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Swat2004 - Bifurcation Analysis Regulatory Modules Mammalian G1 S Lab

About lab

Swat2004 - Bifurcation Analysis Regulatory Modules Mammalian G1 S Lab

Scientific Source

  • Source type: PhysioMe CellML
  • Upstream ID: physiome:swat_kel_herzel_2004
  • Original URL: https://models.physiomeproject.org/workspace/swat_kel_herzel_2004
  • Bundled artifact: data/swat_2004.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_ap_1 (Ap 1) maps to source symbol AP_1; units: substance; evidence: source symbol, component, or units provide a direct public name.
  • initial_cyc_d_a (Cyc D A) maps to source symbol CycD_a; units: substance; 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.
  • ap_1 (Ap 1) maps to source symbol AP_1; units: substance; evidence: source symbol, component, or units provide a direct public name.
  • cyc_d_a (Cyc D A) maps to source symbol CycD_a; units: substance; evidence: source symbol, component, or units provide a direct public name.
  • cyc_d_i (Cyc D I) maps to source symbol CycD_i; units: substance; evidence: source symbol, component, or units provide a direct public name.
  • cyc_e_a (Cyc E A) maps to source symbol CycE_a; units: substance; evidence: source symbol, component, or units provide a direct public name.
  • cyc_e_i (Cyc E I) maps to source symbol CycE_i; units: substance; evidence: source symbol, component, or units provide a direct public name.
  • e2_f1 (E2 F1) maps to source symbol E2F1; units: substance; 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-swat2004-bifurcation-analysis-regulatory-modules-mammalian-g1-s-lab-physiology-r

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 Swat, Kel and Herzel 2004. 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

Packageswat2004-bifurcation-analysis-regulatory-modules-mammalian-g1-s
Created2026-05-23
Updated2026-05-23
physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_ap_1",
        "label": "Initial Ap 1",
        "maps_to": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.initial_ap_1",
        "description": "Initial value for Ap 1. Maps to source symbol `AP_1`. Units: substance. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "substance"
        ]
      },
      {
        "name": "initial_cyc_d_a",
        "label": "Initial Cyc D A",
        "maps_to": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.initial_cyc_d_a",
        "description": "Initial value for Cyc D A. Maps to source symbol `CycD_a`. Units: substance. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "substance"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.variable_labels"
      },
      {
        "name": "ap_1",
        "label": "Ap 1",
        "maps_to": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.ap_1",
        "description": "Ap 1. Maps to source symbol `AP_1`. Units: substance. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "cyc_d_a",
        "label": "Cyc D A",
        "maps_to": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.cyc_d_a",
        "description": "Cyc D A. Maps to source symbol `CycD_a`. Units: substance. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "cyc_d_i",
        "label": "Cyc D I",
        "maps_to": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.cyc_d_i",
        "description": "Cyc D I. Maps to source symbol `CycD_i`. Units: substance. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "cyc_e_a",
        "label": "Cyc E A",
        "maps_to": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.cyc_e_a",
        "description": "Cyc E A. Maps to source symbol `CycE_a`. Units: substance. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "cyc_e_i",
        "label": "Cyc E I",
        "maps_to": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.cyc_e_i",
        "description": "Cyc E I. Maps to source symbol `CycE_i`. Units: substance. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "e2_f1",
        "label": "E2 F1",
        "maps_to": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.e2_f1",
        "description": "E2 F1. Maps to source symbol `E2F1`. Units: substance. Naming evidence: source symbol, component, or units provide a direct public name."
      }
    ]
  },
  "title": "Swat2004 - Bifurcation Analysis Regulatory Modules Mammalian G1 S Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model",
      "alias": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model",
      "parameters": {
        "model_path": "data/swat_2004.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model_state"
      ],
      "from": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model_summary"
      ],
      "from": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model_trajectory"
      ],
      "from": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model_variable_labels"
      ],
      "from": "physiology_cellml_swat_kel_and_herzel_2004_swatkelherzel2004_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Swat, Kel and Herzel 2004. Public controls and outputs are mapped to real source symbols for source-model physiology.",
  "schema_version": "2.0"
}

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