Auckland Bioengineering Institute - The University of Auckland, Auckland, New Zealand

UOA Description of organisation

The University of Auckland is New Zealand's pre-eminent research-led University. The ABI was established in 2001 as a cross-faculty research institute dealing with the application of the mathematical and engineering sciences to biology generally and human physiology in particular. The primary goal of the ABI is to develop anatomically and biophysically based mathematical models for all aspects of human physiology from genes to whole organs, together with the experimental techniques and instrumentation required to measure cell and tissue properties and perform model validation experiments. The understanding of biological function gained through these models is applied to medical diagnosis and treatment planning, drug discovery and medical device manufacture. A major part of this effort is the development of standards, tools and services for the international Physiome Project, including the development of the computational modelling markup languages, CellML and FieldML together with their associated model repositories and computational and visualisation software.


Previous experience

UoA is one of the core partners in the VPH Network of Excellence and is developing the VPH modelling standards CellML and FieldML and the Physiome Model Repository (PMR2). It will provide a resource for translating models developed by the consortium into the CellML and FieldML formats and archiving these models in the PMR2 model repository for use by the consortium and will provide the necessary extensions to the VPH CellML/FieldML framework to support the use of existing data, models & tools where issues of uncertainty in data and model parameters are being addressed and tested in the three demonstrator projects. Role in project: To help coordinate the application of the modelling work by the consortium to the VPH modelling standards (SBML, CellML and FieldML) and to help with the development of multiscale models of tumours.


Profile of staff members

Prof Peter Hunter has a Bachelors degree in Theoretical and Applied Mechanics and a Master of Engineering from the University of Auckland, and a DPhil (PhD) in Physiology from the University of Oxford. As the current co-Chair of the Physiome Committee of the International Union of Physiological Sciences and member of the VPH NoE he is helping to lead the international VPH/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 ABI in 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.



Auckland Bioengineering Institute



Five recent publications relevant to the project

1. Hunter, P.J. and Viceconti, M. The VPH-Physiome Project: Standards and tools for multi-scale modeling in clinical applications. Reviews in BioMedical Engineering, In press 2009.


2. 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.


3. Garny, A., Cooper, J., Hunter, P.J. VPH/Physiome Toolkit. Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2009.


4. Cooling, M.T., Crampin, E.J. and Hunter, P.J. Physiome Mark-up Languages for Systems Biology: Model Modularization and Reuse. Chapter in text book on Systems Biology by Edison Liu and Douglas A Lauffenburger In Press 2009.


5. Lloyd, C.M., Lawson, J.R., Hunter, P.J., Nielsen, P.F. The CellML Model Repository. Bioinformatics Vol. 24 no. 18, pp 2122–2123, 2008.