Gomez Cabrero2011 Atherogenesis Lab

About lab

Gomez Cabrero2011 Atherogenesis

This Biosimulant lab wraps Gomez Cabrero2011 Atherogenesis as a runnable systems biology model with a companion visualization module. This model is from the article: Workflow for generating competing hypothesis from models with parameter uncertainty. 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: Gomez-Cabrero2011_Atherogenesis. 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 SUMRecBcells, Bcells, LDL_blood, HDL_blood, SIGMOID_ACTENDinh, and SIGMOID_ACTENDstim, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, SUMRecBcells moved from 2.68e-07 to 0.6709 across 1.0 simulation windows.

Output Visualizations

Gomez Cabrero2011 Atherogenesis - run interpretation

Summary table for Gomez Cabrero2011 Atherogenesis, reporting the scientific question, observed answer, dominant module, and caveat.

Gomez Cabrero2011 Atherogenesis - timeseries visualization

Trajectories of SUMRecBcells, Bcells, SIGMOID_ACTENDinh, LDL_blood, SIGMOID_ACTENDstim, and HDL_blood across the 1.0 simulation. In this run SUMRecBcells climbed from 2.68e-07 to 0.6709 — the largest movements among the focused observables.

Gomez Cabrero2011 Atherogenesis - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: SUMRecBcells = 0.6709, Bcells = 0.00011, SIGMOID_ACTENDinh = 7.45e-05, with 2 more observables below.

Gomez Cabrero2011 Atherogenesis - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: LDL_blood = 2.500, HDL_blood = 1.000, SUMRecBcells = 0.6709, with 3 more observables below.

Gomez Cabrero2011 Atherogenesis - visualization

Visualization card from the Gomez Cabrero2011 Atherogenesis dark-mode run.

Model Context

Core model: models/core
Visualization model: models/visualisation
Standard: other
Upstream source: biomodels_ebi:MODEL1002160000
License: CC0

Inputs

Input	Maps To	Notes
Initial Sum Rec Bcells	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.initial_sum_rec_bcells`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_14`.
Initial Bcells	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.initial_bcells`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_8`.
Initial Ldl Blood	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.initial_ldl_blood`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_16`.
Initial Hdl Blood	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.initial_hdl_blood`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_15`.
Initial Sigmoid Acten Dinh	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.initial_sigmoid_acten_dinh`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_19`.
Initial Sigmoid Acten Dstim	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.initial_sigmoid_acten_dstim`	Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_18`.

Outputs

Output	Maps To	Role
`state`	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.state`	Available to the visualization model and downstream workflows.
`summary`	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.summary`	Available to the visualization model and downstream workflows.
`species_labels`	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.species_labels`	Available to the visualization model and downstream workflows.
`sum_rec_bcells`	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.sum_rec_bcells`	Available to the visualization model and downstream workflows.
`bcells`	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.bcells`	Available to the visualization model and downstream workflows.
`ldl_blood`	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.ldl_blood`	Available to the visualization model and downstream workflows.
`hdl_blood`	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.hdl_blood`	Available to the visualization model and downstream workflows.
`sigmoid_acten_dinh`	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.sigmoid_acten_dinh`	Available to the visualization model and downstream workflows.
`sigmoid_acten_dstim`	`systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.sigmoid_acten_dstim`	Available to the visualization model and downstream workflows.

Runtime

Duration: 1.0
Communication step: 0.1

Running Locally

biosimulant labs serve

This model is from the article: Workflow for generating competing hypothesis from models with parameter uncertainty. David Gomez-Cabrero, Albert Compte and Jesper Tegner Interface Focus 6 June 2011 vo.

Runtime

Duration1

Comms Step0.1

Runs

Total0

Completed0

Failed0

Metadata

Packagegomez-cabrero2011-atherogenesis-lab

Created2026-05-17

Updated2026-05-17

generegulationsystemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_sum_rec_bcells",
        "label": "Initial Sum Rec Bcells",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.initial_sum_rec_bcells",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_14`."
      },
      {
        "name": "initial_bcells",
        "label": "Initial Bcells",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.initial_bcells",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_8`."
      },
      {
        "name": "initial_ldl_blood",
        "label": "Initial Ldl Blood",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.initial_ldl_blood",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_16`."
      },
      {
        "name": "initial_hdl_blood",
        "label": "Initial Hdl Blood",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.initial_hdl_blood",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_15`."
      },
      {
        "name": "initial_sigmoid_acten_dinh",
        "label": "Initial Sigmoid Acten Dinh",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.initial_sigmoid_acten_dinh",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_19`."
      },
      {
        "name": "initial_sigmoid_acten_dstim",
        "label": "Initial Sigmoid Acten Dstim",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.initial_sigmoid_acten_dstim",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `species_18`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.species_labels"
      },
      {
        "name": "sum_rec_bcells",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.sum_rec_bcells"
      },
      {
        "name": "bcells",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.bcells"
      },
      {
        "name": "ldl_blood",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.ldl_blood"
      },
      {
        "name": "hdl_blood",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.hdl_blood"
      },
      {
        "name": "sigmoid_acten_dinh",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.sigmoid_acten_dinh"
      },
      {
        "name": "sigmoid_acten_dstim",
        "maps_to": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.sigmoid_acten_dstim"
      }
    ]
  },
  "tags": [
    "generegulation",
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Gomez Cabrero2011 Atherogenesis Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model",
      "alias": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model_state"
      ],
      "from": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model_summary"
      ],
      "from": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model_species_labels"
      ],
      "from": "systemsbiology_sbml_gomez_cabrero2011_atherogenesis_model1002160000_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "This model is from the article: Workflow for generating competing hypothesis from models with parameter uncertainty. David Gomez-Cabrero, Albert Compte and Jesper Tegner Interface Focus 6 June 2011 vo.",
  "schema_version": "2.0"
}

Select a run from History to view its results.