About lab
Two-model lab for Chen2006 Endothelial No Release: a core SBML simulator wired into a dedicated visualization sub-model that turns the raw state into friendly timeseries and a plain-language summary. Chen2006 - Nitric Oxide Release fromEndothelial Cells This model is described in the article: Theoretical analysis of biochemical pathways of nitric oxide release from vascular endothelial cells. It can be used to explore cardiac dynamics and compare response patterns across conditions.
Runtime
Duration1
Comms Step0.01
Runs
Total8
Completed3
Failed5
Metadata
Packagechen2006-endothelial-no-release
Created2026-05-05
Updated2026-06-13
cardiovascularscenariostimulussbmlbiomodels_ebifaithfulvisualizationother
Manifest
{
"description": "Two-model lab for Chen2006 Endothelial No Release: a core SBML simulator wired into a dedicated visualization sub-model that turns the raw state into friendly timeseries and a plain-language summary. Chen2006 - Nitric Oxide Release fromEndothelial Cells This model is described in the article: Theoretical analysis of biochemical pathways of nitric oxide release from vascular endothelial cells. It can be used to explore cardiac dynamics and compare response patterns across conditions.",
"io": {
"inputs": [
{
"maps_to": "chen2006_endothelial_no_release_core.integration_step",
"name": "integration_step"
},
{
"maps_to": "chen2006_endothelial_no_release_core.parameter_overrides",
"name": "parameter_overrides"
},
{
"maps_to": "chen2006_endothelial_no_release_core.initial_conditions",
"name": "initial_conditions"
}
],
"outputs": [
{
"maps_to": "chen2006_endothelial_no_release_scenario.scenario_metadata",
"name": "scenario_metadata"
},
{
"maps_to": "chen2006_endothelial_no_release_core.state",
"name": "state"
},
{
"maps_to": "chen2006_endothelial_no_release_viz.run_summary",
"name": "run_summary"
}
]
},
"models": [
{
"alias": "chen2006_endothelial_no_release_scenario",
"parameters": {
"baseline_until": 0.25,
"challenge_until": 0.75,
"scenario_description": "Baseline is followed by a oxygen challenge and recovery period.",
"scenario_name": "Oxygen availability challenge",
"schedule": {
"arg_binding_rate": {
"active": false,
"baseline": 0.1,
"challenge": 0.1,
"description": "Scenario-controlled arg binding rate value.",
"label": "arg binding rate",
"recovery": 0.1,
"unit": "dimensionless"
},
"l_arginine": {
"active": false,
"baseline": 100,
"challenge": 100,
"description": "Scenario-controlled l arginine value.",
"label": "l arginine",
"recovery": 100,
"unit": "dimensionless"
},
"nitric_oxide_synthase_pool": {
"active": false,
"baseline": 0.015,
"challenge": 0.015,
"description": "Scenario-controlled nitric oxide synthase pool value.",
"label": "nitric oxide synthase pool",
"recovery": 0.015,
"unit": "dimensionless"
},
"oxygen": {
"active": true,
"baseline": 150,
"challenge": 75,
"description": "Scenario-controlled oxygen value.",
"label": "oxygen",
"recovery": 150,
"unit": "dimensionless"
},
"oxygen_binding_rate": {
"active": false,
"baseline": 1.89,
"challenge": 1.89,
"description": "Scenario-controlled oxygen binding rate value.",
"label": "oxygen binding rate",
"recovery": 1.89,
"unit": "dimensionless"
}
}
},
"path": "models/scenario"
},
{
"alias": "chen2006_endothelial_no_release_core",
"parameters": {
"integration_step": 0.01,
"model_path": "data/BIOMD0000000676.xml"
},
"path": "models/core"
},
{
"alias": "chen2006_endothelial_no_release_viz",
"parameters": {
"integration_step": 0.01,
"lab_question": "Does the endothelial pathway produce nitric oxide?",
"lab_title": "Chen2006 Endothelial No Release"
},
"path": "models/viz"
}
],
"package": "chen2006-endothelial-no-release",
"runtime": {
"communication_step": 0.01,
"duration": 1,
"initial_inputs": {
"chen2006_endothelial_no_release_core": {
"initial_conditions": {
"payload": {}
},
"integration_step": 0.01,
"parameter_overrides": {
"payload": {}
}
}
}
},
"schema_version": "2.0",
"title": "Chen2006 Endothelial No Release Lab",
"version": "1.0.0",
"wiring": [
{
"from": "chen2006_endothelial_no_release_scenario.l_arginine",
"to": [
"chen2006_endothelial_no_release_core.l_arginine"
]
},
{
"from": "chen2006_endothelial_no_release_scenario.oxygen",
"to": [
"chen2006_endothelial_no_release_core.oxygen"
]
},
{
"from": "chen2006_endothelial_no_release_scenario.nitric_oxide_synthase_pool",
"to": [
"chen2006_endothelial_no_release_core.nitric_oxide_synthase_pool"
]
},
{
"from": "chen2006_endothelial_no_release_scenario.arg_binding_rate",
"to": [
"chen2006_endothelial_no_release_core.arg_binding_rate"
]
},
{
"from": "chen2006_endothelial_no_release_scenario.oxygen_binding_rate",
"to": [
"chen2006_endothelial_no_release_core.oxygen_binding_rate"
]
},
{
"from": "chen2006_endothelial_no_release_scenario.scenario_metadata",
"to": [
"chen2006_endothelial_no_release_viz.scenario_metadata"
]
},
{
"from": "chen2006_endothelial_no_release_core.state",
"to": [
"chen2006_endothelial_no_release_viz.state"
]
},
{
"from": "chen2006_endothelial_no_release_core.species_labels",
"to": [
"chen2006_endothelial_no_release_viz.species_labels"
]
}
]
}Sign in to start your own run. Public-lab history stays visible here.
