PBPK model code associated to the journal article entitled: "Making PBPK models more reproducible in practice"

Elena Domínguez-Romero; Stanislav Mazurenko; Martin Scheringer; Vítor A.P. Martins Dos Santos; Chris T. Evelo; Mihail Anton; John M. Hancock; Anze Zupanič; Maria Suarez-Diez

doi:10.5281/zenodo.12707615

PBPK model code associated to the journal article entitled: "Making PBPK models more reproducible in practice"

Elena Domínguez-Romero^*, Stanislav Mazurenko, Martin Scheringer, Vítor A.P. Martins Dos Santos, Chris T. Evelo, Mihail Anton, John M. Hancock, Anze Zupanič, Maria Suarez-Diez

^*Corresponding author for this work

Research output: Non-textual form › Software

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).

Original language	English
Publisher	Maastricht University
DOIs	https://doi.org/10.5281/zenodo.12707615
Publication status	Published - 25 Sept 2024

Keywords

MATLAB
model code
pharmacokinetics
reproducibility
SBML
systems biology

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10.5281/zenodo.12707615Licence: CC BY

1 Article

Making PBPK models more reproducible in practice
Domínguez-Romero, E., Mazurenko, S., Scheringer, M., Martins Dos Santos, V. A. P., Evelo, C. T., Anton, M., Hancock, J. M., Zupanič, A. & Suarez-Diez, M., Nov 2024, In: Briefings in Bioinformatics. 25, 6, bbae569.
Research output: Contribution to journal › Article › Academic › peer-review

Open Access
2 Citations (Scopus)

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@misc{a6b23e2adec04a4fbadb883607f238ec,

title = "PBPK model code associated to the journal article entitled: {"}Making PBPK models more reproducible in practice{"}",

abstract = "Physiologically-based pharmacokinetic (PBPK) model code associated to the journal article by: E. Dom{\'i}nguez-Romero, S. Mazurenko, M. Scheringer, V. A. P. Martins dos Santos, C. T. Evelo, M. Anton, J. M. Hancock, A. {\v Z}upani{\v c}, 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 Dom{\'i}nguez-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)” (G{\'o}mez et al., 2016) and COPASI tools (Tiwari et al., 2021). More details about the conversion can be found in Dom{\'i}nguez-Romero et al. (2024).",

keywords = "MATLAB, model code, pharmacokinetics, reproducibility, SBML, systems biology",

author = "Elena Dom{\'i}nguez-Romero and Stanislav Mazurenko and Martin Scheringer and {Martins Dos Santos}, {V{\'i}tor A.P.} and Evelo, {Chris T.} and Mihail Anton and Hancock, {John M.} and Anze Zupani{\v c} and Maria Suarez-Diez",

year = "2024",

month = sep,

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doi = "10.5281/zenodo.12707615",

language = "English",

volume = "25",

publisher = "Maastricht University",

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T1 - PBPK model code associated to the journal article entitled: "Making PBPK models more reproducible in practice"

AU - Domínguez-Romero, Elena

AU - Mazurenko, Stanislav

AU - Scheringer, Martin

AU - Martins Dos Santos, Vítor A.P.

AU - Evelo, Chris T.

AU - Anton, Mihail

AU - Hancock, John M.

AU - Zupanič, Anze

AU - Suarez-Diez, Maria

PY - 2024/9/25

Y1 - 2024/9/25

N2 - 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).

AB - 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).

KW - MATLAB

KW - model code

KW - pharmacokinetics

KW - reproducibility

KW - SBML

KW - systems biology

U2 - 10.5281/zenodo.12707615

DO - 10.5281/zenodo.12707615

M3 - Software

VL - 25

PB - Maastricht University

ER -

PBPK model code associated to the journal article entitled: "Making PBPK models more reproducible in practice"

Abstract

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Making PBPK models more reproducible in practice

Cite this