Latest Articles
To explore the effects of diabetes on cardiac function, Musgrave et al. (2025B) developed a pair of non-diabetic and diabetic cross-bridge models. These were parameterised using novel human experimental data, and coupled to thin filament calcium activation and passive force muscle models to enable simulation of muscle mechanoenergetics under work-loop contractions. The present study explores and assesses the reproducibility of the simulations performed with these published models. The authors provide original MATLAB code which reproduces all the figures presented in the Primary Publication. To facilitate broader reuse, they additionally provide CellML code for performing the muscle mechanoenergetics simulations using OpenCOR and Python with a Jupyter Notebook. There were slight discrepancies that could not be adjusted for in the OpenCOR simulations, which were likely due to different solvers used in the two platforms. However, these differences did not markedly affect the output metrics of the model simulations performed in OpenCOR, which are materially equivalent to the original simulation results.
To explore the effects of diabetes on cardiac function, Musgrave et al. (2025B) developed a pair of non-diabetic and diabetic cross-bridge models. These were parameterised using novel human experimental data, and coupled to thin filament calcium activation and passive force muscle models to enable simulation of muscle mechanoenergetics under work-loop contractions. The present study explores and assesses the reproducibility of the simulations performed with these published models. The authors provide original MATLAB code which reproduces all the figures presented in the Primary Publication. To facilitate broader reuse, they additionally provide CellML code for performing the muscle mechanoenergetics simulations using OpenCOR and Python with a Jupyter Notebook. There were slight discrepancies that could not be adjusted for in the OpenCOR simulations, which were likely due to different solvers used in the two platforms. However, these differences did not markedly affect the output metrics of the model simulations performed in OpenCOR, which are materially equivalent to the original simulation 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 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.
Physiome publishes mathematical models of physiological processes where the experimental details have been published or accepted for publication in a recognised ‘primary’ peer-reviewed journal in the field of physiological modelling. A Physiome article thus provides a citable link between the published model and its implementation.
The aim is to confirm the reproducibility and reusability these published models. Therefore, Physiome editors will help as much as is currently possible with model curation and annotation to ensure that the modeling results claimed in the primary paper are consistent with the published model.
Physiome curators will also help authors ensure that models and simulation experiments are made available using appropriate community standards prior to acceptance for publication. When aspects of a computational modelling study are not able to be encoded in standard formats, Physiome curators will help authors ensure their work is as open, reproducible, and reusable as possible.
Physiome is open access with a low Author Processing Charge. All Physiome articles are available on figshare including details on the implementation.
