Bertram2007 - Mathematical Interaction Between Glycolysis Mitochondrial Lab

About lab

Bertram2007 - Mathematical Interaction Between Glycolysis Mitochondrial Lab

Scientific Source

Source type: PhysioMe CellML
Upstream ID: physiome:bertram_satin_pedersen_luciani_sherman_2007
Original URL: https://models.physiomeproject.org/workspace/bertram_satin_pedersen_luciani_sherman_2007
Bundled artifact: data/bertram_satin_pedersen_luciani_sherman_2007.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_voltage_dependent_potassium_current_n_gate (Voltage Dependent Potassium Current N Gate) maps to source symbol n; units: dimensionless; evidence: source metadata names n as voltage-dependent potassium current n gate.
initial_membrane_voltage (Membrane Voltage) maps to source symbol Vm; units: millivolt; evidence: source symbol, component, or units provide a direct public name.
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.
membrane_voltage (Membrane Voltage) maps to source symbol Vm; units: millivolt; evidence: source symbol, component, or units provide a direct public name.
membrane_voltage_v (Membrane Voltage V) maps to source symbol v; units: millivolt; evidence: source symbol, component, or units provide a direct public name.
adp3m (Adp3m) maps to source symbol adp3m; units: micromolar; evidence: source symbol, component, or units provide a direct public name.
mgadp (Mgadp) maps to source symbol mgadp; units: micromolar; evidence: source symbol, component, or units provide a direct public name.
cytosolic_adp_concentration (Cytosolic ADP Concentration) maps to source symbol adp; units: micromolar; evidence: source metadata names adp as cytosolic ADP concentration.
mitochondrial_adp (Mitochondrial ADP) maps to source symbol ADPm; units: millimolar; evidence: source metadata names ADPm as mitochondrial ADP.

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: Glucose, insulin, and regulatory species trajectories; peak glucose/insulin response bars; glycemic recovery 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-bertram2007-mathematical-interaction-between-glycolysis-mitochondrial-lab-physio

02-selected-physiology-trajectories

03-selected-final-observable-values

04-source-and-runtime-evidence

Caveat

This validates source-faithful execution and Biosimulant wiring for glucose-insulin physiology; it does not claim clinical safety or full reproduction of every upstream figure.

Source-faithful physiology lab for Bertram, Satin, Pedersen, Luciani, Sherman, 2007. Public controls and outputs are mapped to real source symbols for glucose-insulin physiology.

Runtime

Duration0.01

Comms Step0.01

Settle Steps1

Runs

Total0

Completed0

Failed0

Metadata

Packagebertram2007-mathematical-interaction-between-glycolysis-mitochon

Created2026-05-23

Updated2026-05-23

physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_voltage_dependent_potassium_current_n_gate",
        "label": "Initial Voltage Dependent Potassium Current N Gate",
        "maps_to": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.initial_voltage_dependent_potassium_current_n_gate",
        "description": "Initial value for Voltage Dependent Potassium Current N Gate. Maps to source symbol `n`. Units: dimensionless. Naming evidence: source metadata names `n` as `voltage-dependent potassium current n gate`.",
        "accepted_units": [
          "dimensionless"
        ]
      },
      {
        "name": "initial_membrane_voltage",
        "label": "Initial Membrane Voltage",
        "maps_to": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.initial_membrane_voltage",
        "description": "Initial value for Membrane Voltage. Maps to source symbol `Vm`. Units: millivolt. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "millivolt"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.variable_labels"
      },
      {
        "name": "membrane_voltage",
        "label": "Membrane Voltage",
        "maps_to": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.membrane_voltage",
        "description": "Membrane Voltage. Maps to source symbol `Vm`. Units: millivolt. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "membrane_voltage_v",
        "label": "Membrane Voltage V",
        "maps_to": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.membrane_voltage_v",
        "description": "Membrane Voltage V. Maps to source symbol `v`. Units: millivolt. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "adp3m",
        "label": "Adp3m",
        "maps_to": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.adp3m",
        "description": "Adp3m. Maps to source symbol `adp3m`. Units: micromolar. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "mgadp",
        "label": "Mgadp",
        "maps_to": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.mgadp",
        "description": "Mgadp. Maps to source symbol `mgadp`. Units: micromolar. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "cytosolic_adp_concentration",
        "label": "Cytosolic ADP Concentration",
        "maps_to": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.cytosolic_adp_concentration",
        "description": "Cytosolic ADP Concentration. Maps to source symbol `adp`. Units: micromolar. Naming evidence: source metadata names `adp` as `cytosolic ADP concentration`."
      },
      {
        "name": "mitochondrial_adp",
        "label": "Mitochondrial ADP",
        "maps_to": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.mitochondrial_adp",
        "description": "Mitochondrial ADP. Maps to source symbol `ADPm`. Units: millimolar. Naming evidence: source metadata names `ADPm` as `mitochondrial ADP`."
      }
    ]
  },
  "title": "Bertram2007 - Mathematical Interaction Between Glycolysis Mitochondrial Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model",
      "alias": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model",
      "parameters": {
        "model_path": "data/bertram_satin_pedersen_luciani_sherman_2007.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model_state"
      ],
      "from": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model_summary"
      ],
      "from": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model_trajectory"
      ],
      "from": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model_variable_labels"
      ],
      "from": "physiology_cellml_bertram_satin_pedersen_luciani_sherman_2007_bertramsatinpedersenlucianisherman2007_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Bertram, Satin, Pedersen, Luciani, Sherman, 2007. Public controls and outputs are mapped to real source symbols for glucose-insulin physiology.",
  "schema_version": "2.0"
}

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