Chen2004 - Mathematical Cell Cyc1e Control Budding Yeast Chencalzonecsi Lab

About lab

Chen2004 - Mathematical Cell Cyc1e Control Budding Yeast Chencalzonecsi Lab

Scientific Source

Source type: PhysioMe CellML
Upstream ID: physiome:chen_calzone_csikasznagy_cross_novak_tyson_2004
Original URL: https://models.physiomeproject.org/workspace/chen_calzone_csikasznagy_cross_novak_tyson_2004
Bundled artifact: data/chen_calzone_csikasznagy_cross_novak_tyson_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_cell_cycle_state_f2 (Cell Cycle State F2 (source F2)) maps to source symbol F2; units: dimensionless; evidence: cell-cycle context supports a conservative source-state label.
initial_cell_cycle_state_f5 (Cell Cycle State F5 (source F5)) maps to source symbol F5; units: dimensionless; evidence: cell-cycle context supports a conservative source-state 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.
apc_p (Apc P) maps to source symbol APC_P; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
bud (Bud) maps to source symbol BUD; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
c2_p (C2 P) maps to source symbol C2P; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
c5_p (C5 P) maps to source symbol C5P; units: dimensionless; evidence: source symbol, component, or units provide a direct public name.
clb2_cyclin_state_c2 (Clb2 Cyclin State C2 (source C2)) maps to source symbol C2; units: dimensionless; evidence: cell-cycle or mitotic context supports a conservative source-state label.
clb5_cyclin_state_c5 (Clb5 Cyclin State C5 (source C5)) maps to source symbol C5; units: dimensionless; evidence: cell-cycle or mitotic context supports a conservative source-state 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: Cyclin/checkpoint trajectories; transition-state bars; cell-cycle progression 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-chen2004-mathematical-cell-cyc1e-control-budding-yeast-chencalzonecsi-lab-physio

02-selected-physiology-trajectories

03-selected-final-observable-values

04-source-and-runtime-evidence

Caveat

This validates source-faithful execution and Biosimulant wiring for cell-cycle dynamics; it does not claim clinical safety or full reproduction of every upstream figure.

Source-faithful physiology lab for Chen, Calzone, Csikasznagy, Cross, Novak, Tyson, 2004. Public controls and outputs are mapped to real source symbols for cell-cycle dynamics.

Runtime

Duration0.01

Comms Step0.01

Settle Steps1

Runs

Total0

Completed0

Failed0

Metadata

Packagechen2004-mathematical-cell-cyc1e-control-budding-yeast-chencalzo

Created2026-05-23

Updated2026-05-23

physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_cell_cycle_state_f2",
        "label": "Initial Cell Cycle State F2 (source F2)",
        "maps_to": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.initial_cell_cycle_state_f2",
        "description": "Initial value for Cell Cycle State F2 (source F2). Maps to source symbol `F2`. Units: dimensionless. Naming evidence: cell-cycle context supports a conservative source-state label.",
        "accepted_units": [
          "dimensionless"
        ]
      },
      {
        "name": "initial_cell_cycle_state_f5",
        "label": "Initial Cell Cycle State F5 (source F5)",
        "maps_to": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.initial_cell_cycle_state_f5",
        "description": "Initial value for Cell Cycle State F5 (source F5). Maps to source symbol `F5`. Units: dimensionless. Naming evidence: cell-cycle context supports a conservative source-state label.",
        "accepted_units": [
          "dimensionless"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.variable_labels"
      },
      {
        "name": "apc_p",
        "label": "Apc P",
        "maps_to": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.apc_p",
        "description": "Apc P. Maps to source symbol `APC_P`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "bud",
        "label": "Bud",
        "maps_to": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.bud",
        "description": "Bud. Maps to source symbol `BUD`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "c2_p",
        "label": "C2 P",
        "maps_to": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.c2_p",
        "description": "C2 P. Maps to source symbol `C2P`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "c5_p",
        "label": "C5 P",
        "maps_to": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.c5_p",
        "description": "C5 P. Maps to source symbol `C5P`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "clb2_cyclin_state_c2",
        "label": "Clb2 Cyclin State C2 (source C2)",
        "maps_to": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.clb2_cyclin_state_c2",
        "description": "Clb2 Cyclin State C2 (source C2). Maps to source symbol `C2`. Units: dimensionless. Naming evidence: cell-cycle or mitotic context supports a conservative source-state label."
      },
      {
        "name": "clb5_cyclin_state_c5",
        "label": "Clb5 Cyclin State C5 (source C5)",
        "maps_to": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.clb5_cyclin_state_c5",
        "description": "Clb5 Cyclin State C5 (source C5). Maps to source symbol `C5`. Units: dimensionless. Naming evidence: cell-cycle or mitotic context supports a conservative source-state label."
      }
    ]
  },
  "title": "Chen2004 - Mathematical Cell Cyc1e Control Budding Yeast Chencalzonecsi Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model",
      "alias": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model",
      "parameters": {
        "model_path": "data/chen_calzone_csikasznagy_cross_novak_tyson_2004.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model_state"
      ],
      "from": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model_summary"
      ],
      "from": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model_trajectory"
      ],
      "from": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model_variable_labels"
      ],
      "from": "physiology_cellml_chen_calzone_csikasznagy_cross_novak_tyson_2004_chencalzonecsikasznagycrossnovaktyson2004_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Chen, Calzone, Csikasznagy, Cross, Novak, Tyson, 2004. Public controls and outputs are mapped to real source symbols for cell-cycle dynamics.",
  "schema_version": "2.0"
}

Select a run from History to view its results.