About lab
Furr2005 - whole-body vitamin A metabolism in humans
Cleaned metabolism SBML ODE lab. The bundled SBML file remains the scientific source of truth.
Validation evidence: Tellurium loaded and simulated 28 floating species
What You'll See
These dark-mode screenshots show the default Furr2005 - whole-body vitamin A metabolism in humans run over 10 model-time units with outputs sampled every 1. The lab exposes 5 inputs (initial_vitamin_a_metabolism_state_1, initial_vitamin_a_metabolism_state_2, initial_vitamin_a_metabolism_state_3, initial_vitamin_a_metabolism_state_4, initial_vitamin_a_metabolism_state_5) and 8 outputs (vitamin_a_metabolism_state_1, vitamin_a_metabolism_state_2, vitamin_a_metabolism_state_3, vitamin_a_metabolism_state_4, vitamin_a_metabolism_state_5, and 3 more). The default input state includes initial_vitamin_a_metabolism_state_1=0.7512690355, initial_vitamin_a_metabolism_state_2=0.5416721566, initial_vitamin_a_metabolism_state_3=3.731098421, initial_vitamin_a_metabolism_state_4=3.17239151. Metabolism Furr2005Whole Body Vitamin AMetabolism In Huma Model2405200001Model represents core biological mechanisms from biomodels_ebi reference biomodels_ebi:MODEL2405200001. When you run it, you can inspect state and compare temporal behavior between baseline and adjusted inputs.
Output Visualizations
The run interpretation table summarizes the configured Furr2005 - whole-body vitamin A metabolism in humans simulation and its reported output statistics.
The observable dynamics plot traces the main reported outputs over the captured run window, including vitamin_a_metabolism_state_1, vitamin_a_metabolism_state_2, vitamin_a_metabolism_state_3, vitamin_a_metabolism_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.
Metabolism Furr2005Whole Body Vitamin AMetabolism In Huma Model2405200001Model represents core biological mechanisms from biomodels_ebi reference biomodels_ebi:MODEL2405200001. When you run it, you can inspect state and compare temporal behavior between baseline and adjusted inputs.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_vitamin_a_metabolism_state_1",
"units": "native SBML value",
"default": 0.7512690355,
"maps_to": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.initial_vitamin_a_metabolism_state_1",
"description": "Initial condition for vitamin a metabolism state 1. Maps to bundled SBML symbol `M_1`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
},
{
"name": "initial_vitamin_a_metabolism_state_2",
"units": "native SBML value",
"default": 0.5416721566,
"maps_to": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.initial_vitamin_a_metabolism_state_2",
"description": "Initial condition for vitamin a metabolism state 2. Maps to bundled SBML symbol `M_2`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
},
{
"name": "initial_vitamin_a_metabolism_state_3",
"units": "native SBML value",
"default": 3.731098421,
"maps_to": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.initial_vitamin_a_metabolism_state_3",
"description": "Initial condition for vitamin a metabolism state 3. Maps to bundled SBML symbol `M_4`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
},
{
"name": "initial_vitamin_a_metabolism_state_4",
"units": "native SBML value",
"default": 3.17239151,
"maps_to": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.initial_vitamin_a_metabolism_state_4",
"description": "Initial condition for vitamin a metabolism state 4. Maps to bundled SBML symbol `M_5`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
},
{
"name": "initial_vitamin_a_metabolism_state_5",
"units": "native SBML value",
"default": 231.4107506,
"maps_to": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.initial_vitamin_a_metabolism_state_5",
"description": "Initial condition for vitamin a metabolism state 5. Maps to bundled SBML symbol `M_6`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
}
],
"outputs": [
{
"name": "vitamin_a_metabolism_state_1",
"maps_to": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.vitamin_a_metabolism_state_1"
},
{
"name": "vitamin_a_metabolism_state_2",
"maps_to": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.vitamin_a_metabolism_state_2"
},
{
"name": "vitamin_a_metabolism_state_3",
"maps_to": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.vitamin_a_metabolism_state_3"
},
{
"name": "vitamin_a_metabolism_state_4",
"maps_to": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.vitamin_a_metabolism_state_4"
},
{
"name": "vitamin_a_metabolism_state_5",
"maps_to": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.vitamin_a_metabolism_state_5"
},
{
"name": "observable_values",
"maps_to": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.observable_values"
},
{
"name": "run_summary",
"maps_to": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.run_summary"
},
{
"name": "observable_labels",
"maps_to": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.observable_labels"
}
]
},
"title": "Furr2005 - whole-body vitamin A metabolism in humans Lab",
"models": [
{
"path": "owned/models/metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model",
"alias": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model",
"parameters": {
"model_path": "data/MODEL2405200001.xml",
"integration_step": 0.1
},
"provenance": {
"owned_path": "owned/models/metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model_observable_values"
],
"from": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.observable_values"
},
{
"to": [
"visualisation.metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model_run_summary"
],
"from": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.run_summary"
},
{
"to": [
"visualisation.metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model_observable_labels"
],
"from": "metabolism_sbml_furr2005_whole_body_vitamin_a_metabolism_in_huma_model2405200001_model.observable_labels"
}
],
"runtime": {
"duration": 10,
"initial_inputs": {},
"communication_step": 1
},
"description": "Metabolism Furr2005Whole Body Vitamin AMetabolism In Huma Model2405200001Model represents core biological mechanisms from biomodels_ebi reference biomodels_ebi:MODEL2405200001. When you run it, you can inspect state and compare temporal behavior between baseline and adjusted inputs.",
"schema_version": "2.0"
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