About lab
Shestov2014 - aerobic glycolysis
Cleaned metabolism SBML ODE lab. The bundled SBML file remains the scientific source of truth.
Validation evidence: Tellurium loaded and simulated 21 floating species
What You'll See
These dark-mode screenshots show the default Shestov2014 - aerobic glycolysis run over 10 model-time units with outputs sampled every 1. The lab exposes 5 inputs (initial_glycolysis_state_1, initial_glucose_6_phosphate, initial_fructose_6_phosphate, initial_fructose_bisphosphate, initial_glycolysis_state_5) and 8 outputs (glycolysis_state_1, glucose_6_phosphate, fructose_6_phosphate, fructose_bisphosphate, glycolysis_state_5, and 3 more). The default input state includes initial_glycolysis_state_1=2.5909, initial_glucose_6_phosphate=0.2263, initial_fructose_6_phosphate=0.0701, initial_fructose_bisphosphate=0.45. Metabolism Shestov2014Aerobic Glycolysis Model1504010000Model models metabolism shestov2014 aerobic glycolysis model1504010000 dynamics as a OTHER simulation curated from biomodels_ebi (biomodels_ebi:MODEL15040. When you run it, you can track state over time and compare response patterns across parameter settings.
Output Visualizations
The run interpretation table summarizes the configured Shestov2014 - aerobic glycolysis simulation and its reported output statistics.
The observable dynamics plot traces the main reported outputs over the captured run window, including glycolysis_state_1, glucose_6_phosphate, fructose_6_phosphate, fructose_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.
Metabolism Shestov2014Aerobic Glycolysis Model1504010000Model models metabolism shestov2014 aerobic glycolysis model1504010000 dynamics as a OTHER simulation curated from biomodels_ebi (biomodels_ebi:MODEL15040. When you run it, you can track state over time and compare response patterns across parameter settings.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_glycolysis_state_1",
"units": "native SBML value",
"default": 2.5909,
"maps_to": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.initial_glycolysis_state_1",
"description": "Initial condition for glycolysis state 1. Maps to bundled SBML symbol `GLU`. 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": 0.2263,
"maps_to": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_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": 0.0701,
"maps_to": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_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_bisphosphate",
"units": "native SBML value",
"default": 0.45,
"maps_to": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.initial_fructose_bisphosphate",
"description": "Initial condition for fructose bisphosphate. Maps to bundled SBML symbol `FBP`. 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": 0.0244,
"maps_to": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.initial_glycolysis_state_5",
"description": "Initial condition for glycolysis state 5. 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": "glycolysis_state_1",
"maps_to": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.glycolysis_state_1"
},
{
"name": "glucose_6_phosphate",
"maps_to": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.glucose_6_phosphate"
},
{
"name": "fructose_6_phosphate",
"maps_to": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.fructose_6_phosphate"
},
{
"name": "fructose_bisphosphate",
"maps_to": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.fructose_bisphosphate"
},
{
"name": "glycolysis_state_5",
"maps_to": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.glycolysis_state_5"
},
{
"name": "observable_values",
"maps_to": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.observable_values"
},
{
"name": "run_summary",
"maps_to": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.run_summary"
},
{
"name": "observable_labels",
"maps_to": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.observable_labels"
}
]
},
"title": "Shestov2014 - aerobic glycolysis Lab",
"models": [
{
"path": "owned/models/metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model",
"alias": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model",
"parameters": {
"model_path": "data/MODEL1504010000.xml",
"integration_step": 0.1
},
"provenance": {
"owned_path": "owned/models/metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model_observable_values"
],
"from": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.observable_values"
},
{
"to": [
"visualisation.metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model_run_summary"
],
"from": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.run_summary"
},
{
"to": [
"visualisation.metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model_observable_labels"
],
"from": "metabolism_sbml_shestov2014_aerobic_glycolysis_model1504010000_model.observable_labels"
}
],
"runtime": {
"duration": 10,
"initial_inputs": {},
"communication_step": 1
},
"description": "Metabolism Shestov2014Aerobic Glycolysis Model1504010000Model models metabolism shestov2014 aerobic glycolysis model1504010000 dynamics as a OTHER simulation curated from biomodels_ebi (biomodels_ebi:MODEL15040. When you run it, you can track state over time and compare response patterns across parameter settings.",
"schema_version": "2.0"
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