About lab
Physiome modularmassact - Primer Modular Mass Action Modelling Cellml Lab
Scientific Source
- Source type:
PhysioMe CellML - Upstream ID:
physiome:modularmassactionprimer - Original URL: https://models.physiomeproject.org/workspace/modularmassactionprimer
- Bundled artifact:
data/BestPractice_Cdecoupled.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_cformation_a(Cformation A) maps to source symbolA; units:uM; evidence: source symbol, component, or units provide a direct public name.initial_cformation_b(Cformation B) maps to source symbolB; units:uM; 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.cformation_a(Cformation A) maps to source symbolA; units:uM; evidence: source symbol, component, or units provide a direct public name.cformation_b(Cformation B) maps to source symbolB; units:uM; evidence: source symbol, component, or units provide a direct public name.eformation_d(Eformation D) maps to source symbolD; units:per_um2; evidence: source symbol, component, or units provide a direct public name.eformation_e(Eformation E) maps to source symbolE; units:per_um2; evidence: source symbol, component, or units provide a direct public name.model_state_c(Model State C (source C)) maps to source symbolC; units:uM; evidence: source symbol is too ambiguous for a stronger public label.cformation_j1(Cformation J1) maps to source symbolJ1; units:uM_per_s; 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 A Primer on Modular Mass Action Modelling with CellML. Public controls and outputs are mapped to real source symbols for source-model physiology.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_cformation_a",
"label": "Initial Cformation A",
"maps_to": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.initial_cformation_a",
"description": "Initial value for Cformation A. Maps to source symbol `A`. Units: uM. Naming evidence: source symbol, component, or units provide a direct public name.",
"accepted_units": [
"uM"
]
},
{
"name": "initial_cformation_b",
"label": "Initial Cformation B",
"maps_to": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.initial_cformation_b",
"description": "Initial value for Cformation B. Maps to source symbol `B`. Units: uM. Naming evidence: source symbol, component, or units provide a direct public name.",
"accepted_units": [
"uM"
]
}
],
"outputs": [
{
"name": "state",
"label": "Selected Source State",
"maps_to": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.state"
},
{
"name": "summary",
"label": "Simulation Summary",
"maps_to": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.summary"
},
{
"name": "trajectory",
"label": "Source Trajectory",
"maps_to": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.trajectory"
},
{
"name": "variable_labels",
"label": "Observable Labels",
"maps_to": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.variable_labels"
},
{
"name": "cformation_a",
"label": "Cformation A",
"maps_to": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.cformation_a",
"description": "Cformation A. Maps to source symbol `A`. Units: uM. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "cformation_b",
"label": "Cformation B",
"maps_to": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.cformation_b",
"description": "Cformation B. Maps to source symbol `B`. Units: uM. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "eformation_d",
"label": "Eformation D",
"maps_to": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.eformation_d",
"description": "Eformation D. Maps to source symbol `D`. Units: per_um2. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "eformation_e",
"label": "Eformation E",
"maps_to": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.eformation_e",
"description": "Eformation E. Maps to source symbol `E`. Units: per_um2. Naming evidence: source symbol, component, or units provide a direct public name."
},
{
"name": "model_state_c",
"label": "Model State C (source C)",
"maps_to": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.model_state_c",
"description": "Model State C (source C). Maps to source symbol `C`. Units: uM. Naming evidence: source symbol is too ambiguous for a stronger public label."
},
{
"name": "cformation_j1",
"label": "Cformation J1",
"maps_to": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.cformation_j1",
"description": "Cformation J1. Maps to source symbol `J1`. Units: uM_per_s. Naming evidence: source symbol, component, or units provide a direct public name."
}
]
},
"title": "Physiome modularmassact - Primer Modular Mass Action Modelling Cellml Lab",
"models": [
{
"path": "owned/models/physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model",
"alias": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model",
"parameters": {
"model_path": "data/BestPractice_Cdecoupled.cellml",
"integration_step": 0.01
},
"provenance": {
"owned_path": "owned/models/physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model_state"
],
"from": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.state"
},
{
"to": [
"visualisation.physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model_summary"
],
"from": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.summary"
},
{
"to": [
"visualisation.physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model_trajectory"
],
"from": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.trajectory"
},
{
"to": [
"visualisation.physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model_variable_labels"
],
"from": "physiology_cellml_a_primer_on_modular_mass_action_modelling_with_c_modularmassactionprimer_model.variable_labels"
}
],
"runtime": {
"duration": 0.01,
"settle_steps": 1,
"initial_inputs": {},
"communication_step": 0.01
},
"description": "Source-faithful physiology lab for A Primer on Modular Mass Action Modelling with CellML. Public controls and outputs are mapped to real source symbols for source-model physiology.",
"schema_version": "2.0"
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