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Smallbone2013 - Glycolysis in S.cerevisiae - Iteration 10 Lab

About lab

Smallbone2013 - Glycolysis in S.cerevisiae - Iteration 10

Cleaned metabolism SBML ODE lab. The bundled SBML file remains the scientific source of truth.

Validation evidence: Tellurium loaded and simulated 20 floating species

What You'll See

These dark-mode screenshots show the default Smallbone2013 - Glycolysis in S.cerevisiae - Iteration 10 run over 10 model-time units with outputs sampled every 1. The lab exposes 5 inputs (initial_adp, initial_atp, initial_acetaldehyde, initial_observable_1_3_bisphosphoglycerate, initial_dihydroxyacetone_phosphate) and 8 outputs (adp, atp, acetaldehyde, observable_1_3_bisphosphoglycerate, dihydroxyacetone_phosphate, and 3 more). The default input state includes initial_adp=1.29, initial_atp=4.29, initial_acetaldehyde=0.178140579850657, initial_observable_1_3_bisphosphoglycerate=0.000736873499865602. Smallbone2013 - Glycolysis in S.cerevisiae - Iteration 10 This model is described in the article: A model of yeast glycolysis based on a consistent kinetic characterization of all its enzymes Kieran S. It can be used to explore metabolic flux dynamics and compare pathway behavior across conditions.

Output Visualizations

The run interpretation table summarizes the configured Smallbone2013 - Glycolysis in S.cerevisiae - Iteration 10 simulation and its reported output statistics.

Smallbone2013 - Glycolysis in S.cerevisiae - Iteration 10 Lab - run interpretation

The observable dynamics plot traces the main reported outputs over the captured run window, including adp, atp, acetaldehyde, observable_1_3_bisphosphoglycerate, and 4 more.

Smallbone2013 - Glycolysis in S.cerevisiae - Iteration 10 observable dynamics

The largest-observable-excursions chart ranks which reported variables moved the most during this simulation.

Largest observable excursions

The phase-relationship plot compares paired observable values to show how the dominant trajectories move relative to one another.

Observable phase relationship

Smallbone2013 - Glycolysis in S.cerevisiae - Iteration 10 This model is described in the article: A model of yeast glycolysis based on a consistent kinetic characterization of all its enzymes Kieran S. It can be used to explore metabolic flux dynamics and compare pathway behavior across conditions.

Runtime

Duration10
Comms Step1

Runs

Total0
Completed0
Failed0

Metadata

Packagesmallbone2013-glycolysis-in-s-cerevisiae-iteration-10-lab
Created2026-05-15
Updated2026-05-15
biomodels_ebifaithfulmetabolismodesbmltelluriumvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_adp",
        "units": "native SBML value",
        "default": 1.29,
        "maps_to": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.initial_adp",
        "description": "Initial condition for adp. Maps to bundled SBML symbol `ADP`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
      },
      {
        "name": "initial_atp",
        "units": "native SBML value",
        "default": 4.29,
        "maps_to": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.initial_atp",
        "description": "Initial condition for atp. Maps to bundled SBML symbol `ATP`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
      },
      {
        "name": "initial_acetaldehyde",
        "units": "native SBML value",
        "default": 0.178140579850657,
        "maps_to": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.initial_acetaldehyde",
        "description": "Initial condition for acetaldehyde. Maps to bundled SBML symbol `AcAld`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
      },
      {
        "name": "initial_observable_1_3_bisphosphoglycerate",
        "units": "native SBML value",
        "default": 0.000736873499865602,
        "maps_to": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.initial_observable_1_3_bisphosphoglycerate",
        "description": "Initial condition for observable 1 3 bisphosphoglycerate. Maps to bundled SBML symbol `BPG`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
      },
      {
        "name": "initial_dihydroxyacetone_phosphate",
        "units": "native SBML value",
        "default": 0.290344213186674,
        "maps_to": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.initial_dihydroxyacetone_phosphate",
        "description": "Initial condition for dihydroxyacetone phosphate. Maps to bundled SBML symbol `DHAP`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
      }
    ],
    "outputs": [
      {
        "name": "adp",
        "maps_to": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.adp"
      },
      {
        "name": "atp",
        "maps_to": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.atp"
      },
      {
        "name": "acetaldehyde",
        "maps_to": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.acetaldehyde"
      },
      {
        "name": "observable_1_3_bisphosphoglycerate",
        "maps_to": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.observable_1_3_bisphosphoglycerate"
      },
      {
        "name": "dihydroxyacetone_phosphate",
        "maps_to": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.dihydroxyacetone_phosphate"
      },
      {
        "name": "observable_values",
        "maps_to": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.observable_values"
      },
      {
        "name": "run_summary",
        "maps_to": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.run_summary"
      },
      {
        "name": "observable_labels",
        "maps_to": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.observable_labels"
      }
    ]
  },
  "title": "Smallbone2013 - Glycolysis in S.cerevisiae - Iteration 10 Lab",
  "models": [
    {
      "path": "owned/models/metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model",
      "alias": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model",
      "parameters": {
        "model_path": "data/MODEL1303260010.xml",
        "integration_step": 0.1
      },
      "provenance": {
        "owned_path": "owned/models/metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model_observable_values"
      ],
      "from": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.observable_values"
    },
    {
      "to": [
        "visualisation.metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model_run_summary"
      ],
      "from": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.run_summary"
    },
    {
      "to": [
        "visualisation.metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model_observable_labels"
      ],
      "from": "metabolism_sbml_smallbone2013_glycolysis_in_s_cerevisiae_iterati_model1303260010_model.observable_labels"
    }
  ],
  "runtime": {
    "duration": 10,
    "initial_inputs": {},
    "communication_step": 1
  },
  "description": "Smallbone2013 - Glycolysis in S.cerevisiae - Iteration 10 This model is described in the article: A model of yeast glycolysis based on a consistent kinetic characterization of all its enzymes Kieran S. It can be used to explore metabolic flux dynamics and compare pathway behavior across conditions.",
  "schema_version": "2.0"
}

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