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JSON
{
"communication_step": 0.01,
"dependency_installs": [
{
"alias": "chen2006_endothelial_no_release_core",
"status": "reused"
}
],
"dependency_policy_enabled": true,
"duration": 1,
"lab_commit": null,
"model_resolutions": [
{
"alias": "chen2006_endothelial_no_release_core",
"commit_sha": null,
"model_id": "/Volumes/dem-ssd/imp/projects/Nitoons/Biosimulant/models/models-cardiovascular/labs/chen2006-endothelial-no-release/models/core",
"repo_full_name": null
},
{
"alias": "chen2006_endothelial_no_release_viz",
"commit_sha": null,
"model_id": "/Volumes/dem-ssd/imp/projects/Nitoons/Biosimulant/models/models-cardiovascular/labs/chen2006-endothelial-no-release/models/viz",
"repo_full_name": null
}
],
"module_ports": {
"chen2006_endothelial_no_release_core": {
"inputs": [
"initial_conditions",
"integration_step",
"parameter_overrides"
],
"outputs": [
"species_labels",
"state"
]
},
"chen2006_endothelial_no_release_viz": {
"inputs": [
"species_labels",
"state"
],
"outputs": [
"run_summary"
]
}
},
"modules": [
"chen2006_endothelial_no_release_core",
"chen2006_endothelial_no_release_viz"
],
"outputs": {
"chen2006_endothelial_no_release_core": {
"species_labels": {
"emitted_at": 1,
"name": "species_labels",
"source": "chen2006_endothelial_no_release_core",
"spec": {
"accepted_profiles": null,
"description": "Static map of SBML species id to human-friendly label.",
"dtype": null,
"emitted_unit": null,
"interpolation": "zoh",
"kind": "state",
"max_age": null,
"schema": {
"payload": "json"
},
"shape": null,
"signal_type": "record",
"stale_policy": "warn"
},
"type": "record",
"value": {
"payload": {
"Arg": "Arg",
"Citrulline": "Citrulline",
"Fe2": "Fe2+",
"Fe2__Arg": "Fe2+_Arg",
"Fe2__NO": "Fe2+_NO",
"Fe2__NOHA": "Fe2+_NOHA",
"Fe3__Arg": "Fe3+_Arg",
"Fe3__NO": "Fe3+_NO",
"Fe3__NOHA": "Fe3+_NOHA",
"Fe3__O2__Arg": "Fe3+_O2-_Arg",
"Fe3__O2__NOHA": "Fe3+_O2-_NOHA",
"Fe3__enos": "Fe3+(enos)",
"NO": "NO",
"NOHA": "NOHA",
"O2": "O2"
}
}
},
"state": {
"emitted_at": 1,
"name": "state",
"source": "chen2006_endothelial_no_release_core",
"spec": {
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"description": "Species concentrations and SBML state variables (mixed units, see SBML file).",
"dtype": null,
"emitted_unit": null,
"interpolation": "zoh",
"kind": "state",
"max_age": null,
"schema": {
"payload": "json"
},
"shape": null,
"signal_type": "record",
"stale_policy": "warn"
},
"type": "record",
"value": {
"payload": {
"Citrulline": 0,
"Fe2": 0,
"Fe2__Arg": 0,
"Fe2__NO": 0,
"Fe2__NOHA": 0,
"Fe3__Arg": 0,
"Fe3__NO": 0,
"Fe3__NOHA": 0,
"Fe3__O2__Arg": 0,
"Fe3__O2__NOHA": 0,
"Fe3__enos": 0,
"NO": 0,
"NOHA": 0
}
}
}
},
"chen2006_endothelial_no_release_viz": {
"run_summary": {
"emitted_at": 1,
"name": "run_summary",
"source": "chen2006_endothelial_no_release_viz",
"spec": {
"accepted_profiles": null,
"description": "Structured Q&A record echoing the rows in the 'What Happened' table.",
"dtype": null,
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"schema": {
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},
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"signal_type": "record",
"stale_policy": "warn"
},
"type": "record",
"value": {
"payload": {
"duration_s": 1,
"point_count": 99,
"rows": [
[
"How long did the simulation run?",
"1 s"
],
[
"How many state variables were tracked?",
"13"
],
[
"Which variable ended at the largest absolute value?",
"Fe3+(enos) = 0"
],
[
"How many time points were recorded?",
"99"
]
],
"state_variable_count": 13
}
}
}
}
},
"state": {
"chen2006_endothelial_no_release_core": {},
"chen2006_endothelial_no_release_viz": {}
},
"visuals": [
{
"module": "chen2006_endothelial_no_release_viz",
"module_class": "Chen2006NitricOxideReleaseFromEndothelialCBiomd0000000676ModelViz",
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}
],
"title": "State Variables Over Time"
},
"description": "How the model's state variables evolve over the simulated window.",
"render": "timeseries"
},
{
"data": {
"columns": [
"Question",
"Answer"
],
"rows": [
[
"How long did the simulation run?",
"1 s"
],
[
"How many state variables were tracked?",
"13"
],
[
"Which variable ended at the largest absolute value?",
"Fe3+(enos) = 0"
],
[
"How many time points were recorded?",
"99"
]
],
"subtitle": "A 1-second window of the Chen2006 Endothelial No Release model, integrated by Tellurium.",
"title": "What Happened"
},
"description": "Plain-language summary of the Chen2006 Endothelial No Release run.",
"render": "table"
}
]
}
]
}