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Grzegorzewski2022 - PBPK model of dextromethorphan Lab

About lab

Grzegorzewski2022 - PBPK model of dextromethorphan

This Biosimulant lab wraps Grzegorzewski2022 - PBPK model of dextromethorphan as a runnable pharmacology model with a companion visualization module. Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan. It can be used to explore drug-exposure and pathway-response dynamics and compare scenario outcomes across configurations.

What You'll See

The lab asks: How do route and CYP2D6 activity shape dextromethorphan and metabolite exposure? It runs for 24.0 time units with a communication step of 1.0. The run uses the model defaults declared by the curated SBML wrapper. The generated visualizations focus on Dextromethorphan Liver Plasma, Dextromethorphan Gut Plasma, Dextromethorphan Kidney Plasma, Dextromethorphan Lung Plasma, Dextorphan Liver Plasma, and Dextorphan Glucuronide Liver Plasma, combining trajectory, endpoint-comparison, and summary-table views from one completed dark-mode run.

In this captured run, dextromethorphan (liver) moved from 0 to 0 across 24.0 simulation windows.

Output Visualizations

Grzegorzewski2022 - PBPK model of dextromethorphan - run interpretation

Summary table for Grzegorzewski2022 - PBPK model of dextromethorphan, reporting the scientific question, observed answer, dominant module, and caveat.

Grzegorzewski2022 - PBPK model of dextromethorphan - timeseries visualization

Trajectories of dextromethorphan (liver), dextromethorphan (gut), dextorphan (liver), dextorphan glucuronide (liver), dextromethorphan (kidney), and dextromethorphan (lung) across the 24.0 simulation. In this run dextromethorphan (liver), dextromethorphan (gut), dextorphan (liver), dextorphan glucuronide (liver) stayed near their initial values — no observable moved appreciably.

Model Context

  • Core model: models/core
  • Visualization model: models/visualisation
  • Standard: sbml
  • Upstream source: biomodels_ebi:MODEL2301090002
  • License: CC0

Inputs

InputMaps ToDefaultNotes
Oral Dextromethorphan Dose Mgpharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.oral_dextromethorphan_dose_mgUses the model default unless overridden at run time.
IV Dextromethorphan Bolus Mgpharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.iv_dextromethorphan_bolus_mgUses the model default unless overridden at run time.
Dextromethorphan Infusion Rate Mg Per Minpharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextromethorphan_infusion_rate_mg_per_minUses the model default unless overridden at run time.
CYP2D6 Custom Activitypharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.cyp2d6_custom_activityUses the model default unless overridden at run time.
CYP2D6 VMAXpharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.cyp2d6_vmaxUses the model default unless overridden at run time.
CYP3A4 VMAXpharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.cyp3a4_vmaxUses the model default unless overridden at run time.

Outputs

OutputMaps ToRole
statepharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.stateAvailable to the visualization model and downstream workflows.
summarypharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.summaryAvailable to the visualization model and downstream workflows.
species_labelspharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.species_labelsAvailable to the visualization model and downstream workflows.
dextromethorphan_liver_plasmapharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextromethorphan_liver_plasmaAvailable to the visualization model and downstream workflows.
dextromethorphan_gut_plasmapharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextromethorphan_gut_plasmaAvailable to the visualization model and downstream workflows.
dextromethorphan_kidney_plasmapharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextromethorphan_kidney_plasmaAvailable to the visualization model and downstream workflows.
dextromethorphan_lung_plasmapharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextromethorphan_lung_plasmaAvailable to the visualization model and downstream workflows.
dextorphan_liver_plasmapharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextorphan_liver_plasmaAvailable to the visualization model and downstream workflows.
dextorphan_glucuronide_liver_plasmapharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextorphan_glucuronide_liver_plasmaAvailable to the visualization model and downstream workflows.

Runtime

  • Duration: 24.0
  • Communication step: 1.0

Running Locally

biosimulant labs serve .

Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan. It can be used to explore dose-response dynamics and compare treatment scenarios across conditions.

