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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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Pharmacokinetic models are mathematical constructs that represent and predict the time course of drug concentrations in the body, providing meaningful pharmacokinetic parameters. These models are categorized into compartment, physiological, and distributed parameter models.
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The link model is a fundamental pharmacokinetic-pharmacodynamic (PK–PD) approach to account for delayed drug responses when the observed effect does not immediately correlate with the drug's plasma concentration peak. This delay is mathematically addressed by introducing an effect compartment concentration, Ce, which is kinetically linked to the plasma concentration, Cp, via a first-order rate constant, ke0. The linkage allows for a more accurate prediction of drug effects over time. A...
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Related Experiment Video

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SEEK: a systems biology data and model management platform.

Katherine Wolstencroft1, Stuart Owen2, Olga Krebs3

  • 1Leiden Institute of Advanced Computer Science Leiden Institute of Advanced Computer Science, Leiden University, 111 Snellius, Niels Bohrweg 1, Leiden, CA, 2333, Netherlands. k.j.wolstencroft@liacs.leidenuniv.nl.

BMC Systems Biology
|July 11, 2015
PubMed
Summary

The SEEK platform offers integrated tools for managing and sharing diverse biological data and models, crucial for systems biology research. It facilitates collaboration and data linking, enhancing biological process modeling and prediction.

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Area of Science:

  • Systems Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Systems biology research necessitates integrating heterogeneous data types for modeling biological processes.
  • Current data and model storage in silos hinders interdependencies crucial for systems biology.
  • Researchers need a unified environment for managing and sharing experimental data and models.

Purpose of the Study:

  • To present the SEEK platform as a solution for managing, sharing, and exploring systems biology data and models.
  • To highlight SEEK's capabilities in linking experiments, protocols, data, and models.
  • To showcase SEEK's utility for both daily collaboration and public data dissemination.

Main Methods:

  • Development of a plug-in architecture for configurable linking of experimental components.
  • Implementation of web-based, access-controlled environment for data and model exchange.
  • Integration of tools for model simulation, data plotting, annotation, and standardization.
  • Utilization of semantic web resources for metadata extraction and RDF generation.

Main Results:

  • SEEK provides a unified platform for managing and sharing diverse systems biology data and models.
  • Its plug-in architecture enables flexible linking of experiments, data, and models.
  • SEEK supports data analysis through integrated tools and facilitates semantic queries via RDF.

Conclusions:

  • The SEEK platform is widely adopted by European systems biology consortia.
  • It offers a low-barrier, collaborative environment for data management.
  • SEEK supports diverse systems biology initiatives like SysMO and the Virtual Liver Network.