BiosimulantBiosimulant
Docs
Search labs...
Sign inGet Started

Abu Soud1999 Nmarginine Lab

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

Abu Soud1999 Nmarginine - run interpretation

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

Abu Soud1999 Nmarginine - timeseries visualization

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.

Abu Soud1999 Nmarginine - excursions bar

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.

Abu Soud1999 Nmarginine - endpoint snapshot bar

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.

Abu Soud1999 Nmarginine - visualization

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

InputMaps ToDefaultNotes
Initial Nm Minus Argininesystemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_nm_minus_arginineSource 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 Nnossystemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_im_minus_nnosSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Im_minus_nNOS.
Initial Imidazolesystemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_imidazoleSource 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 Argininesystemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_nnos_minus_nm_minus_arginineSource 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 Argininesystemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.initial_im_minus_nnos_minus_nm_minus_arginineSource 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

OutputMaps ToRole
statesystemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.stateAvailable to the visualization model and downstream workflows.
summarysystemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.summaryAvailable to the visualization model and downstream workflows.
species_labelssystemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.species_labelsAvailable to the visualization model and downstream workflows.
nm_minus_argininesystemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.nm_minus_arginineAvailable to the visualization model and downstream workflows.
im_minus_nnossystemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.im_minus_nnosAvailable to the visualization model and downstream workflows.
imidazolesystemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.imidazoleAvailable to the visualization model and downstream workflows.
nnos_minus_nm_minus_argininesystemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.nnos_minus_nm_minus_arginineAvailable to the visualization model and downstream workflows.
im_minus_nnos_minus_nm_minus_argininesystemsbiology_sbml_abu_soud1999_nmarginine_model9088169066_model.im_minus_nnos_minus_nm_minus_arginineAvailable 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

Duration1
Comms Step0.1

Runs

Total0
Completed0
Failed0

Metadata

Packageabu-soud1999-nmarginine-lab
Created2026-05-17
Updated2026-05-17
systemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

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"
}

Sign in to start your own run. Public-lab history stays visible here.

Select a run from History to view its results.