Research Articles
A computational model in the form of a whole-body physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model of dapagliflozin was developed to systematically evaluate the influence of patient-specific factors on drug disposition. Based on curated data from 28 clinical studies, the model simulates the absorption, distribution, metabolism and excretion (ADME) of the drug as well as its pharmacodynamics. The model accounts for variability in renal and hepatic function, and effects of food intake. The model is implemented in the Systems Biology Markup Language (SBML) standard. Analysis were performed utilizing the libroadrunner simulation library. Here, we demonstrate the computational reproducibility of the key findings from the primary publication, thereby verifying the consistency of the model implementation with the published results.
A computational model in the form of a whole-body physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model of dapagliflozin was developed to systematically evaluate the influence of patient-specific factors on drug disposition. Based on curated data from 28 clinical studies, the model simulates the absorption, distribution, metabolism and excretion (ADME) of the drug as well as its pharmacodynamics. The model accounts for variability in renal and hepatic function, and effects of food intake. The model is implemented in the Systems Biology Markup Language (SBML) standard. Analysis were performed utilizing the libroadrunner simulation library. Here, we demonstrate the computational reproducibility of the key findings from the primary publication, thereby verifying the consistency of the model implementation with the published results.
A digital twin in the form of a whole-body physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model of losartan was developed to systematically evaluate the influence of patient-specific factors on drug disposition and effects. Based on curated data from 25 clinical studies, the model simulates the absorption, distribution, metabolism and excretion (ADME) as well as pharmacological effects of the drug. The model accounts for variability caused by the differences in renal and hepatic function, and by genetic polymorphisms of CYP2C9 and ABCB1. The model is implemented in the Systems Biology Markup Language (SBML) standard. Simulations were performed utilising the libroadrunner library. Here, we demonstrate the computational reproducibility of the key findings from the primary publication, thereby verifying the consistency and reproducibility of the model implementation with the published results.
A digital twin in the form of a whole-body physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model of losartan was developed to systematically evaluate the influence of patient-specific factors on drug disposition and effects. Based on curated data from 25 clinical studies, the model simulates the absorption, distribution, metabolism and excretion (ADME) as well as pharmacological effects of the drug. The model accounts for variability caused by the differences in renal and hepatic function, and by genetic polymorphisms of CYP2C9 and ABCB1. The model is implemented in the Systems Biology Markup Language (SBML) standard. Simulations were performed utilising the libroadrunner library. Here, we demonstrate the computational reproducibility of the key findings from the primary publication, thereby verifying the consistency and reproducibility of the model implementation with the published results.
A digital twin in the form of a whole-body physiologically based pharmacokinetic (PBPK) model of glimepiride was developed to systematically evaluate the influence of patient-specific factors on drug disposition. Based on curated data from 20 clinical studies, the model simulates the absorption, distribution, metabolism and excretion (ADME) of the drug while accounting for variability in renal and hepatic function, CYP2C9 genetic variants and bodyweight. The model is implemented in the Systems Biology Markup Language (SBML) standard and simulations are perormed using scripts that utilise the libRoadRunner library to run simulations and generate results. Here, we demonstrate the computational reproducibility of the key findings from the primary publication, thereby verifying the consistency and reproducibility of the model implementation with the published results.
A digital twin in the form of a whole-body physiologically based pharmacokinetic (PBPK) model of glimepiride was developed to systematically evaluate the influence of patient-specific factors on drug disposition. Based on curated data from 20 clinical studies, the model simulates the absorption, distribution, metabolism and excretion (ADME) of the drug while accounting for variability in renal and hepatic function, CYP2C9 genetic variants and bodyweight. The model is implemented in the Systems Biology Markup Language (SBML) standard and simulations are perormed using scripts that utilise the libRoadRunner library to run simulations and generate results. Here, we demonstrate the computational reproducibility of the key findings from the primary publication, thereby verifying the consistency and reproducibility of the model implementation with the published results.
This work presents an energy-based modelling framework and presented two exemplar bond graph templates for solute carrier (SLC) transporter families, facilitated diffusion with SLC2A2 (GLUT2) and sodium-glucose cotransport with SLC5A1 (SGLT1).
This work presents an energy-based modelling framework and presented two exemplar bond graph templates for solute carrier (SLC) transporter families, facilitated diffusion with SLC2A2 (GLUT2) and sodium-glucose cotransport with SLC5A1 (SGLT1).
This work studies neural regulation, by simulating the membrane potential oscillations due to phasic slow wave activity and resulting active tension generation within distal gastric interstitial cells of Cajal and smooth muscle cells.
This work studies neural regulation, by simulating the membrane potential oscillations due to phasic slow wave activity and resulting active tension generation within distal gastric interstitial cells of Cajal and smooth muscle cells.
This paper presents a reproduced computational model of lymphatic collecting vessels. The model was originally introduced by Bertram et al. (2011), and comprises a series of contractile segments, known as lymphangions, interconnected by secondary lymphatic valves. The model focused on elucidating the pumping behavior of contracting lymphangions and deriving pump-characteristic curves, by incorporating pressure-dependent valve resistance, passive elasticity, and active contraction terms in multiple lymphangions connected in series.
This paper presents a reproduced computational model of lymphatic collecting vessels. The model was originally introduced by Bertram et al. (2011), and comprises a series of contractile segments, known as lymphangions, interconnected by secondary lymphatic valves. The model focused on elucidating the pumping behavior of contracting lymphangions and deriving pump-characteristic curves, by incorporating pressure-dependent valve resistance, passive elasticity, and active contraction terms in multiple lymphangions connected in series.
The PBPK model of FcRn-mediated recycling of large molecules was developed and studied by deWitte et al. (2023) to characterize and predict Immunoglobulin G (IgG) disposition in plasma and tissues. This study investigated the large-molecule model in PK-Sim and its applicability to molecules with FcRn binding affinity in plasma.
The PBPK model of FcRn-mediated recycling of large molecules was developed and studied by deWitte et al. (2023) to characterize and predict Immunoglobulin G (IgG) disposition in plasma and tissues. This study investigated the large-molecule model in PK-Sim and its applicability to molecules with FcRn binding affinity in plasma.
An effort at reducing the Tong et al. (2011) model into a smaller number of equations for computational efficiency – the 'reduced' Tong model – aims at reproducing the overall behaviour without excessive detail.
An effort at reducing the Tong et al. (2011) model into a smaller number of equations for computational efficiency – the 'reduced' Tong model – aims at reproducing the overall behaviour without excessive detail.
We describe here our implementation of a renal epithelial model as published in Noroozbabaee et al. (2022). The flexible and modular model we presented in Noroozbabaee et al. (2022) can be adapted to specific configurations of epithelial transport.
We describe here our implementation of a renal epithelial model as published in Noroozbabaee et al. (2022). The flexible and modular model we presented in Noroozbabaee et al. (2022) can be adapted to specific configurations of epithelial transport.
The system of equations and figures presented in Imtiaz et al. (2002) are verified and reproduced in the current curation paper.
The system of equations and figures presented in Imtiaz et al. (2002) are verified and reproduced in the current curation paper.
