About lab
Smallbone2015 - Multi-scale model of E. coli metabolism
Cleaned metabolism SBML ODE lab. The bundled SBML file remains the scientific source of truth.
Validation evidence: Tellurium loaded and simulated 144 floating species
What You'll See
These dark-mode screenshots show the default Smallbone2015 - Multi-scale model of E. coli metabolism run over 10 model-time units with outputs sampled every 1. The lab exposes 5 inputs (initial_phosphoenolpyruvate, initial_glucose_6_phosphate, initial_pyruvate, initial_fructose_6_phosphate, initial_microbial_metabolism_state_5) and 8 outputs (phosphoenolpyruvate, glucose_6_phosphate, pyruvate, fructose_6_phosphate, microbial_metabolism_state_5, and 3 more). The default input state includes initial_phosphoenolpyruvate=2.67, initial_glucose_6_phosphate=3.48, initial_pyruvate=2.67, initial_fructose_6_phosphate=0.6. Metabolism Smallbone2015Multi Scale Model Of EColi Metabo Model1503050000Model captures core biological behavior in the context of metabolism, sbml, biomodels_ebi using a biomodels_ebi-sourced OTHER model. When you run it, you can observe state and evaluate how the modeled system changes across runs.
Output Visualizations
The run interpretation table summarizes the configured Smallbone2015 - Multi-scale model of E. coli metabolism simulation and its reported output statistics.
The observable dynamics plot traces the main reported outputs over the captured run window, including phosphoenolpyruvate, glucose_6_phosphate, pyruvate, fructose_6_phosphate, 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 Smallbone2015Multi Scale Model Of EColi Metabo Model1503050000Model captures core biological behavior in the context of metabolism, sbml, biomodels_ebi using a biomodels_ebi-sourced OTHER model. When you run it, you can observe state and evaluate how the modeled system changes across runs.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_phosphoenolpyruvate",
"units": "native SBML value",
"default": 2.67,
"maps_to": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.initial_phosphoenolpyruvate",
"description": "Initial condition for phosphoenolpyruvate. Maps to bundled SBML symbol `PEP`. 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": 3.48,
"maps_to": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_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_pyruvate",
"units": "native SBML value",
"default": 2.67,
"maps_to": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.initial_pyruvate",
"description": "Initial condition for pyruvate. Maps to bundled SBML symbol `PYR`. 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": 0.6,
"maps_to": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_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_microbial_metabolism_state_5",
"units": "native SBML value",
"default": 0.653,
"maps_to": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.initial_microbial_metabolism_state_5",
"description": "Initial condition for microbial metabolism state 5. Maps to bundled SBML symbol `G1P`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
}
],
"outputs": [
{
"name": "phosphoenolpyruvate",
"maps_to": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.phosphoenolpyruvate"
},
{
"name": "glucose_6_phosphate",
"maps_to": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.glucose_6_phosphate"
},
{
"name": "pyruvate",
"maps_to": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.pyruvate"
},
{
"name": "fructose_6_phosphate",
"maps_to": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.fructose_6_phosphate"
},
{
"name": "microbial_metabolism_state_5",
"maps_to": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.microbial_metabolism_state_5"
},
{
"name": "observable_values",
"maps_to": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.observable_values"
},
{
"name": "run_summary",
"maps_to": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.run_summary"
},
{
"name": "observable_labels",
"maps_to": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.observable_labels"
}
]
},
"title": "Smallbone2015 - Multi-scale model of E. coli metabolism Lab",
"models": [
{
"path": "owned/models/metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model",
"alias": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model",
"parameters": {
"model_path": "data/MODEL1503050000.xml",
"integration_step": 0.1
},
"provenance": {
"owned_path": "owned/models/metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model_observable_values"
],
"from": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.observable_values"
},
{
"to": [
"visualisation.metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model_run_summary"
],
"from": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.run_summary"
},
{
"to": [
"visualisation.metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model_observable_labels"
],
"from": "metabolism_sbml_smallbone2015_multi_scale_model_of_e_coli_metabo_model1503050000_model.observable_labels"
}
],
"runtime": {
"duration": 10,
"initial_inputs": {},
"communication_step": 1
},
"description": "Metabolism Smallbone2015Multi Scale Model Of EColi Metabo Model1503050000Model captures core biological behavior in the context of metabolism, sbml, biomodels_ebi using a biomodels_ebi-sourced OTHER model. When you run it, you can observe state and evaluate how the modeled system changes across runs.",
"schema_version": "2.0"
}Sign in to start your own run. Public-lab history stays visible here.
Select a run from History to view its results.