Reed2004 - Mathematical Methionine Cycle Lab

{
  "io": {
    "inputs": [
      {
        "name": "initial_homocysteine",
        "label": "Initial Homocysteine",
        "maps_to": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.initial_homocysteine",
        "description": "Initial value for Homocysteine. Maps to source symbol `Hcy`. Units: micromolar. Naming evidence: source metadata names `Hcy` as `homocysteine`.",
        "accepted_units": [
          "micromolar"
        ]
      },
      {
        "name": "initial_methionine",
        "label": "Initial Methionine",
        "maps_to": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.initial_methionine",
        "description": "Initial value for Methionine. Maps to source symbol `Met`. Units: micromolar. Naming evidence: source metadata names `Met` as `methionine`.",
        "accepted_units": [
          "micromolar"
        ]
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Selected Source State",
        "maps_to": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation Summary",
        "maps_to": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.summary"
      },
      {
        "name": "trajectory",
        "label": "Source Trajectory",
        "maps_to": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.trajectory"
      },
      {
        "name": "variable_labels",
        "label": "Observable Labels",
        "maps_to": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.variable_labels"
      },
      {
        "name": "homocysteine",
        "label": "Homocysteine",
        "maps_to": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.homocysteine",
        "description": "Homocysteine. Maps to source symbol `Hcy`. Units: micromolar. Naming evidence: source metadata names `Hcy` as `homocysteine`."
      },
      {
        "name": "methionine",
        "label": "Methionine",
        "maps_to": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.methionine",
        "description": "Methionine. Maps to source symbol `Met`. Units: micromolar. Naming evidence: source metadata names `Met` as `methionine`."
      },
      {
        "name": "s_adenosylhomocysteine",
        "label": "S Adenosylhomocysteine",
        "maps_to": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.s_adenosylhomocysteine",
        "description": "S Adenosylhomocysteine. Maps to source symbol `AdoHcy`. Units: micromolar. Naming evidence: source metadata names `AdoHcy` as `S-adenosylhomocysteine`."
      },
      {
        "name": "s_adenosylmethionine",
        "label": "S Adenosylmethionine",
        "maps_to": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.s_adenosylmethionine",
        "description": "S Adenosylmethionine. Maps to source symbol `AdoMet`. Units: micromolar. Naming evidence: source metadata names `AdoMet` as `S-adenosylmethionine`."
      },
      {
        "name": "alpha1",
        "label": "Alpha1",
        "maps_to": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.alpha1",
        "description": "Alpha1. Maps to source symbol `alpha1`. Units: first_order_rate_constant. Naming evidence: source symbol, component, or units provide a direct public name."
      },
      {
        "name": "alpha2",
        "label": "Alpha2",
        "maps_to": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.alpha2",
        "description": "Alpha2. Maps to source symbol `alpha2`. Units: dimensionless. Naming evidence: source symbol, component, or units provide a direct public name."
      }
    ]
  },
  "title": "Reed2004 - Mathematical Methionine Cycle Lab",
  "models": [
    {
      "path": "models/core",
      "alias": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model",
      "parameters": {
        "model_path": "data/reed_nijhout_sparks_ulrich_2004.cellml",
        "integration_step": 0.01
      }
    },
    {
      "path": "models/visualisation",
      "alias": "visualisation"
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model_state"
      ],
      "from": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.state"
    },
    {
      "to": [
        "visualisation.physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model_summary"
      ],
      "from": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.summary"
    },
    {
      "to": [
        "visualisation.physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model_trajectory"
      ],
      "from": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.trajectory"
    },
    {
      "to": [
        "visualisation.physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model_variable_labels"
      ],
      "from": "physiology_cellml_reed_nijhout_sparks_ulrich_2004_reednijhoutsparksulrich2004_model.variable_labels"
    }
  ],
  "package": "reed2004-mathematical-methionine-cycle",
  "runtime": {
    "duration": 0.01,
    "settle_steps": 1,
    "initial_inputs": {},
    "communication_step": 0.01
  },
  "version": "1.0.0",
  "description": "Source-faithful physiology lab for Reed, Nijhout, Sparks, Ulrich, 2004. Public controls and outputs are mapped to real source symbols for source-model physiology.",
  "schema_version": "2.0"
}