The IUPS Physiome Project: a framework for computational physiology
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The IUPS Physiome Project is an internationally collaborative open-source project to provide a public domain framework for computational physiology, including the development of modelling standards, computational tools and web-accessible databases of models of structure and function at all spatial scales. A number of papers in this volume deal with the development of specific mathematical models of physiological processes. This paper stands back from the detail of individual models and reviews the current state of the IUPS Physiome Project including organ and organ system continuum models, the interpretation of constitutive law parameters in terms of micro-structural models, and markup languages for standardizing cellular processes. Some current practical applications of the physiome models are given and some of the challenges for the next 5 years of the Physiome Project at the level of organs, cells and proteins are proposed.
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Ignoring most published papers is no longer realistic or necessary in an age of post-genomics, the internet, Web 2.0 and systems biology, and when we are starting to move to integrative models of organisms at a whole organ, genome or whole organism scale.
“This is no longer realistic (nor necessary) in an age of post-genomics, the internet, Web 2.0 and systems biology, and when we are starting to move to integrative (if distributed) models of organisms (including humans) at a whole organ, genome or whole organism scale [118,2135,2407-2416].”
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Self-citationGeneration of an Anatomically Based Three-Dimensional Model of the Conducting Airways
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Self-citationModeling β-Adrenergic Control of Cardiac Myocyte Contractility in Silico
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Strategies for the Physiome Project
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Geometric modeling of the human torso using cubic hermite elements
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The architecture of the heart: a data–based model
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Computational modelling of biological systems: tools and visions
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Towards whole-organ modelling of tumour growth
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Generation of an Anatomically Based Geometric Coronary Model
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A Triaxial-Measurement Shear-Test Device for Soft Biological Tissues
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A Finite Element Method for an Eikonal Equation Model of Myocardial Excitation Wavefront Propagation
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Self-citationModelling gastrointestinal bioelectric activity
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Simulation of ATP metabolism in cardiac excitation–contraction coupling
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Modeling RBC and Neutrophil Distribution Through an Anatomically Based Pulmonary Capillary Network
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A model of cardiac cellular electromechanics
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Self-citationA Deformable Finite Element Derived Finite Difference Method for Cardiac Activation Problems
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Sarcomere length changes in a 3D mathematical model of the pig ventricles
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Modeling the isolated cardiac myocyte
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Integrative models of the heart: achievements and limitations
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Mathematical modelling of the heart: cell to organ
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Characterising respiratory airway gas mixing using a lumped parameter model of the pulmonary acinus
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Self-citation
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Research works printed but not linked: 3
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Biophysical annotation and representation of CellML models
Wimalaratne, S. M., Halstead, M. D. B., Lloyd, C. M., Crampin, E. J., & Nielsen, P. F. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp391 · Cited by 19 · see citing works
- Authors
- Hunter, P. J.
- Affiliations
- University of Auckland (NZ)
- Corresponding author
- Hunter, P.J.
- ORCID
- Hunter, P.J.
- Venue
- Progress in Biophysics and Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2004-06
- Volume
- 85
- Issue
- 2-3
- Pages
- 551-569
- ISSN
- 0079-6107 (ISSN-L)
- OpenAlex
- W2121642757
- Cited by
- 66
- References
- 68
- Citations by year
- 2025: 1 · 2024: 2 · 2023: 1 · 2022: 1 · 2020: 1 · 2019: 2 · 2018: 2 · 2017: 2 · 2016: 7 · 2015: 4 · 2013: 6 · 2012: 4
- FWCI
- 1.31
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Progress in Biophysics and Molecular Biology (publishedVersion, public-domain)
- PubMed (publishedVersion)
- Funders
- Royal Society Te Apārangi
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Social Sciences › Arts and Humanities › History and Philosophy of Science › Philosophy and History of Science
- Keywords
- computational physiology, continuum model, constitutive equations, markup languages, cellular processes, open source software
- MeSH terms
- Cell Physiological Phenomena, Computer Simulation, Database Management Systems, International Cooperation, Models, Biological, Research, Research Design, Viscera, Information Storage and Retrieval, Systems Integration, Computational Biology
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