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 symbolAP_1; units:substance; evidence: source symbol, component, or units provide a direct public name.initial_cyc_d_a(Cyc D A) maps to source symbolCycD_a; units:substance; evidence: source symbol, component, or units provide a direct public name.- The simulator still uses an internal
integration_stepparameter from the model manifest; it is not exposed as a biological lab input.
Selected outputs:
state,summary,trajectory, andvariable_labelsremain available for traceability.ap_1(Ap 1) maps to source symbolAP_1; units:substance; evidence: source symbol, component, or units provide a direct public name.cyc_d_a(Cyc D A) maps to source symbolCycD_a; units:substance; evidence: source symbol, component, or units provide a direct public name.cyc_d_i(Cyc D I) maps to source symbolCycD_i; units:substance; evidence: source symbol, component, or units provide a direct public name.cyc_e_a(Cyc E A) maps to source symbolCycE_a; units:substance; evidence: source symbol, component, or units provide a direct public name.cyc_e_i(Cyc E I) maps to source symbolCycE_i; units:substance; evidence: source symbol, component, or units provide a direct public name.e2_f1(E2 F1) maps to source symbolE2F1; 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




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
Runs
Metadata
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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