Chen2000 - Kinetic Analysis Molecular Budding Yeast Cell Cycle Lab

About lab

Chen2000 - Kinetic Analysis Molecular Budding Yeast Cell Cycle Lab

Scientific Source

Source type: PhysioMe CellML
Upstream ID: physiome:36a
Original URL: https://models.physiomeproject.org/workspace/36a
Bundled artifact: data/chen_csikasz-nagy_gyorffy_val_novak_tyson_2000.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_bud (Bud) maps to source symbol BUD; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
initial_cdc20 (Cdc20) maps to source symbol Cdc20; units: dimensionless; 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.
bud (Bud) maps to source symbol BUD; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
cdc20 (Cdc20) maps to source symbol Cdc20; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
cdc20_t (Cdc20 T) maps to source symbol Cdc20_T; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
clb2_sic1 (Clb2 Sic1) maps to source symbol Clb2_Sic1; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
clb2_t (Clb2 T) maps to source symbol Clb2_T; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
clb5_sic1 (Clb5 Sic1) maps to source symbol Clb5_Sic1; units: dimensionless; 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-chen2000-kinetic-analysis-molecular-budding-yeast-cell-cycle-lab-physiology-run-

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 Chen, Csikasz-Nagy, Gyorffy, Val, Novak, Tyson, 2000. 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

Packagechen2000-kinetic-analysis-molecular-budding-yeast-cell-cycle-lab

Created2026-05-23

Updated2026-05-23

physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_bud",
        "label": "Initial Bud",
        "maps_to": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.initial_bud",
        "description": "Initial value for Bud. Maps to source symbol `BUD`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "dimensionless"
        ]
      },
      {
        "name": "initial_cdc20",
        "label": "Initial Cdc20",
        "maps_to": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.initial_cdc20",
        "description": "Initial value for Cdc20. Maps to source symbol `Cdc20`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "dimensionless"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.variable_labels"
      },
      {
        "name": "bud",
        "label": "Bud",
        "maps_to": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.bud",
        "description": "Bud. Maps to source symbol `BUD`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "cdc20",
        "label": "Cdc20",
        "maps_to": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.cdc20",
        "description": "Cdc20. Maps to source symbol `Cdc20`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "cdc20_t",
        "label": "Cdc20 T",
        "maps_to": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.cdc20_t",
        "description": "Cdc20 T. Maps to source symbol `Cdc20_T`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "clb2_sic1",
        "label": "Clb2 Sic1",
        "maps_to": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.clb2_sic1",
        "description": "Clb2 Sic1. Maps to source symbol `Clb2_Sic1`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "clb2_t",
        "label": "Clb2 T",
        "maps_to": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.clb2_t",
        "description": "Clb2 T. Maps to source symbol `Clb2_T`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "clb5_sic1",
        "label": "Clb5 Sic1",
        "maps_to": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.clb5_sic1",
        "description": "Clb5 Sic1. Maps to source symbol `Clb5_Sic1`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      }
    ]
  },
  "title": "Chen2000 - Kinetic Analysis Molecular Budding Yeast Cell Cycle Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model",
      "alias": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model",
      "parameters": {
        "model_path": "data/chen_csikasz-nagy_gyorffy_val_novak_tyson_2000.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model_state"
      ],
      "from": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model_summary"
      ],
      "from": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model_trajectory"
      ],
      "from": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model_variable_labels"
      ],
      "from": "physiology_cellml_chen_csikasz_nagy_gyorffy_val_novak_tyson_2000_36a_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Chen, Csikasz-Nagy, Gyorffy, Val, Novak, Tyson, 2000. 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.