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Stseranidou2024 Nucleus Pulposus Cell Network Modelling In The Interverteb Lab

About lab

Stseranidou2024 Nucleus Pulposus Cell Network Modelling In The Interverteb

This Biosimulant lab wraps Stseranidou2024 Nucleus Pulposus Cell Network Modelling In The Interverteb as a runnable systems biology model with a companion visualization module. ABSTRACT: Intervertebral disc degeneration (IDD) arises from an intricate imbalance between the anabolic and catabolic processes governing the extracellular matrix (ECM) within the disc. It can be used to explore the configured dynamics and compare scenario outcomes across configurations.

What You'll See

The lab asks: Which gene-regulatory states dominate the source model trajectory? Source model: stseranidou2024 - Nucleus Pulposus Cell Network Modelling in the Intervertebral Disc. 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 TNF, IL-10, IL-1β, TGF-β, IL-8, and IL-6, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, IL-10 moved from 0.9062 to 0.4016 across 1.0 simulation windows.

Output Visualizations

Stseranidou2024 Nucleus Pulposus Cell Network Modelling In The Interverteb - run interpretation

Summary table for Stseranidou2024 Nucleus Pulposus Cell Network Modelling In The Interverteb, reporting the scientific question, observed answer, dominant module, and caveat.

Stseranidou2024 Nucleus Pulposus Cell Network Modelling In The Interverteb - timeseries visualization

Trajectories of IL-10, TGF-β, IL-1β, IL-8, IL-6, and TNF across the 1.0 simulation. In this run TNF climbed from 0.2421 to 0.4257 and IL-10 fell from 0.9062 to 0.4016 — the largest movements among the focused observables.

Stseranidou2024 Nucleus Pulposus Cell Network Modelling In The Interverteb - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: IL-10 = 0.5071, TGF-β = 0.4916, IL-1β = 0.4717, with 3 more observables below.

Stseranidou2024 Nucleus Pulposus Cell Network Modelling In The Interverteb - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: IL-8 = 0.4573, IL-6 = 0.4395, TNF = 0.4257, with 3 more observables below.

Stseranidou2024 Nucleus Pulposus Cell Network Modelling In The Interverteb - visualization

Visualization card from the Stseranidou2024 Nucleus Pulposus Cell Network Modelling In The Interverteb dark-mode run.

Model Context

  • Core model: models/core
  • Visualization model: models/visualisation
  • Standard: other
  • Upstream source: biomodels_ebi:MODEL2407080001
  • License: CC0

Inputs

InputMaps ToDefaultNotes
Initial Model State TNFsystemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.initial_model_state_tnfSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol TNF.
Initial Il 10systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.initial_il_10Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol IL_10.
Initial Il 1systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.initial_il_1Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol IL_1beta.
Initial Model State Tgfsystemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.initial_model_state_tgfSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol TGF_beta.
Initial Il 8systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.initial_il_8Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol IL_8.
Initial Il 6systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.initial_il_6Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol IL_6.

Outputs

OutputMaps ToRole
statesystemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.stateAvailable to the visualization model and downstream workflows.
summarysystemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.summaryAvailable to the visualization model and downstream workflows.
species_labelssystemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.species_labelsAvailable to the visualization model and downstream workflows.
tnfsystemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.tnfAvailable to the visualization model and downstream workflows.
il_10systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.il_10Available to the visualization model and downstream workflows.
il_1systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.il_1Available to the visualization model and downstream workflows.
tgfsystemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.tgfAvailable to the visualization model and downstream workflows.
il_8systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.il_8Available to the visualization model and downstream workflows.
il_6systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.il_6Available to the visualization model and downstream workflows.

Runtime

  • Duration: 1.0
  • Communication step: 0.1

Running Locally

biosimulant labs serve

ABSTRACT: Intervertebral disc degeneration (IDD) arises from an intricate imbalance between the anabolic and catabolic processes governing the extracellular matrix (ECM) within the disc. It can be used to explore systemsbiology stseranidou2024 nucleus pulposus cell network dynamics and compare simulation behavior across conditions.

Runtime

Duration1
Comms Step0.1

Runs

Total0
Completed0
Failed0

Metadata

Packagestseranidou2024-nucleus-pulposus-cell-network-modelling-in-the-i
Created2026-05-17
Updated2026-05-17
generegulationsystemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_model_state_tnf",
        "label": "Initial Model State TNF",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.initial_model_state_tnf",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `TNF`."
      },
      {
        "name": "initial_il_10",
        "label": "Initial Il 10",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.initial_il_10",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `IL_10`."
      },
      {
        "name": "initial_il_1",
        "label": "Initial Il 1",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.initial_il_1",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `IL_1beta`."
      },
      {
        "name": "initial_model_state_tgf",
        "label": "Initial Model State Tgf",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.initial_model_state_tgf",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `TGF_beta`."
      },
      {
        "name": "initial_il_8",
        "label": "Initial Il 8",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.initial_il_8",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `IL_8`."
      },
      {
        "name": "initial_il_6",
        "label": "Initial Il 6",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.initial_il_6",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `IL_6`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.species_labels"
      },
      {
        "name": "tnf",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.tnf"
      },
      {
        "name": "il_10",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.il_10"
      },
      {
        "name": "il_1",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.il_1"
      },
      {
        "name": "tgf",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.tgf"
      },
      {
        "name": "il_8",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.il_8"
      },
      {
        "name": "il_6",
        "maps_to": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.il_6"
      }
    ]
  },
  "tags": [
    "generegulation",
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Stseranidou2024 Nucleus Pulposus Cell Network Modelling In The Interverteb Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model",
      "alias": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model_state"
      ],
      "from": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model_summary"
      ],
      "from": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model_species_labels"
      ],
      "from": "systemsbiology_sbml_stseranidou2024_nucleus_pulposus_cell_network_mo_model2407080001_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "ABSTRACT: Intervertebral disc degeneration (IDD) arises from an intricate imbalance between the anabolic and catabolic processes governing the extracellular matrix (ECM) within the disc. It can be used to explore systemsbiology stseranidou2024 nucleus pulposus cell network dynamics and compare simulation behavior across conditions.",
  "schema_version": "2.0"
}

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