Vilar2006 Tgfbeta Lab

About lab

Vilar2006 Tgfbeta

This Biosimulant lab wraps Vilar2006 Tgfbeta as a runnable systems biology model with a companion visualization module. The model reproduces Fig 5A of the paper. It can be used to explore the configured dynamics and compare scenario outcomes across configurations.

What You'll See

The lab asks: Which signalling variables dominate the simulated network response? Source model: Vilar2006_TGFbeta. 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 ligand receptor complex-endosome, Receptor 2, Receptor 1, ligand receptor complex-plasma membrane, Receptor 2 endosome, and Receptor 1-endosome, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, Receptor 1-endosome moved from 0 to 6.170 across 1.0 simulation windows.

Output Visualizations

Vilar2006 Tgfbeta - run interpretation

Summary table for Vilar2006 Tgfbeta, reporting the scientific question, observed answer, dominant module, and caveat.

Vilar2006 Tgfbeta - timeseries visualization

Trajectories of Receptor 1-endosome, Receptor 2 endosome, Receptor 1, Receptor 2, ligand receptor complex-endosome, and ligand receptor complex-plasma membrane across the 1.0 simulation. In this run Receptor 1-endosome climbed from 0 to 6.170 and Receptor 2 fell from 20.000 to 18.601 — the largest movements among the focused observables.

Vilar2006 Tgfbeta - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: Receptor 1-endosome = 6.170, Receptor 2 endosome = 5.689, Receptor 1 = 1.679, with 3 more observables below.

Vilar2006 Tgfbeta - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: ligand receptor complex-endosome = 38.819, Receptor 1 = 21.679, Receptor 2 = 18.601, with 3 more observables below.

Vilar2006 Tgfbeta - visualization

Visualization card from the Vilar2006 Tgfbeta dark-mode run.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:BIOMD0000000101
License: CC0

Inputs

Input	Maps To	Notes
Initial Ligand Receptor Complex Endosome	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.initial_ligand_receptor_complex_endosome`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `lRIRII_endo`.
Initial Receptor 2	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.initial_receptor_2`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `RII`.
Initial Receptor 1	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.initial_receptor_1`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `RI`.
Initial Ligand Receptor Complex Plasma Membrane	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.initial_ligand_receptor_complex_plasma_membrane`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `lRIRII`.
Initial Receptor 2 Endosome	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.initial_receptor_2_endosome`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `RII_endo`.
Initial Receptor 1 Endosome	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.initial_receptor_1_endosome`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `RI_endo`.

Outputs

Output	Maps To	Role
`state`	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.state`	Available to the visualization model and downstream workflows.
`summary`	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.species_labels`	Available to the visualization model and downstream workflows.
`ligand_receptor_complex_endosome`	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.ligand_receptor_complex_endosome`	Available to the visualization model and downstream workflows.
`receptor_2`	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.receptor_2`	Available to the visualization model and downstream workflows.
`receptor_1`	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.receptor_1`	Available to the visualization model and downstream workflows.
`ligand_receptor_complex_plasma_membrane`	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.ligand_receptor_complex_plasma_membrane`	Available to the visualization model and downstream workflows.
`receptor_2_endosome`	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.receptor_2_endosome`	Available to the visualization model and downstream workflows.
`receptor_1_endosome`	`systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.receptor_1_endosome`	Available to the visualization model and downstream workflows.

Runtime

Duration: 1.0
Communication step: 0.1

Running Locally

biosimulant labs serve

The model reproduces Fig 5A of the paper. The ligand concentration is increased from 3E-5 to 0.01 at time t=2500 to ensure that the system reaches steady state.

Runtime

Duration1

Comms Step0.1

Runs

Total0

Completed0

Failed0

Metadata

Packagevilar2006-tgfbeta-lab

Created2026-05-17

Updated2026-05-17

signalingsystemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_ligand_receptor_complex_endosome",
        "label": "Initial Ligand Receptor Complex Endosome",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.initial_ligand_receptor_complex_endosome",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `lRIRII_endo`."
      },
      {
        "name": "initial_receptor_2",
        "label": "Initial Receptor 2",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.initial_receptor_2",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `RII`."
      },
      {
        "name": "initial_receptor_1",
        "label": "Initial Receptor 1",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.initial_receptor_1",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `RI`."
      },
      {
        "name": "initial_ligand_receptor_complex_plasma_membrane",
        "label": "Initial Ligand Receptor Complex Plasma Membrane",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.initial_ligand_receptor_complex_plasma_membrane",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `lRIRII`."
      },
      {
        "name": "initial_receptor_2_endosome",
        "label": "Initial Receptor 2 Endosome",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.initial_receptor_2_endosome",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `RII_endo`."
      },
      {
        "name": "initial_receptor_1_endosome",
        "label": "Initial Receptor 1 Endosome",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.initial_receptor_1_endosome",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `RI_endo`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.species_labels"
      },
      {
        "name": "ligand_receptor_complex_endosome",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.ligand_receptor_complex_endosome"
      },
      {
        "name": "receptor_2",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.receptor_2"
      },
      {
        "name": "receptor_1",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.receptor_1"
      },
      {
        "name": "ligand_receptor_complex_plasma_membrane",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.ligand_receptor_complex_plasma_membrane"
      },
      {
        "name": "receptor_2_endosome",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.receptor_2_endosome"
      },
      {
        "name": "receptor_1_endosome",
        "maps_to": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.receptor_1_endosome"
      }
    ]
  },
  "tags": [
    "signaling",
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Vilar2006 Tgfbeta Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model",
      "alias": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model_state"
      ],
      "from": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model_summary"
      ],
      "from": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model_species_labels"
      ],
      "from": "systemsbiology_sbml_vilar2006_tgfbeta_biomd0000000101_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "The model reproduces Fig 5A of the paper. The ligand concentration is increased from 3E-5 to 0.01 at time t=2500 to ensure that the system reaches steady state.",
  "schema_version": "2.0"
}

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