| Title: | PBPK model code associated to the journal article entitled: "Making PBPK models more reproducible in practice" : Version v2 |
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| Authors: | ID Domínguez-Romero, Elena (Author)
ID Mazurenko, Stanislav (Author)
ID Scheringer, Martin (Author)
ID Martins dos Santos, Vitor A. P. (Author)
ID Evelo, Chris T (Author)
ID Anton, Mihail (Author)
ID Hancock, John M. (Author)
ID Županič, Anže (Author)
ID Suarez-Diez, Maria (Author) |
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| Files: |  URL - Source URL, visit https://zenodo.org/records/13838845
 ZIP - Software, download (661,21 KB)
MD5: E6926F20DF6BE93E76A3FD2FD4EE57D2
 JSON - Metadata, download (8,54 KB)
MD5: 3FD4276EA3E980A0B4813030D4EF8348
This document has even more files. Complete list of files is available
below. |
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| Language: | English |
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| Typology: | 2.20 - Complete scientific database of research data |
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| Organization: |  NIB - National Institute of Biology
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| Abstract: | 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). |
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| Keywords: | pharmacokinetics, pharmacodynamics, mathematical modelling, standards, model code, reproducibility, SBML, MATLAB, systems biology |
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| Publication status: | Published |
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| Publication version: | Version of Record |
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| Publication date: | 25.09.2024 |
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| Place of publishing: | Genève |
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| Publisher: | Zenodo |
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| Year of publishing: | 2024 |
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| Number of pages: | 1 spletni vir |
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| PID: | 20.500.12556/DiRROS-29333  |
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| UDC: | 659.2:004 |
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| DOI: | 10.5281/zenodo.13838845 |
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| COBISS.SI-ID: | 274282243 |
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| Note: | 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;
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| Publication date in DiRROS: | 08.05.2026 |
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| Views: | 78 |
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| Downloads: | 46 |
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