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Naslov:Making PBPK models more reproducible in practice
Avtorji:ID Domínguez-Romero, Elena (Avtor)
ID Mazurenko, Stanislav (Avtor)
ID Scheringer, Martin (Avtor)
ID Martins dos Santos, Vitor A. P. (Avtor)
ID Evelo, Chris T (Avtor)
ID Anton, Mihail (Avtor)
ID Hancock, John M. (Avtor)
ID Županič, Anže (Avtor)
ID Suarez-Diez, Maria (Avtor)
Datoteke:URL URL - Izvorni URL, za dostop obiščite https://doi.org/10.1093/bib/bbae569
 
.pdf PDF - Predstavitvena datoteka, prenos (1,06 MB)
MD5: 50C68A9D6F794B6A39804254118ECDA9
 
Jezik:Angleški jezik
Tipologija:1.01 - Izvirni znanstveni članek
Organizacija:Logo NIB - Nacionalni inštitut za biologijo
Povzetek: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.
Ključne besede:pharmacokinetics, pharmacodynamics, mathematical modelling, standards, model code, reproducibility, SBML, MATLAB, systems biology
Status publikacije:Objavljeno
Verzija publikacije:Objavljena publikacija
Datum objave:04.11.2024
Leto izida:2024
Št. strani:str.1-13
Številčenje:Vol. 25, iss. 6, [article no.] bbae569
UDK:57
ISSN pri članku:1477-4054
DOI:10.1093/bib/bbae569 Novo okno
COBISS.SI-ID:214014467 Novo okno
Opomba: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;
Datum objave v DiRROS:07.11.2024
Število ogledov:10
Število prenosov:6
Metapodatki:XML DC-XML DC-RDF
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Gradivo je del revije

Naslov:Briefings in bioinformatics
Skrajšan naslov:Brief Bioinform
Založnik:Henry Stewart, Oxford Journals
ISSN:1477-4054
COBISS.SI-ID:3210260 Novo okno

Gradivo je financirano iz projekta

Financer:EC - European Commission
Številka projekta:733032
Naslov:European Human Biomonitoring Initiative
Akronim:HBM4EU

Financer:EC - European Commission
Številka projekta:857560
Naslov:CETOCOEN Excellence
Akronim:CETOCOEN Excellence

Financer:NWO - Netherlands Organisation for Scientific Research
Program financ.:Netherlands Research Agenda: Research on Routes by Consortia
Številka projekta:NWA-ORC 1292.19.272

Financer:Drugi - Drug financer ali več financerjev
Program financ.:Ministry of Education, Youth and Sports of the Czech Republic
Številka projekta:ESFRI RECETOX RI LM2023069 and ESFRI ELIXIR LM2023055

Licence

Licenca:CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
Povezava:http://creativecommons.org/licenses/by/4.0/deed.sl
Opis:To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.

Sekundarni jezik

Jezik:Slovenski jezik
Ključne besede:farmakokinetika, farmakodinamika, matematično modeliranje, standardi, sistemska biologija


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