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Physiome ca5 - Proton Pump Physics Lab

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 symbol q_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 symbol q_2; units: fmol; evidence: source symbol is too ambiguous for a stronger public label.
  • 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.
  • atp_i (ATP I) maps to source symbol ATP_i; units: mM; evidence: source symbol, component, or units provide a direct public name.
  • mu_atpi (Mu Atpi) maps to source symbol mu_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 symbol q_init_ATPi; units: fmol; evidence: source symbol, component, or units provide a direct public name.
  • adp_i (ADP I) maps to source symbol ADP_i; units: mM; evidence: source symbol, component, or units provide a direct public name.
  • mu_adpi (Mu Adpi) maps to source symbol mu_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 symbol q_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

01-physiome-ca5-proton-pump-physics-lab-physiology-run-answer

02-selected-physiology-trajectories

03-selected-final-observable-values

04-source-and-runtime-evidence

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

Duration0.01
Comms Step0.01
Settle Steps1

Runs

Total0
Completed0
Failed0

Metadata

Packagephysiome-ca5-proton-pump-physics-lab
Created2026-05-23
Updated2026-05-23
physiologycellmlphysiomefaithfulvisualisationother

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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