About lab
Koo2013 Shear-Stress Induced Calcium Influx and eNOS Activation Lab
This lab runs the Koo et al. (2013) endothelial mechanotransduction model for shear-stress induced calcium influx. It asks: when endothelial cells experience a shear-stress stimulus, how do IP3 production, calcium-store release, cytosolic calcium, and buffered calcium evolve over ten minutes?
The model wraps the BioModels EBI SBML asset BIOMD0000000464. This submodel is the calcium-influx/eNOS-activation entry point in the Koo2013 series. Its models/core package stays focused on SBML execution and stable numeric outputs, while models/visualisation owns internal grouped charts and narrative logic.
What You'll See
The lab opens as a canvas with one Koo2013 calcium-influx node and a run-results panel. A default run lasts 600 s and produces grouped time-series panels for mechanical inputs/timers and calcium-subsystem species, plus a largest-excursions diagnostic and a What Happened table.
The first screenshot shows the canvas, the mechanical-input/timer panel, and the calcium-subsystem panel. The second scrolls down to the largest-excursions diagnostic and the What Happened table.
How to Read the Visualizations
The mechanical-input panel shows the model's internal step timer and the shear-stress input species. In this curated wrapper, the biologically useful stimulus knob is stimulus_intensity, which maps to the IP3-producing rate constant k1; the SBML shear-stress species itself is decorative and not kinetically wired.
The calcium-subsystem panel tracks extracellular calcium, stored calcium in the ER lumen, cytosolic calcium, buffered calcium, and IP3. In the shown run, stored calcium is the dominant changing pool, while IP3 and cytosolic calcium remain much smaller on the same scale.
The What Happened table summarizes the run without reading every trace. In the screenshot, it reports 7 tracked species observables, a 600 s run, stored calcium in the ER lumen as both the largest signed change and largest peak, and 3 of 7 observables settling within 1% over the final 10% of the run.
What This Lab Contains
lab.yamldescribes the lab, runtime, inputs, outputs, and default model parameters.wiring-layout.jsonplaces the model on the canvas.models/core/model.yamldescribes the SBML execution package, upstream source, parameters, and ports.models/core/src/koo2013_shear_stress_calcium_influx.pywraps the SBML model and publishes stable numeric outputs.models/core/data/BIOMD0000000464.xmlis the curated SBML model file from BioModels EBI.models/visualisation/contains the internal presentation model for charts and narrative logic.models/*/tests/contains smoke tests for core execution and visualisation behavior.
Inputs
stimulus_intensity(1/s): IP3 production rate constantk1, used as the shear-stress-driven mechanotransduction knob.integration_step(s): output sampling step for the Tellurium simulator.
Outputs
cytosolic_calcium: cytosolic Ca2+ amount averaged over the model's headline window.ip3: IP3 amount averaged over the model's headline window.state: latest values of the observed species.summary: final, peak, minimum, and largest-change diagnostics for the run.
Recreate and Run with the Biosim CLI
From this lab folder:
cd /path/to/models-biomechanics/labs/koo2013-calcium-influx
mkdir -p dist
python -m biosim pack build . --out dist/koo2013-calcium-influx.bsilab
python -m biosim pack run dist/koo2013-calcium-influx.bsilab
If you are working from this monorepo without installing biosim, use the local package environment instead:
mkdir -p dist
/path/to/bsim-active/biosim/.venv/bin/python -m biosim pack build . --out dist/koo2013-calcium-influx.bsilab
/path/to/bsim-active/biosim/.venv/bin/python -m biosim pack run dist/koo2013-calcium-influx.bsilab
Run in the Desktop App
- Open Biosimulant Desktop.
- Go to Projects or Labs.
- Choose the option to open or import an existing lab.
- Select this folder's
lab.yaml. - Open the lab and press Run.
The right side of the app should show the mechanical-input, calcium-subsystem, and summary diagnostic panels.
How to Edit It
For scenario changes, start with lab.yaml and models/core/model.yaml.
- Change
runtime.durationinlab.yamlfor a longer or shorter simulation. - Change
runtime.communication_stepif you want more or fewer reported points. - Change
stimulus_intensityto mimic weaker or stronger shear-stress-driven IP3 production. - Change
integration_stepinmodels/core/model.yamlfor finer or coarser Tellurium output sampling.
For downstream nitric-oxide production, wire this lab into koo2013-no-production or use the composed koo2013-shear-to-no lab.
Koo et al. (2013) model of how laminar shear stress at the endothelial surface drives calcium influx and activates endothelial nitric oxide synthase (eNOS).
Runtime
Duration600
Comms Step10
Runs
Total3
Completed3
Failed0
Metadata
Packagekoo2013-shear-stress-induced-calcium-influx-and-enos-activation
Created2026-05-04
Updated2026-05-14
biomechanicsendothelialshear-stressmechanotransductioncalciumsbmlbiomodels_ebifaithfulvisualisationkoo2013
Manifest
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}Sign in to start your own run. Public-lab history stays visible here.
Logs
No logs yet.
JSON
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"description": "What is the shear-stress input doing, and how does the model's internal time tracker evolve?",
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}
],
"title": "Koo2013 Shear-Stress Induced Calcium Influx and eNOS Activation - 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?",
"render": "timeseries"
},
{
"data": {
"categories": [
"Stored calcium (ER lumen)",
"Buffered calcium (protein-bound)",
"Cytosolic calcium (Ca²⁺)",
"Step timer (model internal)",
"IP₃ (inositol 1,4,5-trisphosphate)",
"Extracellular calcium (Ca²⁺)",
"Shear stress (mechanical input)"
],
"title": "Koo2013 Shear-Stress Induced Calcium Influx and eNOS Activation - largest excursions during the run",
"values": [
2410695.665376394,
28486.51910594283,
1001.3192752972,
600.0000000000002,
26.396978990434587,
0,
0
]
},
"description": "Which observables shifted the most during the run?",
"render": "bar"
},
{
"data": {
"columns": [
"Question",
"Answer"
],
"rows": [
[
"What did this run track?",
"7 species observables in the Koo2013 Shear-Stress Induced Calcium Influx and eNOS Activation SBML model"
],
[
"How long did it run?",
"600 s"
],
[
"Which observable changed the most?",
"Stored calcium (ER lumen) (-2.41e+06)"
],
[
"Largest peak?",
"Stored calcium (ER lumen) at 2.83e+06 substance"
],
[
"Did anything reach steady state?",
"3 of 7 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"
}
]
}
]
}