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Physiome modularmassact - Primer Modular Mass Action Modelling Cellml Lab

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 symbol A; units: uM; evidence: source symbol, component, or units provide a direct public name.
  • initial_cformation_b (Cformation B) maps to source symbol B; units: uM; 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.
  • cformation_a (Cformation A) maps to source symbol A; units: uM; evidence: source symbol, component, or units provide a direct public name.
  • cformation_b (Cformation B) maps to source symbol B; units: uM; evidence: source symbol, component, or units provide a direct public name.
  • eformation_d (Eformation D) maps to source symbol D; units: per_um2; evidence: source symbol, component, or units provide a direct public name.
  • eformation_e (Eformation E) maps to source symbol E; 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 symbol C; units: uM; evidence: source symbol is too ambiguous for a stronger public label.
  • cformation_j1 (Cformation J1) maps to source symbol J1; 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

01-physiome-modularmassact-primer-modular-mass-action-modelling-cellml-lab-physiolo

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 A Primer on Modular Mass Action Modelling with CellML. 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

Packagephysiome-modularmassact-primer-modular-mass-action-modelling-cel
Created2026-05-23
Updated2026-05-23
physiologycellmlphysiomefaithfulvisualisationother

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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