Kerkhoven2013 D-ATP Standalone Glycolysis Lab

{
  "io": {
    "inputs": [
      {
        "name": "initial_glycolysis_state_1",
        "units": "native SBML value",
        "default": 0.1,
        "maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.initial_glycolysis_state_1",
        "description": "Initial condition for glycolysis state 1. Maps to bundled SBML symbol `_2PGA_c`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
      },
      {
        "name": "initial_cytosolic_atp",
        "units": "native SBML value",
        "default": 0.3417,
        "maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.initial_cytosolic_atp",
        "description": "Initial condition for cytosolic atp. Maps to bundled SBML symbol `ATP_c`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
      },
      {
        "name": "initial_glycolysis_state_3",
        "units": "native SBML value",
        "default": 2.23132912,
        "maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.initial_glycolysis_state_3",
        "description": "Initial condition for glycolysis state 3. Maps to bundled SBML symbol `DHAP_c`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
      },
      {
        "name": "initial_glycolysis_state_4",
        "units": "native SBML value",
        "default": 0.2405,
        "maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.initial_glycolysis_state_4",
        "description": "Initial condition for glycolysis state 4. Maps to bundled SBML symbol `ATP_g`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
      },
      {
        "name": "initial_glycolysis_state_5",
        "units": "native SBML value",
        "default": 8.483130623,
        "maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.initial_glycolysis_state_5",
        "description": "Initial condition for glycolysis state 5. Maps to bundled SBML symbol `DHAP_g`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
      }
    ],
    "outputs": [
      {
        "name": "glycolysis_state_1",
        "maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.glycolysis_state_1"
      },
      {
        "name": "cytosolic_atp",
        "maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.cytosolic_atp"
      },
      {
        "name": "glycolysis_state_3",
        "maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.glycolysis_state_3"
      },
      {
        "name": "glycolysis_state_4",
        "maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.glycolysis_state_4"
      },
      {
        "name": "glycolysis_state_5",
        "maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.glycolysis_state_5"
      },
      {
        "name": "observable_values",
        "maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.observable_values"
      },
      {
        "name": "run_summary",
        "maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.run_summary"
      },
      {
        "name": "observable_labels",
        "maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.observable_labels"
      }
    ]
  },
  "title": "Kerkhoven2013 D-ATP Standalone Glycolysis Lab",
  "models": [
    {
      "path": "models/core",
      "alias": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model",
      "parameters": {
        "model_path": "data/BIOMD0000000511.xml",
        "integration_step": 0.1
      }
    },
    {
      "path": "models/visualisation",
      "alias": "visualisation"
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model_observable_values"
      ],
      "from": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.observable_values"
    },
    {
      "to": [
        "visualisation.metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model_run_summary"
      ],
      "from": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.run_summary"
    },
    {
      "to": [
        "visualisation.metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model_observable_labels"
      ],
      "from": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000511_model.observable_labels"
    }
  ],
  "runtime": {
    "duration": 10,
    "initial_inputs": {},
    "communication_step": 1
  },
  "description": "Kerkhoven2013 - Glycolysis and Pentose Phosphate Pathway in T.brucei - MODEL D (with ATP:ADP antiporter) There are six models (Model A, B, C, C-fruc, D, D-fruc) described in the paper. It can be used to explore metabolic flux dynamics and compare pathway behavior across conditions.",
  "schema_version": "2.0"
}