Making PBPK models more reproducible in practice

J 2024

Making PBPK models more reproducible in practice

DOMINGUEZ ROMERO, Elena; Stanislav MAZURENKO; Martin SCHERINGER; Martins Vitor A. P. DOS SANTOS; Chris T. EVELO et al.

Základní údaje

Originální název

Making PBPK models more reproducible in practice

Autoři

DOMINGUEZ ROMERO, Elena; Stanislav MAZURENKO; Martin SCHERINGER; Martins Vitor A. P. DOS SANTOS; Chris T. EVELO; Mihail ANTON; John M. HANCOCK; Anze ZUPANIC a Maria SUAREZ-DIEZ

Vydání

Briefings in Bioinformatics, Oxford (UK), Oxford University Press, 2024, 1467-5463

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10609 Biochemical research methods

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 7.700

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/24:00138646

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

systems biology; pharmacokinetics; model code; reproducibility; SBML; MATLAB

Štítky

14314010, 143180, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 23. 6. 2025 19:55, Mgr. Michaela Hylsová, Ph.D.

Anotace

V originále

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.

Návaznosti

LM2023055, projekt VaV

Název: Česká národní infrastruktura pro biologická data

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, ELIXIR-CZ: Česká národní infrastruktura pro biologická data

733032, interní kód MU

Název: European Human Biomonitoring Initiative (Akronym: HBM4EU)

Investor: Evropská unie, European Human Biomonitoring Initiative, Health, demographic change and wellbeing (Societal Challenges)

857560, interní kód MU
(Kód CEP: EF17_043/0009632)

Název: CETOCOEN Excellence (Akronym: CETOCOEN Excellence)

Investor: Evropská unie, CETOCOEN Excellence, Spreading excellence and widening participation

90269, velká výzkumná infrastruktura

Název: RECETOX RI II

Přiložené soubory

2471501.pdf

Citovat

DOMINGUEZ ROMERO, Elena; Stanislav MAZURENKO; Martin SCHERINGER; Martins Vitor A. P. DOS SANTOS; Chris T. EVELO; Mihail ANTON; John M. HANCOCK; Anze ZUPANIC a Maria SUAREZ-DIEZ. Making PBPK models more reproducible in practice. Briefings in Bioinformatics. Oxford (UK): Oxford University Press, 2024, roč. 25, č. 6, s. 1-13. ISSN 1467-5463. Dostupné z: https://doi.org/10.1093/bib/bbae569.

@article{2471501,
   author = {Dominguez Romero, Elena and Mazurenko, Stanislav and Scheringer, Martin and dos Santos, Martins Vitor A. P. and Evelo, Chris T. and Anton, Mihail and Hancock, John M. and Zupanic, Anze and SuarezandDiez, Maria},
   article_location = {Oxford (UK)},
   article_number = {6},
   doi = {https://doi.org/10.1093/bib/bbae569},
   keywords = {systems biology; pharmacokinetics; model code; reproducibility; SBML; MATLAB},
   language = {eng},
   issn = {1467-5463},
   journal = {Briefings in Bioinformatics},
   note = {Nedoplňovat EF17_043/0009632.},
   title = {Making PBPK models more reproducible in practice},
   url = {https://academic.oup.com/bib/article/25/6/bbae569/7874879?login=false},
   volume = {25},
   year = {2024}
}

TY  - JOUR
ID  - 2471501
AU  - Dominguez Romero, Elena - Mazurenko, Stanislav - Scheringer, Martin - dos Santos, Martins Vitor A. P. - Evelo, Chris T. - Anton, Mihail - Hancock, John M. - Zupanic, Anze - Suarez-Diez, Maria
PY  - 2024
TI  - Making PBPK models more reproducible in practice
JF  - Briefings in Bioinformatics
VL  - 25
IS  - 6
SP  - 1-13
EP  - 1-13
PB  - Oxford University Press
SN  - 14675463
N1  - Nedoplňovat EF17_043/0009632.
KW  - systems biology
KW  - pharmacokinetics
KW  - model code
KW  - reproducibility
KW  - SBML
KW  - MATLAB
UR  - https://academic.oup.com/bib/article/25/6/bbae569/7874879?login=false
N2  - 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.
ER  -

DOMINGUEZ ROMERO, Elena; Stanislav MAZURENKO; Martin SCHERINGER; Martins Vitor A. P. DOS SANTOS; Chris T. EVELO; Mihail ANTON; John M. HANCOCK; Anze ZUPANIC a Maria SUAREZ-DIEZ. Making PBPK models more reproducible in practice. \textit{Briefings in Bioinformatics}. Oxford (UK): Oxford University Press, 2024, roč.~25, č.~6, s.~1-13. ISSN~1467-5463. Dostupné z: https://doi.org/10.1093/bib/bbae569.

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