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Updated: Jun 8, 2025

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

Making PBPK models more reproducible in practice.

Elena Domínguez-Romero^1,2, Stanislav Mazurenko^3,4, Martin Scheringer²

¹Department of Bioinformatics-BiGCaT, School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.

Briefings in Bioinformatics

|November 4, 2024

Summary

This summary is machine-generated.

Reproducible physiologically-based pharmacokinetic (PBPK) models are crucial for systems biology. This study proposes reporting recommendations and harmonized abbreviations to enhance PBPK model reproducibility and interoperability.

Keywords:

MATLAB SBML model code pharmacokinetics reproducibility systems biology

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Area of Science:

Systems biology
Computational modeling
Pharmacokinetics

Background:

Systems biology relies on mathematical modeling for understanding biological systems.
Reproducibility of computational models is a significant challenge in the field.
Physiologically-based pharmacokinetic (PBPK) models are essential for assessing chemical exposure effects.

Purpose of the Study:

To address the challenge of reproducibility in PBPK models.
To propose recommendations for PBPK model reporting during development and implementation.
To harmonize abbreviations used in PBPK modeling.

Main Methods:

Summarizing PBPK model reporting guidelines.
Proposing a standardized abbreviation system for PBPK models.
Developing and presenting a reproducible PBPK model code in MATLAB.

Main Results:

An original, reproducible PBPK model code in MATLAB is provided.
An example of converting MATLAB PBPK code to Systems Biology Markup Language (SBML) using MOCCASIN is demonstrated.
Recommendations for PBPK model reporting and abbreviation harmonization are presented.

Conclusions:

Adherence to reporting guidelines and standardized abbreviations enhances PBPK model reproducibility and comprehensibility.
Increased tool development for cross-platform model conversion is needed for better interoperability.
Interdisciplinary collaborations are vital for advancing good modeling practices in systems biology.