{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,13]],"date-time":"2026-06-13T20:29:54Z","timestamp":1781382594636,"version":"3.54.1"},"reference-count":57,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,11,4]],"date-time":"2024-11-04T00:00:00Z","timestamp":1730678400000},"content-version":"vor","delay-in-days":42,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 Research and Innovation Programme","award":["857560"],"award-info":[{"award-number":["857560"]}]},{"DOI":"10.13039\/501100001823","name":"Czech Ministry of Education, Youth and Sports","doi-asserted-by":"crossref","award":["ESFRI ELIXIR LM2023055"],"award-info":[{"award-number":["ESFRI ELIXIR LM2023055"]}],"id":[{"id":"10.13039\/501100001823","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001823","name":"Czech Ministry of Education, Youth and Sports","doi-asserted-by":"crossref","award":["ESFRI RECETOX RI LM2023069"],"award-info":[{"award-number":["ESFRI RECETOX RI LM2023069"]}],"id":[{"id":"10.13039\/501100001823","id-type":"DOI","asserted-by":"crossref"}]},{"name":"European Union\u2019s Horizon 2020","award":["HBM4EU"],"award-info":[{"award-number":["HBM4EU"]}]},{"name":"European Union\u2019s Horizon 2020","award":["733032"],"award-info":[{"award-number":["733032"]}]},{"name":"Netherlands Research Council","award":["NWA-ORC 1292.19.272"],"award-info":[{"award-number":["NWA-ORC 1292.19.272"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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\u2019s 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.<\/jats:p>","DOI":"10.1093\/bib\/bbae569","type":"journal-article","created":{"date-parts":[[2024,11,4]],"date-time":"2024-11-04T12:15:19Z","timestamp":1730722519000},"source":"Crossref","is-referenced-by-count":9,"title":["Making PBPK models more reproducible in practice"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9795-5628","authenticated-orcid":false,"given":"Elena","family":"Dom\u00ednguez-Romero","sequence":"first","affiliation":[{"name":"Department of Bioinformatics\u2014BiGCaT , School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, , P.O. Box 616, 6200 MD, Maastricht ,","place":["The Netherlands"]},{"name":"Maastricht University , School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, , P.O. Box 616, 6200 MD, Maastricht ,","place":["The Netherlands"]},{"name":"RECETOX , Faculty of Science, , Kotlarska 2, 611 37, Brno ,","place":["Czech Republic"]},{"name":"Masaryk University , Faculty of Science, , Kotlarska 2, 611 37, Brno ,","place":["Czech Republic"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3659-4819","authenticated-orcid":false,"given":"Stanislav","family":"Mazurenko","sequence":"additional","affiliation":[{"name":"Loschmidt Laboratories , Department of Experimental Biology and RECETOX, Faculty of Science, , Kamenice 5, 625 00, Brno ,","place":["Czech Republic"]},{"name":"Masaryk University , Department of Experimental Biology and RECETOX, Faculty of Science, , Kamenice 5, 625 00, Brno ,","place":["Czech Republic"]},{"name":"International Clinical Research Center, St. Anne\u2019s University Hospital Brno , Peka\u0159sk\u00e1 53, 656 91, Brno ,","place":["Czech Republic"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0809-7826","authenticated-orcid":false,"given":"Martin","family":"Scheringer","sequence":"additional","affiliation":[{"name":"RECETOX , Faculty of Science, , Kotlarska 2, 611 37, Brno ,","place":["Czech Republic"]},{"name":"Masaryk University , Faculty of Science, , Kotlarska 2, 611 37, Brno ,","place":["Czech Republic"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2352-9017","authenticated-orcid":false,"given":"V\u00edtor A P","family":"Martins dos Santos","sequence":"additional","affiliation":[{"name":"Laboratory of Bioprocess Engineering, Wageningen University and Research , Droevendaalsesteeg 1, 6708 PB, Wageningen ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5301-3142","authenticated-orcid":false,"given":"Chris T","family":"Evelo","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics\u2014BiGCaT , School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, , P.O. Box 616, 6200 MD, Maastricht ,","place":["The Netherlands"]},{"name":"Maastricht University , School of Nutrition and Translational Research in Metabolism, Faculty of Health, Medicine and Life Sciences, , P.O. Box 616, 6200 MD, Maastricht ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7753-9042","authenticated-orcid":false,"given":"Mihail","family":"Anton","sequence":"additional","affiliation":[{"name":"ELIXIR, Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD ,","place":["United Kingdom"]},{"name":"Department of Life Sciences , National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, , Kemig\u00e5rden 1, Gothenburg SE-412 96 ,","place":["Sweden"]},{"name":"Chalmers University of Technology , National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, , Kemig\u00e5rden 1, Gothenburg SE-412 96 ,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2991-2217","authenticated-orcid":false,"given":"John M","family":"Hancock","sequence":"additional","affiliation":[{"name":"Institute of Biochemistry and Molecular Genetics , Faculty of Medicine, , Zalo\u0161ka 4, 1000 Ljubljana ,","place":["Slovenia"]},{"name":"University of Ljubljana , Faculty of Medicine, , Zalo\u0161ka 4, 1000 Ljubljana ,","place":["Slovenia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3303-9086","authenticated-orcid":false,"given":"An\u017ee","family":"\u017dupani\u010d","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Systems Biology, National Institute of Biology , Ve\u010dna pot 121, 1000 Ljubljana ,","place":["Slovenia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5845-146X","authenticated-orcid":false,"given":"Maria","family":"Suarez-Diez","sequence":"additional","affiliation":[{"name":"Laboratory of Systems and Synthetic Biology (SSB), Wageningen University and Research, Agrotechnology and Food Sciences , Stippeneng 4, 6708 WE Wageningen ,","place":["The 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