{"@context": "http://schema.org", "@id": "https://doi.org/10.5281/zenodo.13838845", "@type": "https://schema.org/CreativeWork", "identifier": "https://doi.org/10.5281/zenodo.13838845", "name": "PBPK model code associated to the journal article entitled: \"Making PBPK models more reproducible in practice\"", "creator": [{"name": "Dom\u00ednguez-Romero, Elena", "givenName": "Elena", "familyName": "Dom\u00ednguez-Romero", "affiliation": [{"@type": "Organization", "name": "Maastricht University, Department of Bioinformatics - BiGCaT, Maastricht, The Netherlands"}, {"@type": "Organization", "name": "RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"}], "@id": "https://orcid.org/0000-0001-9795-5628", "@type": "Person"}, {"name": "Mazurenko, Stanislav", "givenName": "Stanislav", "familyName": "Mazurenko", "affiliation": [{"@type": "Organization", "name": "Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"}, {"@type": "Organization", "name": "International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic"}], "@id": "https://orcid.org/0000-0003-3659-4819", "@type": "Person"}, {"name": "Scheringer, Martin", "givenName": "Martin", "familyName": "Scheringer", "affiliation": [{"@type": "Organization", "name": "RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"}], "@id": "https://orcid.org/0000-0002-0809-7826", "@type": "Person"}, {"name": "Martins dos Santos, V\u00edtor A.P.", "givenName": "V\u00edtor A.P.", "familyName": "Martins dos Santos", "affiliation": [{"@type": "Organization", "name": "Laboratory of Bioprocess Engineering, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands"}], "@id": "https://orcid.org/0000-0002-2352-9017", "@type": "Person"}, {"name": "Evelo, Chris", "givenName": "Chris", "familyName": "Evelo", "affiliation": [{"@type": "Organization", "name": "Maastricht University, Department of Bioinformatics - BiGCaT, Maastricht, The Netherlands"}], "@id": "https://orcid.org/0000-0002-5301-3142", "@type": "Person"}, {"name": "Anton, Mihail", "givenName": "Mihail", "familyName": "Anton", "affiliation": [{"@type": "Organization", "name": "ELIXIR, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK"}, {"@type": "Organization", "name": "Department of Life Sciences, NBIS, SciLifeLab, Chalmers University of Technology, Gothenburg SE-412 96, Sweden"}], "@id": "https://orcid.org/0000-0002-7753-9042", "@type": "Person"}, {"name": "Hancock, John", "givenName": "John", "familyName": "Hancock", "affiliation": [{"@type": "Organization", "name": "Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Zalo\u0161ka 4, 1000 Ljubljana, Slovenia"}], "@id": "https://orcid.org/0000-0003-2991-2217", "@type": "Person"}, {"name": "\u017dupani\u010d, An\u017ee", "givenName": "An\u017ee", "familyName": "\u017dupani\u010d", "affiliation": [{"@type": "Organization", "name": "National Institute of Biology, Department of Biotechnology and Systems Biology, Ve\u010dna pot 121, 1000 Ljubljana, Slovenia"}], "@id": "https://orcid.org/0000-0003-3303-9086", "@type": "Person"}, {"name": "Suarez-Diez, Maria", "givenName": "Maria", "familyName": "Suarez-Diez", "affiliation": [{"@type": "Organization", "name": "Wageningen University & Research. Agrotechnology and food sciences. Stippeneng 4, 6708 WE Wageningen"}], "@id": "https://orcid.org/0000-0001-5845-146X", "@type": "Person"}], "author": [{"name": "Dom\u00ednguez-Romero, Elena", "givenName": "Elena", "familyName": "Dom\u00ednguez-Romero", "affiliation": [{"@type": "Organization", "name": "Maastricht University, Department of Bioinformatics - BiGCaT, Maastricht, The Netherlands"}, {"@type": "Organization", "name": "RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"}], "@id": "https://orcid.org/0000-0001-9795-5628", "@type": "Person"}, {"name": "Mazurenko, Stanislav", "givenName": "Stanislav", "familyName": "Mazurenko", "affiliation": [{"@type": "Organization", "name": "Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"}, {"@type": "Organization", "name": "International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic"}], "@id": "https://orcid.org/0000-0003-3659-4819", "@type": "Person"}, {"name": "Scheringer, Martin", "givenName": "Martin", "familyName": "Scheringer", "affiliation": [{"@type": "Organization", "name": "RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"}], "@id": "https://orcid.org/0000-0002-0809-7826", "@type": "Person"}, {"name": "Martins