About lab
Thiaville2016 - Folate pathway model (PanB overexpression)
Cleaned metabolism SBML ODE lab. The bundled SBML file remains the scientific source of truth.
Validation evidence: Tellurium loaded and simulated 7 floating species
What You'll See
These dark-mode screenshots show the default Thiaville2016 - Folate pathway model (PanB overexpression) run over 10 model-time units with outputs sampled every 1. The lab exposes 5 inputs (initial_folate_metabolism_state_1, initial_folate_metabolism_state_2, initial_para_aminobenzoate, initial_folate_metabolism_state_4, initial_dihydrofolate) and 8 outputs (folate_metabolism_state_1, folate_metabolism_state_2, para_aminobenzoate, folate_metabolism_state_4, dihydrofolate, and 3 more). The default input state includes initial_folate_metabolism_state_1=0.000003315, initial_folate_metabolism_state_2=0.00001, initial_para_aminobenzoate=0.00001, initial_folate_metabolism_state_4=0.00001. Henry2016 Folate pathway model with inducedPanB reaction This model is described in the article: Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydrox. It can be used to explore metabolic flux dynamics and compare pathway behavior across conditions.
Output Visualizations
The run interpretation table summarizes the configured Thiaville2016 - Folate pathway model (PanB overexpression) simulation and its reported output statistics.
The observable dynamics plot traces the main reported outputs over the captured run window, including folate_metabolism_state_1, folate_metabolism_state_2, para_aminobenzoate, folate_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.
Henry2016 Folate pathway model with inducedPanB reaction This model is described in the article: Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydrox. It can be used to explore metabolic flux dynamics and compare pathway behavior across conditions.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_folate_metabolism_state_1",
"units": "native SBML value",
"default": 0.000003315,
"maps_to": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.initial_folate_metabolism_state_1",
"description": "Initial condition for folate metabolism state 1. Maps to bundled SBML symbol `H2_HMPt`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
},
{
"name": "initial_folate_metabolism_state_2",
"units": "native SBML value",
"default": 0.00001,
"maps_to": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.initial_folate_metabolism_state_2",
"description": "Initial condition for folate metabolism state 2. Maps to bundled SBML symbol `H2_HMPterinPP`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
},
{
"name": "initial_para_aminobenzoate",
"units": "native SBML value",
"default": 0.00001,
"maps_to": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.initial_para_aminobenzoate",
"description": "Initial condition for para aminobenzoate. Maps to bundled SBML symbol `p_ABA`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
},
{
"name": "initial_folate_metabolism_state_4",
"units": "native SBML value",
"default": 0.00001,
"maps_to": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.initial_folate_metabolism_state_4",
"description": "Initial condition for folate metabolism state 4. Maps to bundled SBML symbol `H2_Pteroate`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
},
{
"name": "initial_dihydrofolate",
"units": "native SBML value",
"default": 0.00001,
"maps_to": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.initial_dihydrofolate",
"description": "Initial condition for dihydrofolate. Maps to bundled SBML symbol `DHF`. Applied before the Tellurium simulation starts; this does not change kinetic parameters or equations. Default from bundled SBML initial value."
}
],
"outputs": [
{
"name": "folate_metabolism_state_1",
"maps_to": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.folate_metabolism_state_1"
},
{
"name": "folate_metabolism_state_2",
"maps_to": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.folate_metabolism_state_2"
},
{
"name": "para_aminobenzoate",
"maps_to": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.para_aminobenzoate"
},
{
"name": "folate_metabolism_state_4",
"maps_to": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.folate_metabolism_state_4"
},
{
"name": "dihydrofolate",
"maps_to": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.dihydrofolate"
},
{
"name": "observable_values",
"maps_to": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.observable_values"
},
{
"name": "run_summary",
"maps_to": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.run_summary"
},
{
"name": "observable_labels",
"maps_to": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.observable_labels"
}
]
},
"title": "Thiaville2016 - Folate pathway model (PanB overexpression) Lab",
"models": [
{
"path": "owned/models/metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model",
"alias": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model",
"parameters": {
"model_path": "data/BIOMD0000000689.xml",
"integration_step": 0.1
},
"provenance": {
"owned_path": "owned/models/metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model_observable_values"
],
"from": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.observable_values"
},
{
"to": [
"visualisation.metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model_run_summary"
],
"from": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.run_summary"
},
{
"to": [
"visualisation.metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model_observable_labels"
],
"from": "metabolism_sbml_thiaville2016_folate_pathway_model_panb_overexpr_biomd0000000689_model.observable_labels"
}
],
"runtime": {
"duration": 10,
"initial_inputs": {},
"communication_step": 1
},
"description": "Henry2016 Folate pathway model with inducedPanB reaction This model is described in the article: Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydrox. It can be used to explore metabolic flux dynamics and compare pathway behavior across conditions.",
"schema_version": "2.0"
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