Friel1995 - Calcium Dynamics Friel1995 Lab

About lab

Friel1995 - Calcium Dynamics Friel1995 Lab

Scientific Source

Source type: PhysioMe CellML
Upstream ID: physiome:friel_1995
Original URL: https://models.physiomeproject.org/workspace/friel_1995
Bundled artifact: data/friel_1995.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_ca_s (Ca S) maps to source symbol Ca_s; units: nanomolar; evidence: source symbol, component, or units provide a direct public name.
initial_intracellular_calcium (Intracellular Calcium) maps to source symbol Ca_i; units: nanomolar; 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.
ca_s (Ca S) maps to source symbol Ca_s; units: nanomolar; evidence: source symbol, component, or units provide a direct public name.
intracellular_calcium (Intracellular Calcium) maps to source symbol Ca_i; units: nanomolar; evidence: source symbol, component, or units provide a direct public name.
ca_i_ss (Ca I Ss) maps to source symbol Ca_i_ss; units: nanomolar; evidence: source symbol, component, or units provide a direct public name.
ca_s_ss (Ca S Ss) maps to source symbol Ca_s_ss; units: nanomolar; evidence: source symbol, component, or units provide a direct public name.
extracellular_calcium (Extracellular Calcium) maps to source symbol Ca_o; units: nanomolar; evidence: source symbol, component, or units provide a direct public name.
gamma (Gamma) maps to source symbol gamma; 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: Calcium-state trajectories; peak calcium response; calcium-store/source evidence table.

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-friel1995-calcium-dynamics-friel1995-lab-physiology-run-answer

02-selected-physiology-trajectories

03-selected-final-observable-values

04-source-and-runtime-evidence

Caveat

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

Source-faithful physiology lab for Friel, 1995. Public controls and outputs are mapped to real source symbols for calcium handling.

Runtime

Duration0.01

Comms Step0.01

Settle Steps1

Runs

Total0

Completed0

Failed0

Metadata

Packagefriel1995-calcium-dynamics-friel1995-lab

Created2026-05-23

Updated2026-05-23

physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_ca_s",
        "label": "Initial Ca S",
        "maps_to": "physiology_cellml_friel_1995_friel1995_model.initial_ca_s",
        "description": "Initial value for Ca S. Maps to source symbol `Ca_s`. Units: nanomolar. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "nanomolar"
        ]
      },
      {
        "name": "initial_intracellular_calcium",
        "label": "Initial Intracellular Calcium",
        "maps_to": "physiology_cellml_friel_1995_friel1995_model.initial_intracellular_calcium",
        "description": "Initial value for Intracellular Calcium. Maps to source symbol `Ca_i`. Units: nanomolar. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "nanomolar"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_friel_1995_friel1995_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_friel_1995_friel1995_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_friel_1995_friel1995_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_friel_1995_friel1995_model.variable_labels"
      },
      {
        "name": "ca_s",
        "label": "Ca S",
        "maps_to": "physiology_cellml_friel_1995_friel1995_model.ca_s",
        "description": "Ca S. Maps to source symbol `Ca_s`. Units: nanomolar. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "intracellular_calcium",
        "label": "Intracellular Calcium",
        "maps_to": "physiology_cellml_friel_1995_friel1995_model.intracellular_calcium",
        "description": "Intracellular Calcium. Maps to source symbol `Ca_i`. Units: nanomolar. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "ca_i_ss",
        "label": "Ca I Ss",
        "maps_to": "physiology_cellml_friel_1995_friel1995_model.ca_i_ss",
        "description": "Ca I Ss. Maps to source symbol `Ca_i_ss`. Units: nanomolar. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "ca_s_ss",
        "label": "Ca S Ss",
        "maps_to": "physiology_cellml_friel_1995_friel1995_model.ca_s_ss",
        "description": "Ca S Ss. Maps to source symbol `Ca_s_ss`. Units: nanomolar. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "extracellular_calcium",
        "label": "Extracellular Calcium",
        "maps_to": "physiology_cellml_friel_1995_friel1995_model.extracellular_calcium",
        "description": "Extracellular Calcium. Maps to source symbol `Ca_o`. Units: nanomolar. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "gamma",
        "label": "Gamma",
        "maps_to": "physiology_cellml_friel_1995_friel1995_model.gamma",
        "description": "Gamma. Maps to source symbol `gamma`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      }
    ]
  },
  "title": "Friel1995 - Calcium Dynamics Friel1995 Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_friel_1995_friel1995_model",
      "alias": "physiology_cellml_friel_1995_friel1995_model",
      "parameters": {
        "model_path": "data/friel_1995.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_friel_1995_friel1995_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_friel_1995_friel1995_model_state"
      ],
      "from": "physiology_cellml_friel_1995_friel1995_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_friel_1995_friel1995_model_summary"
      ],
      "from": "physiology_cellml_friel_1995_friel1995_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_friel_1995_friel1995_model_trajectory"
      ],
      "from": "physiology_cellml_friel_1995_friel1995_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_friel_1995_friel1995_model_variable_labels"
      ],
      "from": "physiology_cellml_friel_1995_friel1995_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Friel, 1995. Public controls and outputs are mapped to real source symbols for calcium handling.",
  "schema_version": "2.0"
}

Select a run from History to view its results.