Gilbert2007 - Case Study Driven Synthetic Biology Lab

{
  "io": {
    "inputs": [
      {
        "name": "initial_bio_env_tfsassociation_tf",
        "label": "Initial Bio Env Tfsassociation Tf",
        "maps_to": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.initial_bio_env_tfsassociation_tf",
        "description": "Initial value for Bio Env Tfsassociation Tf. Maps to source symbol `TF`. Units: uM. Naming evidence: source symbol, component, or units provide a direct public name.",
        "accepted_units": [
          "uM"
        ]
      },
      {
        "name": "initial_phz_ms",
        "label": "Initial Phz Ms",
        "maps_to": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.initial_phz_ms",
        "description": "Initial value for Phz Ms. Maps to source symbol `PhzMS`. 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_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.variable_labels"
      },
      {
        "name": "bio_env_tfsassociation_tf",
        "label": "Bio Env Tfsassociation Tf",
        "maps_to": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.bio_env_tfsassociation_tf",
        "description": "Bio Env Tfsassociation Tf. Maps to source symbol `TF`. Units: uM. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "phz_ms",
        "label": "Phz Ms",
        "maps_to": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.phz_ms",
        "description": "Phz Ms. Maps to source symbol `PhzMS`. Units: uM. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "pyo",
        "label": "Pyo",
        "maps_to": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.pyo",
        "description": "Pyo. Maps to source symbol `PYO`. Units: uM. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "tfs",
        "label": "Tfs",
        "maps_to": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.tfs",
        "description": "Tfs. Maps to source symbol `TFS`. Units: uM. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "alpha_pyo",
        "label": "Alpha Pyo",
        "maps_to": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.alpha_pyo",
        "description": "Alpha Pyo. Maps to source symbol `alphaPYO`. Units: per_second. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "alpha_tf",
        "label": "Alpha Tf",
        "maps_to": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.alpha_tf",
        "description": "Alpha Tf. Maps to source symbol `alphaTF`. Units: uM_per_second. Naming evidence: source symbol, component, or units provide a direct public name."
      }
    ]
  },
  "title": "Gilbert2007 - Case Study Driven Synthetic Biology Lab",
  "models": [
    {
      "path": "models/core",
      "alias": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model",
      "parameters": {
        "model_path": "data/gilbert_heiner_rosser_fulton_gu_trybilo_2007.cellml",
        "integration_step": 0.01
      }
    },
    {
      "path": "models/visualisation",
      "alias": "visualisation"
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model_state"
      ],
      "from": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model_summary"
      ],
      "from": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model_trajectory"
      ],
      "from": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model_variable_labels"
      ],
      "from": "physiology_cellml_gilbert_heiner_rosser_fulton_gu_trybilo_2007_gilbertheinerrosserfultongutrybilo2007_model.variable_labels"
    }
  ],
  "package": "gilbert2007-case-study-driven-synthetic-biology",
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "version": "1.0.0",
  "description": "Source-faithful physiology lab for Gilbert, Heiner, Rosser, Fulton, Gu, Trybilo, 2007. Public controls and outputs are mapped to real source symbols for source-model physiology.",
  "schema_version": "2.0"
}