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Title:Making PBPK models more reproducible in practice
Authors:ID Domínguez-Romero, Elena (Author)
ID Mazurenko, Stanislav (Author)
ID Scheringer, Martin (Author)
ID Martins dos Santos, Vitor A. P. (Author)
ID Evelo, Chris T (Author)
ID Anton, Mihail (Author)
ID Hancock, John M. (Author)
ID Županič, Anže (Author)
ID Suarez-Diez, Maria (Author)
Files:URL URL - Source URL, visit https://doi.org/10.1093/bib/bbae569
 
.pdf PDF - Presentation file, download (1,06 MB)
MD5: 50C68A9D6F794B6A39804254118ECDA9
 
Language:English
Typology:1.01 - Original Scientific Article
Organization:Logo NIB - National Institute of Biology
Abstract:Systems biology aims to understand living organisms through mathematically modeling their behaviors at different organizational levels, ranging from molecules to populations. Modeling involves several steps, from determining the model purpose to developing the mathematical model, implementing it computationally, simulating the model’s behavior, evaluating, and refining the model. Importantly, model simulation results must be reproducible, ensuring that other researchers can obtain the same results after writing the code de novo and/or using different software tools. Guidelines to increase model reproducibility have been published. However, reproducibility remains a major challenge in this field. In this paper, we tackle this challenge for physiologically-based pharmacokinetic (PBPK) models, which represent the pharmacokinetics of chemicals following exposure in humans or animals. We summarize recommendations for PBPK model reporting that should apply during model development and implementation, in order to ensure model reproducibility and comprehensibility. We make a proposal aiming to harmonize abbreviations used in PBPK models. To illustrate these recommendations, we present an original and reproducible PBPK model code in MATLAB, alongside an example of MATLAB code converted to Systems Biology Markup Language format using MOCCASIN. As directions for future improvement, more tools to convert computational PBPK models from different software platforms into standard formats would increase the interoperability of these models. The application of other systems biology standards to PBPK models is encouraged. This work is the result of an interdisciplinary collaboration involving the ELIXIR systems biology community. More interdisciplinary collaborations like this would facilitate further harmonization and application of good modeling practices in different systems biology fields.
Keywords:pharmacokinetics, pharmacodynamics, mathematical modelling, standards, model code, reproducibility, SBML, MATLAB, systems biology
Publication status:Published
Publication version:Version of Record
Publication date:04.11.2024
Year of publishing:2024
Number of pages:str.1-13
Numbering:Vol. 25, iss. 6, [article no.] bbae569
UDC:57
ISSN on article:1477-4054
DOI:10.1093/bib/bbae569 New window
COBISS.SI-ID:214014467 New window
Note:Soavtorji: Stanislav Mazurenko, Martin Scheringer, Vítor A. P. Martins dos Santos, Chris T. Evelo, Mihail Anton, John M. Hancock, Anže Županič, Maria Suarez-Diez; Nasl. z nasl. zaslona; Opis vira z dne 7. 11. 2024;
Publication date in DiRROS:07.11.2024
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Downloads:6
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Record is a part of a journal

Title:Briefings in bioinformatics
Shortened title:Brief Bioinform
Publisher:Henry Stewart, Oxford Journals
ISSN:1477-4054
COBISS.SI-ID:3210260 New window

Document is financed by a project

Funder:EC - European Commission
Project number:733032
Name:European Human Biomonitoring Initiative
Acronym:HBM4EU

Funder:EC - European Commission
Project number:857560
Name:CETOCOEN Excellence
Acronym:CETOCOEN Excellence

Funder:NWO - Netherlands Organisation for Scientific Research
Funding programme:Netherlands Research Agenda: Research on Routes by Consortia
Project number:NWA-ORC 1292.19.272

Funder:Other - Other funder or multiple funders
Funding programme:Ministry of Education, Youth and Sports of the Czech Republic
Project number:ESFRI RECETOX RI LM2023069 and ESFRI ELIXIR LM2023055

Licences

License:CC BY 4.0, Creative Commons Attribution 4.0 International
Link:http://creativecommons.org/licenses/by/4.0/
Description:This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

Language:Slovenian
Keywords:farmakokinetika, farmakodinamika, matematično modeliranje, standardi, sistemska biologija


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