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
{
"io": {
"inputs": [
{
"name": "integration_step",
"maps_to": "chen2006_endothelial_no_release_core.integration_step"
},
{
"name": "parameter_overrides",
"maps_to": "chen2006_endothelial_no_release_core.parameter_overrides"
},
{
"name": "initial_conditions",
"maps_to": "chen2006_endothelial_no_release_core.initial_conditions"
}
],
"outputs": [
{
"name": "scenario_metadata",
"maps_to": "chen2006_endothelial_no_release_scenario.scenario_metadata"
},
{
"name": "state",
"maps_to": "chen2006_endothelial_no_release_core.state"
},
{
"name": "run_summary",
"maps_to": "chen2006_endothelial_no_release_viz.run_summary"
}
]
},
"title": "Chen2006 Endothelial No Release Lab",
"models": [
{
"path": "models/scenario",
"alias": "chen2006_endothelial_no_release_scenario",
"parameters": {
"schedule": {
"oxygen": {
"unit": "dimensionless",
"label": "oxygen",
"active": true,
"baseline": 150,
"recovery": 150,
"challenge": 75,
"description": "Scenario-controlled oxygen value."
},
"l_arginine": {
"unit": "dimensionless",
"label": "l arginine",
"active": false,
"baseline": 100,
"recovery": 100,
"challenge": 100,
"description": "Scenario-controlled l arginine value."
},
"arg_binding_rate": {
"unit": "dimensionless",
"label": "arg binding rate",
"active": false,
"baseline": 0.1,
"recovery": 0.1,
"challenge": 0.1,
"description": "Scenario-controlled arg binding rate value."
},
"oxygen_binding_rate": {
"unit": "dimensionless",
"label": "oxygen binding rate",
"active": false,
"baseline": 1.89,
"recovery": 1.89,
"challenge": 1.89,
"description": "Scenario-controlled oxygen binding rate value."
},
"nitric_oxide_synthase_pool": {
"unit": "dimensionless",
"label": "nitric oxide synthase pool",
"active": false,
"baseline": 0.015,
"recovery": 0.015,
"challenge": 0.015,
"description": "Scenario-controlled nitric oxide synthase pool value."
}
},
"scenario_name": "Oxygen availability challenge",
"baseline_until": 0.25,
"challenge_until": 0.75,
"scenario_description": "Baseline is followed by a oxygen challenge and recovery period."
}
},
{
"path": "models/core",
"alias": "chen2006_endothelial_no_release_core",
"parameters": {
"model_path": "data/BIOMD0000000676.xml",
"integration_step": 0.01
}
},
{
"path": "models/viz",
"alias": "chen2006_endothelial_no_release_viz",
"parameters": {
"lab_title": "Chen2006 Endothelial No Release",
"lab_question": "Does the endothelial pathway produce nitric oxide?",
"integration_step": 0.01
}
}
],
"wiring": [
{
"to": [
"chen2006_endothelial_no_release_core.l_arginine"
],
"from": "chen2006_endothelial_no_release_scenario.l_arginine"
},
{
"to": [
"chen2006_endothelial_no_release_core.oxygen"
],
"from": "chen2006_endothelial_no_release_scenario.oxygen"
},
{
"to": [
"chen2006_endothelial_no_release_core.nitric_oxide_synthase_pool"
],
"from": "chen2006_endothelial_no_release_scenario.nitric_oxide_synthase_pool"
},
{
"to": [
"chen2006_endothelial_no_release_core.arg_binding_rate"
],
"from": "chen2006_endothelial_no_release_scenario.arg_binding_rate"
},
{
"to": [
"chen2006_endothelial_no_release_core.oxygen_binding_rate"
],
"from": "chen2006_endothelial_no_release_scenario.oxygen_binding_rate"
},
{
"to": [
"chen2006_endothelial_no_release_viz.scenario_metadata"
],
"from": "chen2006_endothelial_no_release_scenario.scenario_metadata"
},
{
"to": [
"chen2006_endothelial_no_release_viz.state"
],
"from": "chen2006_endothelial_no_release_core.state"
},
{
"to": [
"chen2006_endothelial_no_release_viz.species_labels"
],
"from": "chen2006_endothelial_no_release_core.species_labels"
}
],
"package": "chen2006-endothelial-no-release",
"runtime": {
"duration": 1,
"initial_inputs": {
"chen2006_endothelial_no_release_core": {
"integration_step": 0.01,
"initial_conditions": {
"payload": {}
},
"parameter_overrides": {
"payload": {}
}
}
},
"communication_step": 0.01
},
"version": "1.0.0",
"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.",
"schema_version": "2.0"
}Sign in to start your own run. Public-lab history stays visible here.
Logs
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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_scenario",
"commit_sha": null,
"model_id": "/Volumes/dem-ssd/imp/projects/Nitoons/Biosimulant/models/models-cardiovascular/labs/chen2006-endothelial-no-release/models/scenario",
"repo_full_name": null
},
{
"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": [
"arg_binding_rate",
"initial_conditions",
"integration_step",
"l_arginine",
"nitric_oxide_synthase_pool",
"oxygen",
"oxygen_binding_rate",
"parameter_overrides"
],
"outputs": [
"species_labels",
"state"
]
},
"chen2006_endothelial_no_release_scenario": {
"inputs": [],
"outputs": [
"arg_binding_rate",
"l_arginine",
"nitric_oxide_synthase_pool",
"oxygen",
"oxygen_binding_rate",
"scenario_metadata"
]
},
"chen2006_endothelial_no_release_viz": {
"inputs": [
"scenario_metadata",
"species_labels",
"state"
],
"outputs": [
"run_summary"
]
}
},
"modules": [
"chen2006_endothelial_no_release_scenario",
"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": {
"accepted_profiles": null,
"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": {
"Arg": 100,
"Citrulline": 0.010198928835021385,
"Fe3__Arg": 0.09004700015878561,
"Fe3__NO": 0.0005288741934220948,
"Fe3__enos": 0.013841594686710108,
"NO": 0.009509504564535688,
"O2": 150
}
}
}
},
"chen2006_endothelial_no_release_scenario": {
"arg_binding_rate": {
"emitted_at": 1,
"name": "arg_binding_rate",
"source": "chen2006_endothelial_no_release_scenario",
"spec": {
"accepted_profiles": null,
"description": "Scenario-controlled arg binding rate value.",
"dtype": "float64",
"emitted_unit": "dimensionless",
"interpolation": "zoh",
"kind": "state",
"max_age": null,
"schema": null,
"shape": null,
"signal_type": "scalar",
"stale_policy": "warn"
},
"type": "scalar",
"value": 0.1
},
"l_arginine": {
"emitted_at": 1,
"name": "l_arginine",
"source": "chen2006_endothelial_no_release_scenario",
"spec": {
"accepted_profiles": null,
"description": "Scenario-controlled l arginine value.",
"dtype": "float64",
"emitted_unit": "dimensionless",
"interpolation": "zoh",
"kind": "state",
"max_age": null,
"schema": null,
"shape": null,
"signal_type": "scalar",
"stale_policy": "warn"
},
"type": "scalar",
"value": 100
},
"nitric_oxide_synthase_pool": {
"emitted_at": 1,
"name": "nitric_oxide_synthase_pool",
"source": "chen2006_endothelial_no_release_scenario",
"spec": {
"accepted_profiles": null,
"description": "Scenario-controlled nitric oxide synthase pool value.",
"dtype": "float64",
"emitted_unit": "dimensionless",
"interpolation": "zoh",
"kind": "state",
"max_age": null,
"schema": null,
"shape": null,
"signal_type": "scalar",
"stale_policy": "warn"
},
"type": "scalar",
"value": 0.015
},
"oxygen": {
"emitted_at": 1,
"name": "oxygen",
"source": "chen2006_endothelial_no_release_scenario",
"spec": {
"accepted_profiles": null,
"description": "Scenario-controlled oxygen value.",
"dtype": "float64",
"emitted_unit": "dimensionless",
"interpolation": "zoh",
"kind": "state",
"max_age": null,
"schema": null,
"shape": null,
"signal_type": "scalar",
"stale_policy": "warn"
},
"type": "scalar",
"value": 150
},
"oxygen_binding_rate": {
"emitted_at": 1,
"name": "oxygen_binding_rate",
"source": "chen2006_endothelial_no_release_scenario",
"spec": {
"accepted_profiles": null,
"description": "Scenario-controlled oxygen binding rate value.",
"dtype": "float64",
"emitted_unit": "dimensionless",
"interpolation": "zoh",
"kind": "state",
"max_age": null,
"schema": null,
"shape": null,
