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Model Approaches for Pharmacokinetic Data: Physiological Models01:15

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Physiological models in pharmacokinetics are instrumental in understanding the distribution and elimination of drugs within the body. These models describe the drug concentration within target organs, influenced by factors such as drug uptake, tissue volume, and blood flow. Drug uptake is governed by the partition coefficient, which signifies the drug concentration ratio in tissue to that in the blood. The blood flow rate to a specific tissue is expressed as Qt, and the rate of change in tissue...
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Mechanistic models, a category encompassing both physiological and compartmental modeling, differ from empirical models' approaches to incorporating known factors about the systems being modeled. Empirical models describe data with minimal assumptions, while mechanistic models aim to provide a robust description of available data by specifying assumptions and integrating known factors about the system. Compartmental analysis is a key example of a mechanistic model in pharmacokinetics and...
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Modular modelling with Physiome standards.

Michael T Cooling1, David P Nickerson1, Poul M F Nielsen1,2

  • 1Auckland Bioengineering Institute, the University of Auckland, New Zealand.

The Journal of Physiology
|June 30, 2016
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Summary
This summary is machine-generated.

We propose new design principles for building complex computational models using CellML. These principles ensure models are reusable and extensible, facilitating the creation of integrated physiological systems for virtual experiments.

Keywords:
modellingmodularityphysiomestandards

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Area of Science:

  • Computational Biology
  • Systems Biology
  • Physiology

Background:

  • Computational models are increasingly complex, yet design principles for their construction are underdeveloped.
  • Reuse of existing models is crucial for developing large-scale, multi-scale physiological frameworks.

Purpose of the Study:

  • To establish a set of design principles for constructing complex, reusable, and extensible computational models in CellML.
  • To demonstrate these principles through an integrated whole-cell model prototype.

Main Methods:

  • Development of a novel set of design principles for CellML model construction.
  • Illustration of principles with an architectural prototype linking electrophysiology, metabolism, signaling, gene regulation, and synthetic biology.

Main Results:

  • Generated models are extensible and suitable for reuse in larger, more complex models.
  • An architectural prototype demonstrating the integration of diverse biological processes in a single CellML model was created.

Conclusions:

  • The proposed design principles facilitate the creation of composable, characterized, and simulatable quantitative descriptions of physiology.
  • These principles complement existing Physiome tools and frameworks, enhancing their utility for the modeling community.