dos Santos, V\u00edtor A.P.", "givenName": "V\u00edtor A.P.", "familyName": "Martins dos Santos", "affiliation": [{"@type": "Organization", "name": "Laboratory of Bioprocess Engineering, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands"}], "@id": "https://orcid.org/0000-0002-2352-9017", "@type": "Person"}, {"name": "Evelo, Chris", "givenName": "Chris", "familyName": "Evelo", "affiliation": [{"@type": "Organization", "name": "Maastricht University, Department of Bioinformatics - BiGCaT, Maastricht, The Netherlands"}], "@id": "https://orcid.org/0000-0002-5301-3142", "@type": "Person"}, {"name": "Anton, Mihail", "givenName": "Mihail", "familyName": "Anton", "affiliation": [{"@type": "Organization", "name": "ELIXIR, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK"}, {"@type": "Organization", "name": "Department of Life Sciences, NBIS, SciLifeLab, Chalmers University of Technology, Gothenburg SE-412 96, Sweden"}], "@id": "https://orcid.org/0000-0002-7753-9042", "@type": "Person"}, {"name": "Hancock, John", "givenName": "John", "familyName": "Hancock", "affiliation": [{"@type": "Organization", "name": "Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Zalo\u0161ka 4, 1000 Ljubljana, Slovenia"}], "@id": "https://orcid.org/0000-0003-2991-2217", "@type": "Person"}, {"name": "\u017dupani\u010d, An\u017ee", "givenName": "An\u017ee", "familyName": "\u017dupani\u010d", "affiliation": [{"@type": "Organization", "name": "National Institute of Biology, Department of Biotechnology and Systems Biology, Ve\u010dna pot 121, 1000 Ljubljana, Slovenia"}], "@id": "https://orcid.org/0000-0003-3303-9086", "@type": "Person"}, {"name": "Suarez-Diez, Maria", "givenName": "Maria", "familyName": "Suarez-Diez", "affiliation": [{"@type": "Organization", "name": "Wageningen University & Research. Agrotechnology and food sciences. Stippeneng 4, 6708 WE Wageningen"}], "@id": "https://orcid.org/0000-0001-5845-146X", "@type": "Person"}], "publisher": {"@type": "Organization", "name": "Zenodo"}, "dateCreated": "2024-09-25T14:35:11.201232+00:00", "dateModified": "2024-11-04T18:40:49.600463+00:00", "datePublished": "2024-09-25", "contentSize": "660.62 KB", "size": "660.62 KB", "license": "https://creativecommons.org/licenses/by/4.0/legalcode", "description": "<p>Physiologically-based pharmacokinetic (PBPK) model code associated to the journal article by: E. Dom&iacute;nguez-Romero, S. Mazurenko, M. Scheringer, V. A. P. Martins dos Santos, C. T. Evelo, M. Anton, J. M. Hancock, A. \u017dupani\u010d, M. Suarez-Diez, entitled: <em>Making PBPK models more reproducible in practice</em> (<em>Briefings in Bioinformatics</em>, Volume 25, Issue 6, November 2024, bbae569, <a href=\"https://doi.org/10.1093/bib/bbae569\">https://doi.org/10.1093/bib/bbae569</a>).</p>\n<p>The code is provided in MATLAB and SBML formats. The following files can be found here:</p>\n<p>\"PBPK_code_EDR_et_al_vs4.m\": model code in <strong>MATLAB</strong> format. This is the 4th version of the code. The mathematical model is described by Dom&iacute;nguez-Romero et al., and more succinctly explained within the code (annotations). When this code is run in MATLAB, we obtain the next file:</p>\n<p>\"Model_variables_numeric_results.xls\": numeric results obtained by model simulation in MATLAB.</p>\n<p>\"SM2_PBPK_code_EDR_et_al_final4_test_trigger.xml\": model code in <strong>SBML</strong> format, obtained by conversion of the MATLAB code, by using&nbsp;<em>\"Model ODE Converter for Creating Automated SBML Interoperability (MOCCASIN)&rdquo;</em> (G&oacute;mez et al., 2016) and COPASI tools (Tiwari et al., 2021). More details about the conversion can be found in Dom&iacute;nguez-Romero et al. (2024).</p>", "isPartOf": [{"@type": "CreativeWork", "@id": "https://doi.org/10.1093/bib/bbae569"}], "url": "https://zenodo.org/records/13838845", "container_title": "Briefings in Bioinformatics", "page": "bbae569", "volume": "25", "issue": "6"}