About lab
Oliveira2020 - Extended E. coli Central Carbon Metabolism from Glucose
Cleaned metabolism SBML ODE lab. The bundled SBML file remains the scientific source of truth.
Validation evidence: Tellurium loaded and simulated 76 floating species
What You'll See
These dark-mode screenshots show the default Oliveira2020 - Extended E. coli Central Carbon Metabolism from Glucose run over 10 model-time units with outputs sampled every 1. The lab exposes 5 inputs (initial_glycolysis_state_1, initial_glycolysis_state_2, initial_glycolysis_state_3, initial_glycolysis_state_4, initial_glycolysis_state_5) and 8 outputs (glycolysis_state_1, glycolysis_state_2, glycolysis_state_3, glycolysis_state_4, glycolysis_state_5, and 3 more). The default input state includes initial_glycolysis_state_1=0.154743005197164, initial_glycolysis_state_2=0.0321498018175313, initial_glycolysis_state_3=0.0143909273594558, initial_glycolysis_state_4=0.59787032384441. The kinetic model of E. coli central carbon metabolism developed by Millard et al.
Output Visualizations
The run interpretation table summarizes the configured Oliveira2020 - Extended E. coli Central Carbon Metabolism from Glucose simulation and its reported output statistics.
The observable dynamics plot traces the main reported outputs over the captured run window, including glycolysis_state_1, glycolysis_state_2, glycolysis_state_3, glycolysis_state_4, 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.
The kinetic model of E. coli central carbon metabolism developed by Millard et al.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_glycolysis_state_1",
"units": "native SBML value",
"default": 0.154743005197164,
"maps_to": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.initial_glycolysis_state_1",
"description": "Initial condition for glycolysis state 1. Maps to bundled SBML symbol `ACCOA`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
},
{
"name": "initial_glycolysis_state_2",
"units": "native SBML value",
"default": 0.0321498018175313,
"maps_to": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.initial_glycolysis_state_2",
"description": "Initial condition for glycolysis state 2. Maps to bundled SBML symbol `ACO`. 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": 0.0143909273594558,
"maps_to": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.initial_glycolysis_state_3",
"description": "Initial condition for glycolysis state 3. Maps to bundled SBML symbol `ACP`. 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": 0.59787032384441,
"maps_to": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.initial_glycolysis_state_4",
"description": "Initial condition for glycolysis state 4. Maps to bundled SBML symbol `AKG`. 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": 0.0654105657862152,
"maps_to": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.initial_glycolysis_state_5",
"description": "Initial condition for glycolysis state 5. 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."
}
],
"outputs": [
{
"name": "glycolysis_state_1",
"maps_to": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.glycolysis_state_1"
},
{
"name": "glycolysis_state_2",
"maps_to": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.glycolysis_state_2"
},
{
"name": "glycolysis_state_3",
"maps_to": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.glycolysis_state_3"
},
{
"name": "glycolysis_state_4",
"maps_to": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.glycolysis_state_4"
},
{
"name": "glycolysis_state_5",
"maps_to": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.glycolysis_state_5"
},
{
"name": "observable_values",
"maps_to": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.observable_values"
},
{
"name": "run_summary",
"maps_to": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.run_summary"
},
{
"name": "observable_labels",
"maps_to": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.observable_labels"
}
]
},
"title": "Oliveira2020 - Extended E. coli Central Carbon Metabolism from Glucose Lab",
"models": [
{
"path": "owned/models/metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model",
"alias": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model",
"parameters": {
"model_path": "data/MODEL2010030001.xml",
"integration_step": 0.1
},
"provenance": {
"owned_path": "owned/models/metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model_observable_values"
],
"from": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.observable_values"
},
{
"to": [
"visualisation.metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model_run_summary"
],
"from": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.run_summary"
},
{
"to": [
"visualisation.metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model_observable_labels"
],
"from": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model.observable_labels"
}
],
"runtime": {
"duration": 10,
"initial_inputs": {},
"communication_step": 1
},
"description": "The kinetic model of E. coli central carbon metabolism developed by Millard et al.",
"schema_version": "2.0"
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