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Kuhn2009 Endomesodermnetwork Lab

About lab

Kuhn2009 Endomesodermnetwork

This Biosimulant lab wraps Kuhn2009 Endomesodermnetwork as a runnable systems biology model with a companion visualization module. This a model from the article: Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network. 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: Kuhn2009_EndoMesodermNetwork. 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 mRNA_P_VEGFR, mRNA_M_VEGFR, mRNA_E_VEGFR, PROTEIN_P_VEGFSignal, PROTEIN_P_VEGFR, and PROTEIN_M_VEGFSignal, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, mRNA_P_VEGFR moved from 0 to 1.298 across 1.0 simulation windows.

Output Visualizations

Kuhn2009 Endomesodermnetwork - run interpretation

Summary table for Kuhn2009 Endomesodermnetwork, reporting the scientific question, observed answer, dominant module, and caveat.

Kuhn2009 Endomesodermnetwork - timeseries visualization

Trajectories of mRNA_P_VEGFR, PROTEIN_P_VEGFSignal, PROTEIN_P_VEGFR, mRNA_M_VEGFR, mRNA_E_VEGFR, and PROTEIN_M_VEGFSignal across the 1.0 simulation. In this run mRNA_P_VEGFR climbed from 0 to 1.298 — the largest movements among the focused observables.

Kuhn2009 Endomesodermnetwork - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: mRNA_P_VEGFR = 1.298, PROTEIN_P_VEGFSignal = 0.7128, PROTEIN_P_VEGFR = 0.2879.

Kuhn2009 Endomesodermnetwork - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: mRNA_P_VEGFR = 1.298, PROTEIN_P_VEGFSignal = 0.7128, PROTEIN_P_VEGFR = 0.2238.

Kuhn2009 Endomesodermnetwork - visualization

Visualization card from the Kuhn2009 Endomesodermnetwork dark-mode run.

Model Context

  • Core model: models/core
  • Visualization model: models/visualisation
  • Standard: other
  • Upstream source: biomodels_ebi:BIOMD0000000235
  • License: CC0

Inputs

InputMaps ToDefaultNotes
Initial MRNA P Vegfrsystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.initial_mrna_p_vegfrSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol mRNA_P_VEGFR.
Initial MRNA M Vegfrsystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.initial_mrna_m_vegfrSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol mRNA_M_VEGFR.
Initial MRNA E Vegfrsystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.initial_mrna_e_vegfrSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol mRNA_E_VEGFR.
Initial Protein P Vegf Signalsystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.initial_protein_p_vegf_signalSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol PROTEIN_P_VEGFSignal.
Initial Protein P Vegfrsystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.initial_protein_p_vegfrSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol PROTEIN_P_VEGFR.
Initial Protein M Vegf Signalsystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.initial_protein_m_vegf_signalSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol PROTEIN_M_VEGFSignal.

Outputs

OutputMaps ToRole
statesystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.stateAvailable to the visualization model and downstream workflows.
summarysystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.summaryAvailable to the visualization model and downstream workflows.
species_labelssystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.species_labelsAvailable to the visualization model and downstream workflows.
mrna_p_vegfrsystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.mrna_p_vegfrAvailable to the visualization model and downstream workflows.
mrna_m_vegfrsystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.mrna_m_vegfrAvailable to the visualization model and downstream workflows.
mrna_e_vegfrsystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.mrna_e_vegfrAvailable to the visualization model and downstream workflows.
protein_p_vegf_signalsystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.protein_p_vegf_signalAvailable to the visualization model and downstream workflows.
protein_p_vegfrsystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.protein_p_vegfrAvailable to the visualization model and downstream workflows.
protein_m_vegf_signalsystemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.protein_m_vegf_signalAvailable to the visualization model and downstream workflows.

Runtime

  • Duration: 1.0
  • Communication step: 0.1

Running Locally

biosimulant labs serve

This a model from the article: Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network. Kühn C, Wierling C, Kühn A, Klipp E, Panopoulou G, Lehrach H, Poustka AJ.

Runtime

Duration1
Comms Step0.1

Runs

Total0
Completed0
Failed0

Metadata

Packagekuhn2009-endomesodermnetwork-lab
Created2026-05-17
Updated2026-05-17
systemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_mrna_p_vegfr",
        "label": "Initial MRNA P Vegfr",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.initial_mrna_p_vegfr",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `mRNA_P_VEGFR`."
      },
      {
        "name": "initial_mrna_m_vegfr",
        "label": "Initial MRNA M Vegfr",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.initial_mrna_m_vegfr",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `mRNA_M_VEGFR`."
      },
      {
        "name": "initial_mrna_e_vegfr",
        "label": "Initial MRNA E Vegfr",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.initial_mrna_e_vegfr",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `mRNA_E_VEGFR`."
      },
      {
        "name": "initial_protein_p_vegf_signal",
        "label": "Initial Protein P Vegf Signal",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.initial_protein_p_vegf_signal",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `PROTEIN_P_VEGFSignal`."
      },
      {
        "name": "initial_protein_p_vegfr",
        "label": "Initial Protein P Vegfr",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.initial_protein_p_vegfr",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `PROTEIN_P_VEGFR`."
      },
      {
        "name": "initial_protein_m_vegf_signal",
        "label": "Initial Protein M Vegf Signal",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.initial_protein_m_vegf_signal",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `PROTEIN_M_VEGFSignal`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.species_labels"
      },
      {
        "name": "mrna_p_vegfr",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.mrna_p_vegfr"
      },
      {
        "name": "mrna_m_vegfr",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.mrna_m_vegfr"
      },
      {
        "name": "mrna_e_vegfr",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.mrna_e_vegfr"
      },
      {
        "name": "protein_p_vegf_signal",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.protein_p_vegf_signal"
      },
      {
        "name": "protein_p_vegfr",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.protein_p_vegfr"
      },
      {
        "name": "protein_m_vegf_signal",
        "maps_to": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.protein_m_vegf_signal"
      }
    ]
  },
  "tags": [
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Kuhn2009 Endomesodermnetwork Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model",
      "alias": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model_state"
      ],
      "from": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model_summary"
      ],
      "from": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model_species_labels"
      ],
      "from": "systemsbiology_sbml_kuhn2009_endomesodermnetwork_biomd0000000235_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "This a model from the article: Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network. Kühn C, Wierling C, Kühn A, Klipp E, Panopoulou G, Lehrach H, Poustka AJ.",
  "schema_version": "2.0"
}

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