Reproducible, reusable models for physiological research

Latest Articles

Original Research
Reproducibility Study on a PBPK Model of FcRn-Mediated Recycling for Large Molecules
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Soroush Safaei, Veronique De Brabandere, Wilhelmus E. A. de Witte, Lindsay B. Avery, Tom Van Bogaert, Maria Laura Sargentini-Maier
Feb 12, 2024

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.

Original Research
Steady-state Approximations for Hodgkin-Huxley Cell Models: Towards Multi-scale Models of Uterine Smooth Muscle
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Shawn A. Means, Alys R. Clark, Leo K. Cheng
Dec 4, 2023

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.

Original Research
Reproducibility study of the modular and reusable model of epithelial transport in the proximal convoluted tubule
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Leyla Noroozbabaee, Pablo J. Blanco, Soroush Safaei, David P. Nickerson
May 27, 2023

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.

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.

Funding and support by:
International Union of Physiological SciencesAuckland Bioengineering InstituteDigital ScienceVPH Institute