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Brown1997 - Mathematical Diurnal Variations Human Plasma Melatonin Lab

About lab

Brown1997 - Mathematical Diurnal Variations Human Plasma Melatonin Lab

Scientific Source

  • Source type: PhysioMe CellML
  • Upstream ID: physiome:57f
  • Original URL: https://models.physiomeproject.org/workspace/57f
  • Bundled artifact: data/brown_choe_shanahan_czeisler_1997.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_concentration_h1 (Concentration H1 (source H1)) maps to source symbol H1; units: picomolar; evidence: amount concentration units identify a concentration state.
  • initial_concentration_h2 (Concentration H2 (source H2)) maps to source symbol H2; units: picomolar; evidence: amount concentration units identify a concentration state.
  • 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.
  • concentration_h1 (Concentration H1 (source H1)) maps to source symbol H1; units: picomolar; evidence: amount concentration units identify a concentration state.
  • concentration_h2 (Concentration H2 (source H2)) maps to source symbol H2; units: picomolar; evidence: amount concentration units identify a concentration state.
  • alpha (Alpha) maps to source symbol alpha; units: first_order_rate_constant; evidence: source symbol, component, or units provide a direct public name.
  • beta_c (Beta C) maps to source symbol beta_C; units: first_order_rate_constant; evidence: source symbol, component, or units provide a direct public name.
  • beta_i (Beta I) maps to source symbol beta_I; units: first_order_rate_constant; evidence: source symbol, component, or units provide a direct public name.
  • lamda (Lamda) maps to source symbol lamda; units: first_order_rate_constant; 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: Selected source-variable trajectories; final observable ranking; source/runtime evidence table; scientific 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-brown1997-mathematical-diurnal-variations-human-plasma-melatonin-lab-physiology-

02-selected-physiology-trajectories

03-selected-final-observable-values

04-source-and-runtime-evidence

Caveat

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

Source-faithful physiology lab for Brown, Choe, Shanahan, Czeisler, 1997. Public controls and outputs are mapped to real source symbols for source-model physiology.

Runtime

Duration0.01
Comms Step0.01
Settle Steps1

Runs

Total0
Completed0
Failed0

Metadata

Packagebrown1997-mathematical-diurnal-variations-human-plasma-melatonin
Created2026-05-23
Updated2026-05-23
physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_concentration_h1",
        "label": "Initial Concentration H1 (source H1)",
        "maps_to": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.initial_concentration_h1",
        "description": "Initial value for Concentration H1 (source H1). Maps to source symbol `H1`. Units: picomolar. Naming evidence: amount concentration units identify a concentration state.",
        "accepted_units": [
          "picomolar"
        ]
      },
      {
        "name": "initial_concentration_h2",
        "label": "Initial Concentration H2 (source H2)",
        "maps_to": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.initial_concentration_h2",
        "description": "Initial value for Concentration H2 (source H2). Maps to source symbol `H2`. Units: picomolar. Naming evidence: amount concentration units identify a concentration state.",
        "accepted_units": [
          "picomolar"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.variable_labels"
      },
      {
        "name": "concentration_h1",
        "label": "Concentration H1 (source H1)",
        "maps_to": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.concentration_h1",
        "description": "Concentration H1 (source H1). Maps to source symbol `H1`. Units: picomolar. Naming evidence: amount concentration units identify a concentration state."
      },
      {
        "name": "concentration_h2",
        "label": "Concentration H2 (source H2)",
        "maps_to": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.concentration_h2",
        "description": "Concentration H2 (source H2). Maps to source symbol `H2`. Units: picomolar. Naming evidence: amount concentration units identify a concentration state."
      },
      {
        "name": "alpha",
        "label": "Alpha",
        "maps_to": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.alpha",
        "description": "Alpha. Maps to source symbol `alpha`. Units: first_order_rate_constant. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "beta_c",
        "label": "Beta C",
        "maps_to": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.beta_c",
        "description": "Beta C. Maps to source symbol `beta_C`. Units: first_order_rate_constant. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "beta_i",
        "label": "Beta I",
        "maps_to": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.beta_i",
        "description": "Beta I. Maps to source symbol `beta_I`. Units: first_order_rate_constant. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "lamda",
        "label": "Lamda",
        "maps_to": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.lamda",
        "description": "Lamda. Maps to source symbol `lamda`. Units: first_order_rate_constant. Naming evidence: source symbol, component, or units provide a direct public name."
      }
    ]
  },
  "title": "Brown1997 - Mathematical Diurnal Variations Human Plasma Melatonin Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model",
      "alias": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model",
      "parameters": {
        "model_path": "data/brown_choe_shanahan_czeisler_1997.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model_state"
      ],
      "from": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model_summary"
      ],
      "from": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model_trajectory"
      ],
      "from": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model_variable_labels"
      ],
      "from": "physiology_cellml_brown_choe_shanahan_czeisler_1997_57f_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Brown, Choe, Shanahan, Czeisler, 1997. Public controls and outputs are mapped to real source symbols for source-model physiology.",
  "schema_version": "2.0"
}

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