About lab
Kerkhoven2013 - Glycolysis and Pentose Phosphate Pathway in T.brucei - MODEL C (with glucosomal ribokinase)
Cleaned metabolism SBML ODE lab. The bundled SBML file remains the scientific source of truth.
Validation evidence: Tellurium loaded and simulated 38 floating species
What You'll See
These dark-mode screenshots show the default Kerkhoven2013 - Glycolysis and Pentose Phosphate Pathway in T.brucei - MODEL C (with glucosomal ribokinase) 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=0.1, initial_glycolysis_state_2=2.23132912, initial_glycolysis_state_3=0.2405, initial_glycolysis_state_4=8.483130623. Kerkhoven2013 - Glycolysis and Pentose Phosphate Pathway in T.brucei -MODEL C (with glucosomal ribokinase) There are six models (Model A, B, C, C-fruc, D, D-fruc) described in the paper. It can be used to explore metabolic flux dynamics and compare pathway behavior across conditions.
Output Visualizations
The run interpretation table summarizes the configured Kerkhoven2013 - Glycolysis and Pentose Phosphate Pathway in T.brucei - MODEL C (with glucosomal ribokinase) 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.
Kerkhoven2013 - Glycolysis and Pentose Phosphate Pathway in T.brucei -MODEL C (with glucosomal ribokinase) There are six models (Model A, B, C, C-fruc, D, D-fruc) described in the paper. It can be used to explore metabolic flux dynamics and compare pathway behavior across conditions.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_glycolysis_state_1",
"units": "native SBML value",
"default": 0.1,
"maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.initial_glycolysis_state_1",
"description": "Initial condition for glycolysis state 1. Maps to bundled SBML symbol `_2PGA_c`. 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": 2.23132912,
"maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.initial_glycolysis_state_2",
"description": "Initial condition for glycolysis state 2. Maps to bundled SBML symbol `DHAP_c`. 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": 0.2405,
"maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.initial_glycolysis_state_3",
"description": "Initial condition for glycolysis state 3. Maps to bundled SBML symbol `ATP_g`. 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": 8.483130623,
"maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.initial_glycolysis_state_4",
"description": "Initial condition for glycolysis state 4. Maps to bundled SBML symbol `DHAP_g`. 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": 1.519,
"maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.initial_glycolysis_state_5",
"description": "Initial condition for glycolysis state 5. Maps to bundled SBML symbol `ADP_g`. 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_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.glycolysis_state_1"
},
{
"name": "glycolysis_state_2",
"maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.glycolysis_state_2"
},
{
"name": "glycolysis_state_3",
"maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.glycolysis_state_3"
},
{
"name": "glycolysis_state_4",
"maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.glycolysis_state_4"
},
{
"name": "glycolysis_state_5",
"maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.glycolysis_state_5"
},
{
"name": "observable_values",
"maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.observable_values"
},
{
"name": "run_summary",
"maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.run_summary"
},
{
"name": "observable_labels",
"maps_to": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.observable_labels"
}
]
},
"title": "Kerkhoven2013 C-Glucose Standalone Glycolysis Lab",
"models": [
{
"path": "models/core",
"alias": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model",
"parameters": {
"model_path": "data/BIOMD0000000510.xml",
"integration_step": 0.1
}
},
{
"path": "models/visualisation",
"alias": "visualisation"
}
],
"wiring": [
{
"to": [
"visualisation.metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model_observable_values"
],
"from": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.observable_values"
},
{
"to": [
"visualisation.metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model_run_summary"
],
"from": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.run_summary"
},
{
"to": [
"visualisation.metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model_observable_labels"
],
"from": "metabolism_sbml_kerkhoven2013_glycolysis_and_pentose_phosphate_p_biomd0000000510_model.observable_labels"
}
],
"runtime": {
"duration": 10,
"initial_inputs": {},
"communication_step": 1
},
"description": "Kerkhoven2013 - Glycolysis and Pentose Phosphate Pathway in T.brucei -MODEL C (with glucosomal ribokinase) There are six models (Model A, B, C, C-fruc, D, D-fruc) described in the paper. It can be used to explore metabolic flux dynamics and compare pathway behavior across conditions.",
"schema_version": "2.0"
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