About lab
Koo2013 Shear-Stress Induced NO Production Lab
This lab wraps the Koo et al. (2013) NO-production submodel from BioModels source BIOMD0000000467. The screenshots below were checked against the visible run alias koo2013_shear_stress_no_production, which matches this lab and its model package. The models/core package handles SBML execution and numeric outputs, while models/visualisation owns internal grouped charts and narrative logic.
Use this lab for the downstream half of the endothelial shear-stress pathway: cytosolic calcium is treated as an external input, then the model follows eNOS activation and nitric oxide production.
Results Preview
The default run spans 600 s and renders six visualization panels. The first view shows the canvas wiring beside the calcium subsystem, PI3K/AKT signalling axis, and eNOS activation-chain panels. The model input is cytosolic_calcium, so these panels are best read as the downstream response to a fixed or upstream-supplied calcium signal.
The summary view highlights the nitric oxide output. In the captured run, NO rises across the 600 s simulation; the What Happened table reports 16 species observables, names nitric oxide as the largest-changing observable (+1.3e+04), and notes that 15 of 16 observables settled within 1% over the final 10% of the run.
Model Files
| Path | Purpose |
|---|---|
lab.yaml | Lab title, IO wiring, runtime defaults, and canvas metadata. |
models/core/model.yaml | Core SBML execution package metadata, parameters, inputs, outputs, and units. |
models/core/src/koo2013_shear_stress_no_production.py | Tellurium-backed SBML execution wrapper. |
models/core/data/BIOMD0000000467.xml | Curated SBML model file from BioModels. |
models/visualisation/ | Internal presentation model for charts and narrative logic. |
models/*/tests/ | Smoke coverage for core execution and visualisation behavior. |
Inputs and Outputs
Inputs:
cytosolic_calcium(substance): external calcium signal used by the NO-production submodel.integration_step(s): Tellurium output sampling interval.
Outputs:
active_eNOS: active eNOS-CaM-Ca4 complex amount, averaged over the wrapper's headline window.nitric_oxide: nitric oxide amount, averaged over the wrapper's headline window.state: latest values for the 16 tracked named species.summary: final, peak, minimum, and excursion diagnostics for the run.
Notes
This is the downstream Koo2013 submodel. It does not include the calcium-influx pathway; compose it with koo2013-calcium-influx or use koo2013-integrated when the experiment needs the full shear-stress-to-NO chain.
Koo et al. (2013) model of nitric oxide (NO) production downstream of shear-stress-driven calcium and eNOS activation in endothelial cells.
Runtime
Duration600
Comms Step10
Runs
Total4
Completed4
Failed0
Metadata
Packagekoo2013-shear-stress-induced-no-production-lab
Created2026-05-04
Updated2026-05-04
Manifest
{
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{
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{
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"title": "Koo2013 Shear-Stress Induced NO Production Lab",
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"description": "Koo et al. (2013) model of nitric oxide (NO) production downstream of shear-stress-driven calcium and eNOS activation in endothelial cells.",
"schema_version": "2.0"
}Sign in to start your own run. Public-lab history stays visible here.
Logs
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JSON
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"title": "Koo2013 Shear-Stress Induced NO Production - Calcium subsystem (Ca²⁺ pools, IP₃, calmodulin)",
"x_unit": "s"
},
"description": "How do extracellular, stored, cytosolic, and buffered Ca²⁺ pools shift, and how does IP₃-driven release propagate through calmodulin?",
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],
"title": "Koo2013 Shear-Stress Induced NO Production - PI3K / AKT signalling axis",
"x_unit": "s"
},
"description": "How does shear-stimulated PI3K activate AKT through PI3P and PDK kinases?",
"render": "timeseries"
},
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],
"title": "Koo2013 Shear-Stress Induced NO Production - eNOS activation chain (eNOS · CaM · Ca₄ · Hsp90 complexes)",
"x_unit": "s"
},
"description": "How does the eNOS enzyme assemble with calmodulin, calcium, and Hsp90 into its active complex?",
"render": "timeseries"
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],
"title": "Koo2013 Shear-Stress Induced NO Production - Nitric oxide production",
"x_unit": "s"
},
"description": "How quickly does the active eNOS complex produce nitric oxide from L-arginine?",
"render": "timeseries"
},
{
"data": {
"categories": [
"Nitric oxide (NO)",
"eNOS·caveolin-1 (inhibited)",
"Calmodulin",
"Hsp90 (heat shock protein 90)",
"Hsp90·eNOS·CaM·Ca₂",
"eNOS·CaM·Ca₂ complex",
"Hsp90·eNOS·CaM·Ca₄ (active)",
"Calmodulin·Ca₂ complex"
],
"title": "Koo2013 Shear-Stress Induced NO Production - largest excursions during the run",
"values": [
13004.396575736266,
1.9354643916510457,
0.769796356507868,
0.6995576311892364,
0.6232331084085025,
0.11958382443765236,
0.05861333177102146,
0.03523238159891662
]
},
"description": "Which observables shifted the most during the run?",
"render": "bar"
},
{
"data": {
"columns": [
"Question",
"Answer"
],
"rows": [
[
"What did this run track?",
"16 species observables in the Koo2013 Shear-Stress Induced NO Production SBML model"
],
[
"How long did it run?",
"600 s"
],
[
"Which observable changed the most?",
"Nitric oxide (NO) (+1.3e+04)"
],
[
"Largest peak?",
"Hsp90 (heat shock protein 90) at 2e+05 substance"
],
[
"Did anything reach steady state?",
"15 of 16 observables settled within 1% over the last 10% of the run."
]
],
"title": "What Happened"
},
"description": "What did this simulation actually show, in plain language?",
"render": "table"
}
]
}
]
}