol is too ambiguous for a stronger public label.",
"accepted_units": [
"fmol"
]
},
{
"name": "initial_model_state_q_2",
"label": "Initial Model State Q 2 (source q_2)",
"maps_to": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.initial_model_state_q_2",
"description": "Initial value for Model State Q 2 (source q_2). Maps to source symbol `q_2`. Units: fmol. Naming evidence: source symbol is too ambiguous for a stronger public label.",
"accepted_units": [
"fmol"
]
}
],
"outputs": [
{
"name": "state",
"label": "Selected Source State",
"maps_to": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.state"
},
{
"name": "summary",
"label": "Simulation Summary",
"maps_to": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.summary"
},
{
"name": "trajectory",
"label": "Source Trajectory",
"maps_to": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.trajectory"
},
{
"name": "variable_labels",
"label": "Observable Labels",
"maps_to": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.variable_labels"
},
{
"name": "atp_i",
"label": "ATP I",
"maps_to": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.atp_i",
"description": "ATP I. Maps to source symbol `ATP_i`. Units: mM. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "mu_atpi",
"label": "Mu Atpi",
"maps_to": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.mu_atpi",
"description": "Mu Atpi. Maps to source symbol `mu_ATPi`. Units: J_per_mol. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "q_init_atpi",
"label": "Q Init Atpi",
"maps_to": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.q_init_atpi",
"description": "Q Init Atpi. Maps to source symbol `q_init_ATPi`. Units: fmol. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "adp_i",
"label": "ADP I",
"maps_to": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.adp_i",
"description": "ADP I. Maps to source symbol `ADP_i`. Units: mM. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "mu_adpi",
"label": "Mu Adpi",
"maps_to": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.mu_adpi",
"description": "Mu Adpi. Maps to source symbol `mu_ADPi`. Units: J_per_mol. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "q_init_adpi",
"label": "Q Init Adpi",
"maps_to": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.q_init_adpi",
"description": "Q Init Adpi. Maps to source symbol `q_init_ADPi`. Units: fmol. Naming evidence: source symbol, component, or units provide a direct public name."
}
]
},
"title": "Physiome ca5 - Proton Pump Physics Lab",
"models": [
{
"path": "owned/models/physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model",
"alias": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model",
"parameters": {
"model_path": "data/BG_H_pump.cellml",
"integration_step": 0.01
},
"provenance": {
"owned_path": "owned/models/physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model_state"
],
"from": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.state"
},
{
"to": [
"visualisation.physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model_summary"
],
"from": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.summary"
},
{
"to": [
"visualisation.physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model_trajectory"
],
"from": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.trajectory"
},
{
"to": [
"visualisation.physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model_variable_labels"
],
"from": "physiology_cellml_proton_pump_the_physics_of_physiology_ca5_model.variable_labels"
}
],
"runtime": {
"duration": 0.01,
"settle_steps": 1,
"initial_inputs": {},
"communication_step": 0.01
},
"description": "Source-faithful physiology lab for Proton pump - The Physics of Physiology. Public controls and outputs are mapped to real source symbols for transport physiology.",
"schema_version": "2.0"
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