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Tran2009 - Thermodynamic Cardiac Sarcoplasmic Endoplasmic Calcium 2 Lab

About lab

Source-faithful physiology lab for Tran, Smith, Loiselle, Crampin, 2009. Public controls and outputs are mapped to real source symbols for electrophysiology.

Runtime

Duration0.01
Comms Step0.01
Settle Steps1

Runs

Total0
Completed0
Failed0

Metadata

Packagetran2009-thermodynamic-cardiac-sarcoplasmic-endoplasmic-calcium
Created2026-05-23
Updated2026-05-23
physiologycellmlphysiomefaithfulvisualisationother

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_ca_sr",
        "label": "Initial Ca Sr",
        "maps_to": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.initial_ca_sr",
        "description": "Initial value for Ca Sr. Maps to source symbol `Ca_sr`. Units: millimolar. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "millimolar"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.variable_labels"
      },
      {
        "name": "intracellular_calcium",
        "label": "Intracellular Calcium",
        "maps_to": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.intracellular_calcium",
        "description": "Intracellular Calcium. Maps to source symbol `Ca_i`. Units: millimolar. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "atp_concentration",
        "label": "ATP Concentration",
        "maps_to": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.atp_concentration",
        "description": "ATP Concentration. Maps to source symbol `ATP`. Units: millimolar. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "adp_concentration",
        "label": "ADP Concentration",
        "maps_to": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.adp_concentration",
        "description": "ADP Concentration. Maps to source symbol `ADP`. Units: millimolar. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "ca_sr",
        "label": "Ca Sr",
        "maps_to": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.ca_sr",
        "description": "Ca Sr. Maps to source symbol `Ca_sr`. Units: millimolar. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "concentration_h_i",
        "label": "Concentration H I (source H_i)",
        "maps_to": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.concentration_h_i",
        "description": "Concentration H I (source H_i). Maps to source symbol `H_i`. Units: millimolar. Naming evidence: amount concentration units identify a concentration state."
      },
      {
        "name": "concentration_p_i",
        "label": "Concentration P I (source P_i)",
        "maps_to": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.concentration_p_i",
        "description": "Concentration P I (source P_i). Maps to source symbol `P_i`. Units: millimolar. Naming evidence: amount concentration units identify a concentration state."
      }
    ]
  },
  "title": "Tran2009 - Thermodynamic Cardiac Sarcoplasmic Endoplasmic Calcium 2 Lab",
  "models": [
    {
      "path": "owned/models/physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model",
      "alias": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model",
      "parameters": {
        "model_path": "data/tran_smith_loiselle_crampin_2009.cellml",
        "integration_step": 0.01
      },
      "provenance": {
        "owned_path": "owned/models/physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model_state"
      ],
      "from": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model_summary"
      ],
      "from": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model_trajectory"
      ],
      "from": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model_variable_labels"
      ],
      "from": "physiology_cellml_tran_smith_loiselle_crampin_2009_transmithloisellecrampin2009_model.variable_labels"
    }
  ],
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "description": "Source-faithful physiology lab for Tran, Smith, Loiselle, Crampin, 2009. Public controls and outputs are mapped to real source symbols for electrophysiology.",
  "schema_version": "2.0"
}

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