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Komarova2003 - Wodarz Mathematical Evolutionary Dynamics Mutator Lab

About lab

Komarova2003 - Wodarz Mathematical Evolutionary Dynamics Mutator Lab

Scientific Source

  • Source type: PhysioMe CellML
  • Upstream ID: physiome:komarova_wodarz_2003
  • Original URL: https://models.physiomeproject.org/workspace/komarova_wodarz_2003
  • Bundled artifact: data/komarova_wodarz_2003_complex.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_m_1_2 (M 1 2) maps to source symbol M_1_2; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
  • initial_model_state_m_0 (Model State M 0 (source M_0)) maps to source symbol M_0; units: dimensionless; evidence: source symbol is dimensionless but lacks enough evidence for a biological 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_m_0 (Model State M 0 (source M_0)) maps to source symbol M_0; units: dimensionless; evidence: source symbol is dimensionless but lacks enough evidence for a biological label.
  • model_state_m_1 (Model State M 1 (source M_1)) maps to source symbol M_1; units: dimensionless; evidence: source symbol is dimensionless but lacks enough evidence for a biological label.
  • model_state_m_2 (Model State M 2 (source M_2)) maps to source symbol M_2; units: dimensionless; evidence: source symbol is dimensionless but lacks enough evidence for a biological label.
  • model_state_m_3 (Model State M 3 (source M_3)) maps to source symbol M_3; units: dimensionless; evidence: source symbol is dimensionless but lacks enough evidence for a biological label.
  • model_state_m_4 (Model State M 4 (source M_4)) maps to source symbol M_4; units: dimensionless; evidence: source symbol is dimensionless but lacks enough evidence for a biological label.
  • model_state_m_5 (Model State M 5 (source M_5)) maps to source symbol M_5; 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-komarova2003-wodarz-mathematical-evolutionary-dynamics-mutator-lab-physiology-ru

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 Komarova, Wodarz, 2003. 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

Packagekomarova2003-wodarz-mathematical-evolutionary-dynamics-mutator-l
Created2026-05-23
Updated2026-05-23
physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_m_1_2",
        "label": "Initial M 1 2",
        "maps_to": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.initial_m_1_2",
        "description": "Initial value for M 1 2. Maps to source symbol `M_1_2`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "dimensionless"
        ]
      },
      {
        "name": "initial_model_state_m_0",
        "label": "Initial Model State M 0 (source M_0)",
        "maps_to": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.initial_model_state_m_0",
        "description": "Initial value for Model State M 0 (source M_0). Maps to source symbol `M_0`. Units: dimensionless. Naming evidence: source symbol is dimensionless but lacks enough evidence for a biological label.",
        "accepted_units": [
          "dimensionless"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.variable_labels"
      },
      {
        "name": "model_state_m_0",
        "label": "Model State M 0 (source M_0)",
        "maps_to": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.model_state_m_0",
        "description": "Model State M 0 (source M_0). Maps to source symbol `M_0`. Units: dimensionless. Naming evidence: source symbol is dimensionless but lacks enough evidence for a biological label."
      },
      {
        "name": "model_state_m_1",
        "label": "Model State M 1 (source M_1)",
        "maps_to": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.model_state_m_1",
        "description": "Model State M 1 (source M_1). Maps to source symbol `M_1`. Units: dimensionless. Naming evidence: source symbol is dimensionless but lacks enough evidence for a biological label."
      },
      {
        "name": "model_state_m_2",
        "label": "Model State M 2 (source M_2)",
        "maps_to": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.model_state_m_2",
        "description": "Model State M 2 (source M_2). Maps to source symbol `M_2`. Units: dimensionless. Naming evidence: source symbol is dimensionless but lacks enough evidence for a biological label."
      },
      {
        "name": "model_state_m_3",
        "label": "Model State M 3 (source M_3)",
        "maps_to": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.model_state_m_3",
        "description": "Model State M 3 (source M_3). Maps to source symbol `M_3`. Units: dimensionless. Naming evidence: source symbol is dimensionless but lacks enough evidence for a biological label."
      },
      {
        "name": "model_state_m_4",
        "label": "Model State M 4 (source M_4)",
        "maps_to": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.model_state_m_4",
        "description": "Model State M 4 (source M_4). Maps to source symbol `M_4`. Units: dimensionless. Naming evidence: source symbol is dimensionless but lacks enough evidence for a biological label."
      },
      {
        "name": "model_state_m_5",
        "label": "Model State M 5 (source M_5)",
        "maps_to": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.model_state_m_5",
        "description": "Model State M 5 (source M_5). Maps to source symbol `M_5`. Units: dimensionless. Naming evidence: source symbol is dimensionless but lacks enough evidence for a biological label."
      }
    ]
  },
  "title": "Komarova2003 - Wodarz Mathematical Evolutionary Dynamics Mutator Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model",
      "alias": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model",
      "parameters": {
        "model_path": "data/komarova_wodarz_2003_complex.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model_state"
      ],
      "from": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model_summary"
      ],
      "from": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model_trajectory"
      ],
      "from": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model_variable_labels"
      ],
      "from": "physiology_cellml_komarova_wodarz_2003_komarovawodarz2003_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Komarova, Wodarz, 2003. Public controls and outputs are mapped to real source symbols for source-model physiology.",
  "schema_version": "2.0"
}

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