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Proctor2008 P53 Mdm2 Circuit P53 Stabilisation By Atm Lab

About lab

Proctor2008 P53 Mdm2 Circuit P53 Stabilisation By Atm

This Biosimulant lab wraps Proctor2008 P53 Mdm2 Circuit P53 Stabilisation By Atm as a runnable systems biology model with a companion visualization module. Proctor2008 - p53/Mdm2 circuit - p53 stabilisation by ATM This model is described in the article: Explaining oscillations and variability in the p53-Mdm2 system. 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: Proctor2008 - p53/Mdm2 circuit - p53 stabilisation by ATM. 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 P53 MRNA, Mdm2 MRNA, ATMI, Mdm2 P53, P53, and Mdm2, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, Mdm2 moved from 5.000 to 5.048 across 1.0 simulation windows.

Output Visualizations

Proctor2008 P53 Mdm2 Circuit P53 Stabilisation By Atm - run interpretation

Summary table for Proctor2008 P53 Mdm2 Circuit P53 Stabilisation By Atm, reporting the scientific question, observed answer, dominant module, and caveat.

Proctor2008 P53 Mdm2 Circuit P53 Stabilisation By Atm - timeseries visualization

Trajectories of Mdm2, Mdm2 P53, P53, Mdm2 MRNA, P53 MRNA, and ATMI across the 1.0 simulation. In this run Mdm2 climbed from 5.000 to 5.048 and Mdm2 P53 fell from 95.000 to 94.955 — the largest movements among the focused observables.

Proctor2008 P53 Mdm2 Circuit P53 Stabilisation By Atm - excursions bar

Largest-excursion ranking of the focused observables — the absolute movement magnitude during the run. Top 3: Mdm2 = 0.0478, Mdm2 P53 = 0.0453, P53 = 0.0288, with 1 more observable below.

Proctor2008 P53 Mdm2 Circuit P53 Stabilisation By Atm - endpoint snapshot bar

Endpoint snapshot of the focused observables — final values from the captured run. Top 3 by value: ATMI = 200.0, Mdm2 P53 = 94.955, P53 MRNA = 10.000, with 3 more observables below.

Proctor2008 P53 Mdm2 Circuit P53 Stabilisation By Atm - visualization

Visualization card from the Proctor2008 P53 Mdm2 Circuit P53 Stabilisation By Atm dark-mode run.

Model Context

  • Core model: models/core
  • Visualization model: models/visualisation
  • Standard: other
  • Upstream source: biomodels_ebi:BIOMD0000000188
  • License: CC0

Inputs

InputMaps ToDefaultNotes
Initial P53 MRNAsystemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.initial_p53_mrnaSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol p53_mRNA.
Initial Mdm2 MRNAsystemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.initial_mdm2_mrnaSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Mdm2_mRNA.
Initial Atmisystemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.initial_atmiSource state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol ATMI.
Initial Mdm2 P53systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.initial_mdm2_p53Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Mdm2_p53.
Initial Model State P53systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.initial_model_state_p53Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol p53.
Initial Mdm2systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.initial_mdm2Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol Mdm2.

Outputs

OutputMaps ToRole
statesystemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.stateAvailable to the visualization model and downstream workflows.
summarysystemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.summaryAvailable to the visualization model and downstream workflows.
species_labelssystemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.species_labelsAvailable to the visualization model and downstream workflows.
p53_mrnasystemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.p53_mrnaAvailable to the visualization model and downstream workflows.
mdm2_mrnasystemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.mdm2_mrnaAvailable to the visualization model and downstream workflows.
atmisystemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.atmiAvailable to the visualization model and downstream workflows.
mdm2_p53systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.mdm2_p53Available to the visualization model and downstream workflows.
p53systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.p53Available to the visualization model and downstream workflows.
mdm2systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.mdm2Available to the visualization model and downstream workflows.

Runtime

  • Duration: 1.0
  • Communication step: 0.1

Running Locally

biosimulant labs serve

Proctor2008 - p53/Mdm2 circuit - p53 stabilisation by ATM This model is described in the article: Explaining oscillations and variability in the p53-Mdm2 system. It can be used to explore systemsbiology proctor2008 p53 mdm2 circuit p53 dynamics and compare simulation behavior across conditions.

Runtime

Duration1
Comms Step0.1

Runs

Total0
Completed0
Failed0

Metadata

Packageproctor2008-p53-mdm2-circuit-p53-stabilisation-by-atm-lab
Created2026-05-17
Updated2026-05-17
systemsbiologysbmlbiomodels_ebifaithfulcuratedvisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "initial_p53_mrna",
        "label": "Initial P53 MRNA",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.initial_p53_mrna",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `p53_mRNA`."
      },
      {
        "name": "initial_mdm2_mrna",
        "label": "Initial Mdm2 MRNA",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.initial_mdm2_mrna",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Mdm2_mRNA`."
      },
      {
        "name": "initial_atmi",
        "label": "Initial Atmi",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.initial_atmi",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `ATMI`."
      },
      {
        "name": "initial_mdm2_p53",
        "label": "Initial Mdm2 P53",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.initial_mdm2_p53",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Mdm2_p53`."
      },
      {
        "name": "initial_model_state_p53",
        "label": "Initial Model State P53",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.initial_model_state_p53",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `p53`."
      },
      {
        "name": "initial_mdm2",
        "label": "Initial Mdm2",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.initial_mdm2",
        "description": "Source state initial condition exposed as a model-specific control because no explicit intervention parameter is identifiable. Maps to SBML symbol `Mdm2`."
      }
    ],
    "outputs": [
      {
        "name": "state",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.state"
      },
      {
        "name": "summary",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.summary"
      },
      {
        "name": "species_labels",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.species_labels"
      },
      {
        "name": "p53_mrna",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.p53_mrna"
      },
      {
        "name": "mdm2_mrna",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.mdm2_mrna"
      },
      {
        "name": "atmi",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.atmi"
      },
      {
        "name": "mdm2_p53",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.mdm2_p53"
      },
      {
        "name": "p53",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.p53"
      },
      {
        "name": "mdm2",
        "maps_to": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.mdm2"
      }
    ]
  },
  "tags": [
    "systemsbiology",
    "sbml",
    "biomodels_ebi",
    "faithful",
    "curated"
  ],
  "title": "Proctor2008 P53 Mdm2 Circuit P53 Stabilisation By Atm Lab",
  "models": [
    {
      "path": "owned/models/systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model",
      "alias": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model",
      "provenance": {
        "owned_path": "owned/models/systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model_state"
      ],
      "from": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.state"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model_summary"
      ],
      "from": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.summary"
    },
    {
      "to": [
        "visualisation.systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model_species_labels"
      ],
      "from": "systemsbiology_sbml_proctor2008_p53_mdm2_circuit_p53_stabilisation_b_biomd0000000188_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 1,
    "initial_inputs": {},
    "communication_step": 0.1
  },
  "description": "Proctor2008 - p53/Mdm2 circuit - p53 stabilisation by ATM This model is described in the article: Explaining oscillations and variability in the p53-Mdm2 system. It can be used to explore systemsbiology proctor2008 p53 mdm2 circuit p53 dynamics and compare simulation behavior across conditions.",
  "schema_version": "2.0"
}

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