About lab
Bruck2008_Glycolysis
Cleaned metabolism SBML ODE lab. The bundled SBML file remains the scientific source of truth.
Validation evidence: Tellurium loaded and simulated 17 floating species
What You'll See
These dark-mode screenshots show the default Bruck2008_Glycolysis run over 10 model-time units with outputs sampled every 1. The lab exposes 5 inputs (initial_intracellular_glucose, initial_glucose_6_phosphate, initial_fructose_6_phosphate, initial_fructose_1_6_bisphosphate, initial_triose_phosphate) and 8 outputs (intracellular_glucose, glucose_6_phosphate, fructose_6_phosphate, fructose_1_6_bisphosphate, triose_phosphate, and 3 more). The default input state includes initial_intracellular_glucose=0.087, initial_glucose_6_phosphate=1.39, initial_fructose_6_phosphate=0.28, initial_fructose_1_6_bisphosphate=0.1. Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis Jozsef Bruck, Wolfram Liebermeister, Edda Klipp, Genome Inform 2008 20:1-14 Abstract: Metabolism is one of. It can be used to explore metabolic flux dynamics and compare pathway behavior across conditions.
Output Visualizations
The run interpretation table summarizes the configured Bruck2008_Glycolysis simulation and its reported output statistics.
The observable dynamics plot traces the main reported outputs over the captured run window, including intracellular_glucose, glucose_6_phosphate, fructose_6_phosphate, fructose_1_6_bisphosphate, and 4 more.
The largest-observable-excursions chart ranks which reported variables moved the most during this simulation.
The phase-relationship plot compares paired observable values to show how the dominant trajectories move relative to one another.
Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis Jozsef Bruck, Wolfram Liebermeister, Edda Klipp, Genome Inform 2008 20:1-14 Abstract: Metabolism is one of. It can be used to explore metabolic flux dynamics and compare pathway behavior across conditions.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_intracellular_glucose",
"units": "native SBML value",
"default": 0.087,
"maps_to": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.initial_intracellular_glucose",
"description": "Initial condition for intracellular glucose. Maps to bundled SBML symbol `GLCi`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
},
{
"name": "initial_glucose_6_phosphate",
"units": "native SBML value",
"default": 1.39,
"maps_to": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.initial_glucose_6_phosphate",
"description": "Initial condition for glucose 6 phosphate. Maps to bundled SBML symbol `G6P`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
},
{
"name": "initial_fructose_6_phosphate",
"units": "native SBML value",
"default": 0.28,
"maps_to": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.initial_fructose_6_phosphate",
"description": "Initial condition for fructose 6 phosphate. Maps to bundled SBML symbol `F6P`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
},
{
"name": "initial_fructose_1_6_bisphosphate",
"units": "native SBML value",
"default": 0.1,
"maps_to": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.initial_fructose_1_6_bisphosphate",
"description": "Initial condition for fructose 1 6 bisphosphate. Maps to bundled SBML symbol `F16P`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
},
{
"name": "initial_triose_phosphate",
"units": "native SBML value",
"default": 5.17,
"maps_to": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.initial_triose_phosphate",
"description": "Initial condition for triose phosphate. Maps to bundled SBML symbol `TRIO`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
}
],
"outputs": [
{
"name": "intracellular_glucose",
"maps_to": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.intracellular_glucose"
},
{
"name": "glucose_6_phosphate",
"maps_to": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.glucose_6_phosphate"
},
{
"name": "fructose_6_phosphate",
"maps_to": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.fructose_6_phosphate"
},
{
"name": "fructose_1_6_bisphosphate",
"maps_to": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.fructose_1_6_bisphosphate"
},
{
"name": "triose_phosphate",
"maps_to": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.triose_phosphate"
},
{
"name": "observable_values",
"maps_to": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.observable_values"
},
{
"name": "run_summary",
"maps_to": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.run_summary"
},
{
"name": "observable_labels",
"maps_to": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.observable_labels"
}
]
},
"title": "Bruck2008_Glycolysis Lab",
"models": [
{
"path": "owned/models/metabolism_sbml_bruck2008_glycolysis_model1011010000_model",
"alias": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model",
"parameters": {
"model_path": "data/MODEL1011010000.xml",
"integration_step": 0.1
},
"provenance": {
"owned_path": "owned/models/metabolism_sbml_bruck2008_glycolysis_model1011010000_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.metabolism_sbml_bruck2008_glycolysis_model1011010000_model_observable_values"
],
"from": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.observable_values"
},
{
"to": [
"visualisation.metabolism_sbml_bruck2008_glycolysis_model1011010000_model_run_summary"
],
"from": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.run_summary"
},
{
"to": [
"visualisation.metabolism_sbml_bruck2008_glycolysis_model1011010000_model_observable_labels"
],
"from": "metabolism_sbml_bruck2008_glycolysis_model1011010000_model.observable_labels"
}
],
"runtime": {
"duration": 10,
"initial_inputs": {},
"communication_step": 1
},
"description": "Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis Jozsef Bruck, Wolfram Liebermeister, Edda Klipp, Genome Inform 2008 20:1-14 Abstract: Metabolism is one of. It can be used to explore metabolic flux dynamics and compare pathway behavior across conditions.",
"schema_version": "2.0"
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