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Preparing exact examples…
The model should reproduce the figure 2F of the article. The equation 7 has been split into equations 7a-7c, in order to take into account the different flux rates of Lysine and CML formation from Sch.
Manifest
{
"io": {
"inputs": [
{
"name": "initial_glucose",
"label": "Initial Glucose",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.initial_glucose",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Glucose`."
},
{
"name": "initial_lysine",
"label": "Initial Lysine",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.initial_lysine",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Lysine`."
},
{
"name": "initial_schiff",
"label": "Initial Schiff",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.initial_schiff",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Schiff`."
},
{
"name": "initial_glyoxal",
"label": "Initial Glyoxal",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.initial_glyoxal",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Glyoxal`."
},
{
"name": "initial_model_state_cml",
"label": "Initial Model State Cml",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.initial_model_state_cml",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `CML`."
},
{
"name": "initial_amadori",
"label": "Initial Amadori",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.initial_amadori",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Amadori`."
}
],
"outputs": [
{
"name": "state",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.state"
},
{
"name": "summary",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.summary"
},
{
"name": "species_labels",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.species_labels"
},
{
"name": "glucose",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.glucose"
},
{
"name": "lysine",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.lysine"
},
{
"name": "schiff",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.schiff"
},
{
"name": "glyoxal",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.glyoxal"
},
{
"name": "cml",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.cml"
},
{
"name": "amadori",
"maps_to": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.amadori"
}
]
},
"tags": [
"generegulation",
"systemsbiology",
"sbml",
"biomodels_ebi",
"faithful",
"curated"
],
"title": "Ferreira2003 Cml Generation2 Lab",
"models": [
{
"path": "models/core",
"alias": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model"
},
{
"path": "models/visualisation",
"alias": "visualisation"
}
],
"wiring": [
{
"to": [
"visualisation.systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model_state"
],
"from": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.state"
},
{
"to": [
"visualisation.systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model_summary"
],
"from": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.summary"
},
{
"to": [
"visualisation.systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model_species_labels"
],
"from": "systemsbiology_sbml_ferreira2003_cml_generation2_biomd0000000053_model.species_labels"
}
],
"package": "ferreira2003-cml-generation2",
"runtime": {
"duration": 1,
"initial_inputs": {},
"communication_step": 0.1
},
"version": "1.0.0",
"description": "The model should reproduce the figure 2F of the article. The equation 7 has been split into equations 7a-7c, in order to take into account the different flux rates of Lysine and CML formation from Sch.",
"schema_version": "2.0"
}Runtime
Duration1
Comms Step0.1
Runs
Total0
Completed0
Failed0
Metadata
Packageferreira2003-cml-generation2
Created2026-05-17
Updated2026-06-13
generegulationsystemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisationother