About lab
Abu Soud1999 Nmarginine
This Biosimulant lab wraps Abu Soud1999 Nmarginine as a runnable systems biology model with a companion visualization module.
This model is taken from the referenced publication. It can be used to explore the configured dynamics and compare scenario outcomes across configurations.
What You'll See
The lab asks: Which source-defined system states dominate this SBML model trajectory? Source model: Abu-Soud1999_NMArginine. It runs for 1.0 time units with a communication step of 0.1. The run uses the model defaults declared by the curated SBML wrapper. The generated visualizations focus on NM Minus Arginine, Im Minus NNOS, Imidazole, NNOS Minus NM Minus Arginine, and Im Minus NNOS Minus NM Minus Arginine, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.
In this captured run, NM Minus Arginine moved from 1e-14 to 1e-14 across 1.0 simulation windows.
Output Visualizations

Summary table for Abu Soud1999 Nmarginine, reporting the scientific question, observed answer, dominant module, and caveat.

Trajectories of NM Minus Arginine, Im Minus NNOS, Imidazole, NNOS Minus NM Minus Arginine, and Im Minus NNOS Minus NM Minus Arginine across the 1.0 simulation. In this run Imidazole climbed from 0 to 1.65e-18 and NM Minus Arginine fell from 1e-14 to 1e-14 — the largest movements among the focused observables.

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: NM Minus Arginine = 1.66e-18, Im Minus NNOS = 1.66e-18, Imidazole = 1.65e-18, with 2 more observables below.

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: NM Minus Arginine = 1e-14, Imidazole = 1.65e-18, NNOS Minus NM Minus Arginine = 1.65e-18, with 2 more observables below.

Visualization card from the Abu Soud1999 Nmarginine dark-mode run.
Model Context
- Core model:
models/core - Visualization model:
models/visualisation - Standard:
other - Upstream source:
biomodels_ebi:MODEL9088169066 - License:
CC0
Inputs
| Input | Maps To | Default | Notes |
|---|---|---|---|
| Initial Nm Minus Arginine | systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_nm_minus_arginine | Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol NM_minus_Arginine. | |
| Initial Im Minus Nnos | systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_im_minus_nnos | Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Im_minus_nNOS. | |
| Initial Imidazole | systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_imidazole | Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Imidazole. | |
| Initial Nnos Minus Nm Minus Arginine | systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_nnos_minus_nm_minus_arginine | Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol nNOS_minus_NM_minus_Arginine. | |
| Initial Im Minus Nnos Minus Nm Minus Arginine | systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_im_minus_nnos_minus_nm_minus_arginine | Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Im_minus_nNOS_minus_NM_minus_Arginine. |
Outputs
| Output | Maps To | Role |
|---|---|---|
state | systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.state | Available to the visualization model and downstream workflows. |
summary | systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.summary | Available to the visualization model and downstream workflows. |
species_labels | systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.species_labels | Available to the visualization model and downstream workflows. |
nm_minus_arginine | systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.nm_minus_arginine | Available to the visualization model and downstream workflows. |
im_minus_nnos | systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.im_minus_nnos | Available to the visualization model and downstream workflows. |
imidazole | systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.imidazole | Available to the visualization model and downstream workflows. |
nnos_minus_nm_minus_arginine | systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.nnos_minus_nm_minus_arginine | Available to the visualization model and downstream workflows. |
im_minus_nnos_minus_nm_minus_arginine | systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.im_minus_nnos_minus_nm_minus_arginine | Available to the visualization model and downstream workflows. |
Runtime
- Duration:
1.0 - Communication step:
0.1
Running Locally
biosimulant labs serve
This model is taken from the <a href = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=7559438&dopt=Abstract'>Peer-reviewed publication>Husam M. It can be used to explore systemsbiology abu soud1999 nmarginine model9088169066 dynamics and compare simulation behavior across conditions.
Runtime
Runs
Metadata
Manifest
{
"io": {
"inputs": [
{
"name": "initial_nm_minus_arginine",
"label": "Initial Nm Minus Arginine",
"maps_to": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_nm_minus_arginine",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `NM_minus_Arginine`."
},
{
"name": "initial_im_minus_nnos",
"label": "Initial Im Minus Nnos",
"maps_to": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_im_minus_nnos",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Im_minus_nNOS`."
},
{
"name": "initial_imidazole",
"label": "Initial Imidazole",
"maps_to": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_imidazole",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Imidazole`."
},
{
"name": "initial_nnos_minus_nm_minus_arginine",
"label": "Initial Nnos Minus Nm Minus Arginine",
"maps_to": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_nnos_minus_nm_minus_arginine",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `nNOS_minus_NM_minus_Arginine`."
},
{
"name": "initial_im_minus_nnos_minus_nm_minus_arginine",
"label": "Initial Im Minus Nnos Minus Nm Minus Arginine",
"maps_to": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_im_minus_nnos_minus_nm_minus_arginine",
"description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Im_minus_nNOS_minus_NM_minus_Arginine`."
}
],
"outputs": [
{
"name": "state",
"maps_to": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.state"
},
{
"name": "summary",
"maps_to": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.summary"
},
{
"name": "species_labels",
"maps_to": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.species_labels"
},
{
"name": "nm_minus_arginine",
"maps_to": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.nm_minus_arginine"
},
{
"name": "im_minus_nnos",
"maps_to": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.im_minus_nnos"
},
{
"name": "imidazole",
"maps_to": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.imidazole"
},
{
"name": "nnos_minus_nm_minus_arginine",
"maps_to": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.nnos_minus_nm_minus_arginine"
},
{
"name": "im_minus_nnos_minus_nm_minus_arginine",
"maps_to": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.im_minus_nnos_minus_nm_minus_arginine"
}
]
},
"tags": [
"systemsbiology",
"sbml",
"biomodels_ebi",
"faithful",
"curated"
],
"title": "Abu Soud1999 Nmarginine Lab",
"models": [
{
"path": "owned/models/systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model",
"alias": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model",
"provenance": {
"owned_path": "owned/models/systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model"
}
},
{
"path": "owned/models/visualisation",
"alias": "visualisation",
"provenance": {
"owned_path": "owned/models/visualisation"
}
}
],
"wiring": [
{
"to": [
"visualisation.systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model_state"
],
"from": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.state"
},
{
"to": [
"visualisation.systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model_summary"
],
"from": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.summary"
},
{
"to": [
"visualisation.systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model_species_labels"
],
"from": "systemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.species_labels"
}
],
"runtime": {
"duration": 1,
"initial_inputs": {},
"communication_step": 0.1
},
"description": "This model is taken from the <a href = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=7559438&dopt=Abstract'>Peer-reviewed publication>Husam M. It can be used to explore systemsbiology abu soud1999 nmarginine model9088169066 dynamics and compare simulation behavior across conditions.",
"schema_version": "2.0"
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