Wodarz2003 - Jansen Mathematical Ctl Dynamics Lab

About lab

Wodarz2003 - Jansen Mathematical Ctl Dynamics Lab

Scientific Source

Source type: PhysioMe CellML
Upstream ID: physiome:wodarz_jansen_2003
Original URL: https://models.physiomeproject.org/workspace/wodarz_jansen_2003
Bundled artifact: data/wodarz_jansen_2003.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_antigen_presenting_cells (Antigen Presenting Cells) maps to source symbol A; units: dimensionless; evidence: source metadata names A as antigen presenting cells.
initial_cytotoxic_t_lymphocytes (Cytotoxic T Lymphocytes) maps to source symbol C; units: dimensionless; evidence: source metadata names C as cytotoxic T lymphocytes.
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.
antigen_presenting_cells (Antigen Presenting Cells) maps to source symbol A; units: dimensionless; evidence: source metadata names A as antigen presenting cells.
cytotoxic_t_lymphocytes (Cytotoxic T Lymphocytes) maps to source symbol C; units: dimensionless; evidence: source metadata names C as cytotoxic T lymphocytes.
target_cells (Target Cells) maps to source symbol T; units: dimensionless; evidence: source metadata names T as target cells.
a_star (A Star) maps to source symbol A_star; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
alpha (Alpha) maps to source symbol alpha; units: first_order_rate_constant; evidence: source symbol, component, or units provide a direct public name.
delta_1 (Delta 1) maps to source symbol delta_1; 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-wodarz2003-jansen-mathematical-ctl-dynamics-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 source-model physiology; it does not claim clinical safety or full reproduction of every upstream figure.

Source-faithful physiology lab for Wodarz, Jansen, 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

Packagewodarz2003-jansen-mathematical-ctl-dynamics-lab

Created2026-05-23

Updated2026-05-23

physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_antigen_presenting_cells",
        "label": "Initial Antigen Presenting Cells",
        "maps_to": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.initial_antigen_presenting_cells",
        "description": "Initial value for Antigen Presenting Cells. Maps to source symbol `A`. Units: dimensionless. Naming evidence: source metadata names `A` as `antigen presenting cells`.",
        "accepted_units": [
          "dimensionless"
        ]
      },
      {
        "name": "initial_cytotoxic_t_lymphocytes",
        "label": "Initial Cytotoxic T Lymphocytes",
        "maps_to": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.initial_cytotoxic_t_lymphocytes",
        "description": "Initial value for Cytotoxic T Lymphocytes. Maps to source symbol `C`. Units: dimensionless. Naming evidence: source metadata names `C` as `cytotoxic T lymphocytes`.",
        "accepted_units": [
          "dimensionless"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.variable_labels"
      },
      {
        "name": "antigen_presenting_cells",
        "label": "Antigen Presenting Cells",
        "maps_to": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.antigen_presenting_cells",
        "description": "Antigen Presenting Cells. Maps to source symbol `A`. Units: dimensionless. Naming evidence: source metadata names `A` as `antigen presenting cells`."
      },
      {
        "name": "cytotoxic_t_lymphocytes",
        "label": "Cytotoxic T Lymphocytes",
        "maps_to": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.cytotoxic_t_lymphocytes",
        "description": "Cytotoxic T Lymphocytes. Maps to source symbol `C`. Units: dimensionless. Naming evidence: source metadata names `C` as `cytotoxic T lymphocytes`."
      },
      {
        "name": "target_cells",
        "label": "Target Cells",
        "maps_to": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.target_cells",
        "description": "Target Cells. Maps to source symbol `T`. Units: dimensionless. Naming evidence: source metadata names `T` as `target cells`."
      },
      {
        "name": "a_star",
        "label": "A Star",
        "maps_to": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.a_star",
        "description": "A Star. Maps to source symbol `A_star`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "alpha",
        "label": "Alpha",
        "maps_to": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_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": "delta_1",
        "label": "Delta 1",
        "maps_to": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.delta_1",
        "description": "Delta 1. Maps to source symbol `delta_1`. Units: first_order_rate_constant. Naming evidence: source symbol, component, or units provide a direct public name."
      }
    ]
  },
  "title": "Wodarz2003 - Jansen Mathematical Ctl Dynamics Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model",
      "alias": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model",
      "parameters": {
        "model_path": "data/wodarz_jansen_2003.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model_state"
      ],
      "from": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model_summary"
      ],
      "from": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model_trajectory"
      ],
      "from": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model_variable_labels"
      ],
      "from": "physiology_cellml_wodarz_jansen_2003_wodarzjansen2003_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Wodarz, Jansen, 2003. Public controls and outputs are mapped to real source symbols for source-model physiology.",
  "schema_version": "2.0"
}

Select a run from History to view its results.