Runtime

Duration24
Comms Step1

Runs

Total0
Completed0
Failed0

Metadata

Packagegrzegorzewski2022-pbpk-model-of-dextromethorphan-lab
Created2026-05-16
Updated2026-05-16
pharmacologypbpkpharmacokineticsphysiologycyp-metabolismsbmltelluriumfaithfulbiomodels_ebivisualisation

Manifest

{
  "io": {
    "inputs": [
      {
        "name": "oral_dextromethorphan_dose_mg",
        "label": "Oral Dextromethorphan Dose Mg",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.oral_dextromethorphan_dose_mg"
      },
      {
        "name": "iv_dextromethorphan_bolus_mg",
        "label": "IV Dextromethorphan Bolus Mg",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.iv_dextromethorphan_bolus_mg"
      },
      {
        "name": "dextromethorphan_infusion_rate_mg_per_min",
        "label": "Dextromethorphan Infusion Rate Mg Per Min",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextromethorphan_infusion_rate_mg_per_min"
      },
      {
        "name": "cyp2d6_custom_activity",
        "label": "CYP2D6 Custom Activity",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.cyp2d6_custom_activity"
      },
      {
        "name": "cyp2d6_vmax",
        "label": "CYP2D6 VMAX",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.cyp2d6_vmax"
      },
      {
        "name": "cyp3a4_vmax",
        "label": "CYP3A4 VMAX",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.cyp3a4_vmax"
      }
    ],
    "outputs": [
      {
        "name": "state",
        "label": "Tracked source state",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.state"
      },
      {
        "name": "summary",
        "label": "Simulation summary",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.summary"
      },
      {
        "name": "species_labels",
        "label": "Observable labels",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.species_labels"
      },
      {
        "name": "dextromethorphan_liver_plasma",
        "label": "Dextromethorphan Liver Plasma",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextromethorphan_liver_plasma"
      },
      {
        "name": "dextromethorphan_gut_plasma",
        "label": "Dextromethorphan Gut Plasma",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextromethorphan_gut_plasma"
      },
      {
        "name": "dextromethorphan_kidney_plasma",
        "label": "Dextromethorphan Kidney Plasma",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextromethorphan_kidney_plasma"
      },
      {
        "name": "dextromethorphan_lung_plasma",
        "label": "Dextromethorphan Lung Plasma",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextromethorphan_lung_plasma"
      },
      {
        "name": "dextorphan_liver_plasma",
        "label": "Dextorphan Liver Plasma",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextorphan_liver_plasma"
      },
      {
        "name": "dextorphan_glucuronide_liver_plasma",
        "label": "Dextorphan Glucuronide Liver Plasma",
        "maps_to": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.dextorphan_glucuronide_liver_plasma"
      }
    ]
  },
  "tags": [
    "pharmacology",
    "pbpk",
    "pharmacokinetics",
    "physiology",
    "cyp-metabolism",
    "sbml",
    "tellurium",
    "faithful",
    "biomodels_ebi"
  ],
  "title": "Grzegorzewski2022 - PBPK model of dextromethorphan Lab",
  "models": [
    {
      "path": "owned/models/pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model",
      "alias": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model",
      "parameters": {
        "model_path": "data/MODEL2301090002.xml",
        "integration_step": 0.1
      },
      "provenance": {
        "owned_path": "owned/models/pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model"
      }
    },
    {
      "path": "owned/models/visualisation",
      "alias": "visualisation",
      "provenance": {
        "owned_path": "owned/models/visualisation"
      }
    }
  ],
  "wiring": [
    {
      "to": [
        "visualisation.pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model_state"
      ],
      "from": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.state"
    },
    {
      "to": [
        "visualisation.pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model_summary"
      ],
      "from": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.summary"
    },
    {
      "to": [
        "visualisation.pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model_species_labels"
      ],
      "from": "pharmacology_sbml_grzegorzewski2022_pbpk_model_of_dextromethorphan_model2301090002_model.species_labels"
    }
  ],
  "runtime": {
    "duration": 24,
    "initial_inputs": {},
    "communication_step": 1
  },
  "description": "Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan. It can be used to explore dose-response dynamics and compare treatment scenarios across conditions.",
  "schema_version": "2.0"
}

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