2nd INCF Congress of Neuroinformatics: September 6-8, 2009
- Kenji Doya
- Alon Halevy
- Astrid Prinz
- Andrew Schwartz
- Shankar Subramaniam
- Arthur Toga
- Bart ter Haar Romeny
- Uri Eden
- Klaus Linkenkaer-Hansen
- Tim Clark
- Alan Ruttenberg
- Jeffrey Grethe
- Arnd Roth
- Wulfram Gerstner
- Peter Hunter
- Markus Diesmann
- Andrey Semin
- Pietro Liò
- Albert Cardona
- Giorgio Ascoli
- Rolf Kötter
Workshop 3, How should a neuron be modeled: Biophysical detail vs. abstraction
Title: Model abstraction and multiscale physiological modelling: Examples from the Physiome Project.
University of Auckland, Auckland, New Zealand
Abstract: The Physiome Project of the International Union of Physiological Sciences (IUPS) is attempting to provide a comprehensive framework for modelling the human body using computational methods that can incorporate the biochemistry, biophysics and anatomy of cells, tissues and organs. A major goal of the project is to use computational modelling to analyse integrative biological function in terms of underlying structure and molecular mechanisms. It is also establishing web-accessible physiological databases dealing with model-related data at the cell, tissue, organ and organ system levels. A newly formed EU Network of Excellence for the Virtual Physiological Human (VPH) is also contributing and, in particular, addressing clinical applications of the project.
The application of this framework to modeling the heart and other organs will be discussed, with particular reference to model abstraction and multi-scale physiological modeling.
The talk will also briefly describe current progress in the development of XML markup languages, such as CellML and FieldML, for standardised encoding of models, and the model repositories, graphical user interfaces and the open source computational software being developed under the VPH/IUPS Physiome Project for computational physiology.
1. Hunter, P.J. and Borg, T.K. Integration from proteins to organs: The Physiome Project. Nature Reviews Molecular and Cell Biology. 4, 237-243, 2003.
2. Hunter, P.J. and Nielsen, P.M.F. A strategy for integrative computational physiology. Physiology. 20,316-325, 2005.
3. Hunter, P.J., Crampin, E.J. and Nielsen, P.M.F. Bioinformatics, multiscale modelling and the IUPS Physiome Project. Briefings in Bioinformatics. 9 (4), 333-343, 2008.
4. Cooling, M., Hunter, P. J. and Crampin, E. J., Modeling biological modularity with CellML, IET Systems Biology Journal, 2, 73-79, 2008.
5. Christie, R., Nielsen, P.M.F., Blackett, S., Bradley, C. and Hunter, P.J. FieldML: Standards, tools and repositories. Phil. Trans. Roy. Soc. A 367, 1869-1884, 2009.
Bio sketch: Prof. Hunter completed an engineering degree in 1971 in Theoretical and Applied Mechanics (now Engineering Science) at the University of Auckland, New Zealand, a Master of Engineering degree in 1972 (Auckland) on solving the equations of arterial blood flow, and a D. Phil. (Ph.D.) in Physiology at the University of Oxford in 1975 on finite element modeling of ventricular mechanics.
His major research interests since then have been modelling many aspects of the human body using specially developed computational algorithms and an anatomically and biophysically based approach which incorporates detailed anatomical and microstructural measurements and material properties into the continuum models. The interrelated electrical, mechanical and biochemical functions of the heart, for example, have been modelled in the first 'physiome' model of an organ.
As the current co-Chair of the Physiome Committee of the International Union of Physiological Sciences he is helping to lead the international Physiome Project which aims to use computational methods for understanding the integrated physiological function of the body in terms of the structure and function of tissues, cells and proteins.
He is currently a Professor of Engineering Science and Director of the Bioengineering Institute at the University of Auckland, Director of Computational Physiology at Oxford University and holds honorary or visiting Professorships at a number of Universities. He is on the scientific advisory boards of a number of Research Institutes in Europe, the US and the Asia-Pacific region. He is an elected Fellow of the Royal Society (London and NZ), the World Council for Biomechanics, the American Institute for Medical and Biological Engineering, and the International Academy of Medical & Biological Engineering.