About lab
The kinetic model of E. coli central carbon metabolism developed by Millard et al.
Runtime
Duration10
Comms Step1
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Total0
Completed0
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Metadata
Packageoliveira2020-extended-e-coli-central-carbon-metabolism-30e6ac5d
Created2026-05-15
Updated2026-06-13
biomodels_ebifaithfulmetabolismodesbmltelluriumvisualisationother
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": "models/core",
"alias": "metabolism_sbml_oliveira2020_extended_e_coli_central_carbon_meta_model2010030001_model",
"parameters": {
"model_path": "data/MODEL2010030001.xml",
"integration_step": 0.1
}
},
{
"path": "models/visualisation",
"alias": "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"
}
],
"package": "oliveira2020-extended-e-coli-central-carbon-metabolism-30e6ac5d",
"runtime": {
"duration": 10,
"initial_inputs": {},
"communication_step": 1
},
"version": "1.0.0",
"description": "The kinetic model of E. coli central carbon metabolism developed by Millard et al.",
"schema_version": "2.0"
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