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Phillips2007 - Quantitative Sleep Wake Dynamics Based Brainst Phillips2007 Lab

About lab

Phillips2007 - Quantitative Sleep Wake Dynamics Based Brainst Phillips2007 Lab

Scientific Source

  • Source type: PhysioMe CellML
  • Upstream ID: physiome:phillips_2007
  • Original URL: https://models.physiomeproject.org/workspace/phillips_2007
  • Bundled artifact: data/phillips_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_model_state_vm (Model State Vm (source Vm)) maps to source symbol Vm; units: mV; evidence: source symbol is too ambiguous for a stronger public label.
  • initial_model_state_vv (Model State Vv (source Vv)) maps to source symbol Vv; units: mV; 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.
  • model_state_vm (Model State Vm (source Vm)) maps to source symbol Vm; units: mV; evidence: source symbol is too ambiguous for a stronger public label.
  • model_state_vv (Model State Vv (source Vv)) maps to source symbol Vv; units: mV; evidence: source symbol is too ambiguous for a stronger public label.
  • somnogen_level (Somnogen Level) maps to source symbol H; units: nM; evidence: source metadata names H as somnogen level.
  • chi (Chi) maps to source symbol chi; units: hour; evidence: source symbol, component, or units provide a direct public name.
  • model_parameter_c (Model Parameter C (source C)) maps to source symbol C; units: dimensionless; evidence: source symbol is dimensionless but lacks enough evidence for a biological label.
  • model_parameter_c0 (Model Parameter C0 (source c0)) maps to source symbol c0; units: dimensionless; evidence: source symbol is dimensionless but lacks enough evidence for a biological label.

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-phillips2007-quantitative-sleep-wake-dynamics-based-brainst-phillips2007-lab-phy

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 Phillips 2007. 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

Packagephillips2007-quantitative-sleep-wake-dynamics-based-brainst-phil
Created2026-05-23
Updated2026-05-23
physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_model_state_vm",
        "label": "Initial Model State Vm (source Vm)",
        "maps_to": "physiology_cellml_phillips_2007_phillips2007_model.initial_model_state_vm",
        "description": "Initial value for Model State Vm (source Vm). Maps to source symbol `Vm`. Units: mV. Naming evidence: source symbol is too ambiguous for a stronger public label.",
        "accepted_units": [
          "mV"
        ]
      },
      {
        "name": "initial_model_state_vv",
        "label": "Initial Model State Vv (source Vv)",
        "maps_to": "physiology_cellml_phillips_2007_phillips2007_model.initial_model_state_vv",
        "description": "Initial value for Model State Vv (source Vv). Maps to source symbol `Vv`. Units: mV. Naming evidence: source symbol is too ambiguous for a stronger public label.",
        "accepted_units": [
          "mV"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_phillips_2007_phillips2007_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_phillips_2007_phillips2007_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_phillips_2007_phillips2007_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_phillips_2007_phillips2007_model.variable_labels"
      },
      {
        "name": "model_state_vm",
        "label": "Model State Vm (source Vm)",
        "maps_to": "physiology_cellml_phillips_2007_phillips2007_model.model_state_vm",
        "description": "Model State Vm (source Vm). Maps to source symbol `Vm`. Units: mV. Naming evidence: source symbol is too ambiguous for a stronger public label."
      },
      {
        "name": "model_state_vv",
        "label": "Model State Vv (source Vv)",
        "maps_to": "physiology_cellml_phillips_2007_phillips2007_model.model_state_vv",
        "description": "Model State Vv (source Vv). Maps to source symbol `Vv`. Units: mV. Naming evidence: source symbol is too ambiguous for a stronger public label."
      },
      {
        "name": "somnogen_level",
        "label": "Somnogen Level",
        "maps_to": "physiology_cellml_phillips_2007_phillips2007_model.somnogen_level",
        "description": "Somnogen Level. Maps to source symbol `H`. Units: nM. Naming evidence: source metadata names `H` as `somnogen level`."
      },
      {
        "name": "chi",
        "label": "Chi",
        "maps_to": "physiology_cellml_phillips_2007_phillips2007_model.chi",
        "description": "Chi. Maps to source symbol `chi`. Units: hour. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "model_parameter_c",
        "label": "Model Parameter C (source C)",
        "maps_to": "physiology_cellml_phillips_2007_phillips2007_model.model_parameter_c",
        "description": "Model Parameter C (source C). Maps to source symbol `C`. Units: dimensionless. Naming evidence: source symbol is dimensionless but lacks enough evidence for a biological label."
      },
      {
        "name": "model_parameter_c0",
        "label": "Model Parameter C0 (source c0)",
        "maps_to": "physiology_cellml_phillips_2007_phillips2007_model.model_parameter_c0",
        "description": "Model Parameter C0 (source c0). Maps to source symbol `c0`. Units: dimensionless. Naming evidence: source symbol is dimensionless but lacks enough evidence for a biological label."
      }
    ]
  },
  "title": "Phillips2007 - Quantitative Sleep Wake Dynamics Based Brainst Phillips2007 Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_phillips_2007_phillips2007_model",
      "alias": "physiology_cellml_phillips_2007_phillips2007_model",
      "parameters": {
        "model_path": "data/phillips_2007.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_phillips_2007_phillips2007_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_phillips_2007_phillips2007_model_state"
      ],
      "from": "physiology_cellml_phillips_2007_phillips2007_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_phillips_2007_phillips2007_model_summary"
      ],
      "from": "physiology_cellml_phillips_2007_phillips2007_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_phillips_2007_phillips2007_model_trajectory"
      ],
      "from": "physiology_cellml_phillips_2007_phillips2007_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_phillips_2007_phillips2007_model_variable_labels"
      ],
      "from": "physiology_cellml_phillips_2007_phillips2007_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Phillips 2007. Public controls and outputs are mapped to real source symbols for source-model physiology.",
  "schema_version": "2.0"
}

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