20.500.12556/DiRROS-29333 PBPK model code associated to the journal article entitled: "Making PBPK models more reproducible in practice" Version v2 Physiologically-based pharmacokinetic (PBPK) model code associated to the journal article by: E. Domínguez-Romero, S. Mazurenko, M. Scheringer, V. A. P. Martins dos Santos, C. T. Evelo, M. Anton, J. M. Hancock, A. Županič, M. Suarez-Diez, entitled: Making PBPK models more reproducible in practice (Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae569, https://doi.org/10.1093/bib/bbae569). The code is provided in MATLAB and SBML formats. The following files can be found here: "PBPK_code_EDR_et_al_vs4.m": model code in MATLAB format. This is the 4th version of the code. The mathematical model is described by Domínguez-Romero et al., and more succinctly explained within the code (annotations). When this code is run in MATLAB, we obtain the next file: "Model_variables_numeric_results.xls": numeric results obtained by model simulation in MATLAB. "SM2_PBPK_code_EDR_et_al_final4_test_trigger.xml": model code in SBML format, obtained by conversion of the MATLAB code, by using "Model ODE Converter for Creating Automated SBML Interoperability (MOCCASIN)” (Gómez et al., 2016) and COPASI tools (Tiwari et al., 2021). More details about the conversion can be found in Domínguez-Romero et al. (2024). pharmacokinetics pharmacodynamics mathematical modelling standards model code reproducibility SBML MATLAB systems biology farmakokinetika farmakodinamika matematično modeliranje standardi sistemska biologija true false false Zenodo Angleški jezik Slovenski jezik Neznano 2026-05-08 14:22:33 2026-05-08 14:27:57 2026-05-09 03:44:22 0000-00-00 00:00:00 2024 0 Genève 0 Nasl. z nasl. zaslona; Opis vira z dne 6. 4. 2026; Soavtorji: Stanislav Mazurenko, Martin Scheringer, Vítor A. P. Martins dos Santos, Chris T. Evelo, Mihail Anton, John M. Hancock, Anže Županič, Maria Suarez-Diez; 1 spletni vir 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 2024-09-25 659.2:004 10.5281/zenodo.13838845 274282243 https://zenodo.org/records/13838845 1 9c14d0a4-4ad8-11f1-8a5a-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=43919 RAZ_Dominguez-Romero_Elena_2024.zip RAZ_Dominguez-Romero_Elena_2024.zip 1 E6926F20DF6BE93E76A3FD2FD4EE57D2 8e17e06167526bdd5b026c80eefa659e19065a8a154f90e42b384e0a116fa7d1 eb6754bf-4ad8-11f1-8a5a-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=43920 RAZ_Dominguez-Romero_Elena_2024.json RAZ_Dominguez-Romero_Elena_2024.json 1 3FD4276EA3E980A0B4813030D4EF8348 11a55b83c3a1670bf67c69257c3d52d7312186ab60529da7339d110151bd2393 fadf157e-4ad8-11f1-8a5a-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=43921 https://doi.org/10.1093/bib/bbae569 Making PBPK models more reproducible in practice (Raziskovalni članek) Making PBPK models more reproducible in practice (Research article) 0 1944e29d-4ad9-11f1-8a5a-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=43922 Nacionalni inštitut za biologijo Making PBPK models more reproducible in practice 0 0 0