"signal_type": "scalar",
"stale_policy": "warn"
},
"type": "scalar",
"value": 1.89
},
"scenario_metadata": {
"emitted_at": 1,
"name": "scenario_metadata",
"source": "chen2006_endothelial_no_release_scenario",
"spec": {
"accepted_profiles": null,
"description": "Plain-language scenario name, timing, active input, and event markers.",
"dtype": null,
"emitted_unit": null,
"interpolation": "zoh",
"kind": "state",
"max_age": null,
"schema": {
"payload": "json"
},
"shape": null,
"signal_type": "record",
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},
"type": "record",
"value": {
"payload": {
"active_label": "oxygen",
"active_port": "oxygen",
"baseline_until": 0.25,
"baseline_value": 150,
"challenge_until": 0.75,
"challenge_value": 75,
"events": [
{
"label": "Challenge starts",
"time": 0.25
},
{
"label": "Recovery starts",
"time": 0.75
}
],
"phase": "recovery",
"recovery_value": 150,
"scenario_description": "Baseline is followed by a oxygen challenge and recovery period.",
"scenario_name": "Oxygen availability challenge",
"unit": "dimensionless"
}
}
}
},
"chen2006_endothelial_no_release_viz": {
"run_summary": {
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"name": "run_summary",
"source": "chen2006_endothelial_no_release_viz",
"spec": {
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"description": "Structured Q&A record echoing the rows in the 'What Happened' table.",
"dtype": null,
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"interpolation": "zoh",
"kind": "state",
"max_age": null,
"schema": {
"payload": "json"
},
"shape": null,
"signal_type": "record",
"stale_policy": "warn"
},
"type": "record",
"value": {
"payload": {
"duration_s": 1,
"point_count": 99,
"response_metrics": [
{
"baseline": 0.01639047586771081,
"delta": 0.07312242587435111,
"direction": "increased",
"final": 0.08951290174206192,
"id": "Fe3__Arg",
"label": "Arginine-bound nitric oxide synthase",
"peak": 0.08951290174206192,
"percent_change": 446.12753445677606
},
{
"baseline": 0.00003316300622496897,
"delta": 0.009869713610101477,
"direction": "increased",
"final": 0.009902876616326446,
"id": "Citrulline",
"label": "Citrulline",
"peak": 0.009902876616326446,
"percent_change": 29761.21508149164
},
{
"baseline": 0.00002398106300444923,
"delta": 0.009202751254973716,
"direction": "increased",
"final": 0.009226732317978166,
"id": "NO",
"label": "Nitric oxide",
"peak": 0.009226732317978166,
"percent_change": 38375.07642286883
},
{
"baseline": 0.000008777068130834239,
"delta": 0.0005115912300437794,
"direction": "increased",
"final": 0.0005203682981746137,
"id": "Fe3__NO",
"label": "Nitric-oxide-bound nitric oxide synthase",
"peak": 0.0005203682981746137,
"percent_change": 5828.725747798814
},
{
"baseline": 0.013469762923696024,
"delta": 0.00036639046228331,
"direction": "increased",
"final": 0.013836153385979334,
"id": "Fe3__enos",
"label": "Ferric endothelial nitric oxide synthase pool",
"peak": 0.013836153385979334,
"percent_change": 2.720095849933301
},
{
"baseline": 100,
"delta": 0,
"direction": "stayed near baseline",
"final": 100,
"id": "Arg",
"label": "Arg",
"peak": 100,
"percent_change": 0
},
{
"baseline": 150,
"delta": 0,
"direction": "stayed near baseline",
"final": 150,
"id": "O2",
"label": "Oxygen",
"peak": 75,
"percent_change": 0
}
],
"rows": [
[
"What question did this run answer?",
"Does the endothelial pathway produce nitric oxide?"
],
[
"What challenge was applied?",
"Oxygen availability challenge: oxygen changed from 150.0 to 75.0 dimensionless."
],
[
"How much simulated time was evaluated?",
"1 s across 99 recorded time points"
],
[
"Which variable responded most?",
"Arginine-bound nitric oxide synthase increased by 0.0731 (446% from baseline)."
],
[
"How should this be interpreted?",
"Treat this as a modelled physiological challenge, not a clinical prediction; inspect the absolute and baseline-relative plots together."
]
],
"scenario": {
"active_label": "oxygen",
"active_port": "oxygen",
"baseline_until": 0.25,
"baseline_value": 150,
"challenge_until": 0.75,
"challenge_value": 75,
"events": [
{
"label": "Challenge starts",
"time": 0.25
},
{
"label": "Recovery starts",
"time": 0.75
}
],
"phase": "recovery",
"recovery_value": 150,
"scenario_description": "Baseline is followed by a oxygen challenge and recovery period.",
"scenario_name": "Oxygen availability challenge",
"unit": "dimensionless"
},
"state_variable_count": 7
}
}
}
}
},
"state": {
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"chen2006_endothelial_no_release_scenario": {},
"chen2006_endothelial_no_release_viz": {}
},
"visuals": [
{
"module": "chen2006_endothelial_no_release_viz",
"module_class": "Chen2006NitricOxideReleaseFromEndothelialCBiomd0000000676ModelViz",
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{
"data": {
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{
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},
{
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}
],
"reference_lines": [
{
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}
],
"series": [
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"title": "What did the model simulate?",
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"x_label": "Time (s)",
"y_label": "Native SBML value"
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"description": "Absolute model state values in their native SBML scale, annotated with the scenario timing.",
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0.9800000000000006,
0
],
[
0.9900000000000008,
0
],
[
1,
0
]
]
}
],
"title": "What changed after the challenge?",
"value_mode": "percent_change",
"x_label": "Time (s)",
"y_label": "Change from baseline",
"y_unit": "% when baseline is nonzero; native delta otherwise"
},
"description": "Baseline-relative trajectories show which signals moved after the challenge instead of hiding small changes on an absolute scale.",
"render": "timeseries"
},
{
"data": {
"items": [
{
"color": "#0f766e",
"label": "Arginine-bound nitric oxide synthase",
"unit": "native SBML units",
"value": 0.07312242587435111
},
{
"color": "#0f766e",
"label": "Citrulline",
"unit": "native SBML units",
"value": 0.009869713610101477
},
{
"color": "#0f766e",
"label": "Nitric oxide",
"unit": "native SBML units",
"value": 0.009202751254973716
},
{
"color": "#0f766e",
"label": "Nitric-oxide-bound nitric oxide synthase",
"unit": "native SBML units",
"value": 0.0005115912300437794
},
{
"color": "#0f766e",
"label": "Ferric endothelial nitric oxide synthase pool",
"unit": "native SBML units",
"value": 0.00036639046228331
},
{
"color": "#0f766e",
"label": "Arg",
"unit": "native SBML units",
"value": 0
},
{
"color": "#0f766e",
"label": "Oxygen",
"unit": "native SBML units",
"value": 0
}
],
"title": "Which variables responded most?",
"x_label": "Model variable",
"y_label": "Final minus baseline",
"y_unit": "native SBML units"
},
"description": "Signed final-minus-baseline changes rank the strongest responses in the selected model outputs.",
"render": "bar"
},
{
"data": {
"columns": [
"Question",
"Answer"
],
"rows": [
[
"What question did this run answer?",
"Does the endothelial pathway produce nitric oxide?"
],
[
"What challenge was applied?",
"Oxygen availability challenge: oxygen changed from 150.0 to 75.0 dimensionless."
],
[
"How much simulated time was evaluated?",
"1 s across 99 recorded time points"
],
[
"Which variable responded most?",
"Arginine-bound nitric oxide synthase increased by 0.0731 (446% from baseline)."
],
[
"How should this be interpreted?",
"Treat this as a modelled physiological challenge, not a clinical prediction; inspect the absolute and baseline-relative plots together."
]
],
"subtitle": "Answers `Does the endothelial pathway produce nitric oxide?` using oxygen availability challenge over a 1-second Tellurium run.",
"title": "What Happened"
},
"description": "Answers `Does the endothelial pathway produce nitric oxide?` for the Chen2006 Endothelial No Release run.",
"render": "table"
}
]
}
]
}