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Abstract

A web-based 3D "virtual kidney" interface has been developed for access to experimental data and parameter values abstracted within a quantitative kidney database and to a repository of mathematical models of kidney function. A translucent multi-scale reconstruction of a rat kidney shows major anatomical structures as well as renal arteries and veins to several levels of branching. Within the kidney are examples of reconstructed serially sectioned nephrons. The user can rotate the kidney, display or hide individual structures, and zoom in on any portion. Selection of a structure provides a link to the search facility of QKDB and thence to relevant parameter values and extracts from the literature.

A menu lists the repository of mathematical models, such as segmental (e.g., proximal or distal tubule) or medullary transport models, which may be run on the local machine or, via a Grid Portal (KidneyGrid), simultaneously on several remote machines. The use of a grid resource broker demonstrates the ability to compose, schedule, monitor and visualize the results of the simulation and simplifies the development of application, credential and resource management while decoupling the launch platform from the underlying grid middleware.

The simulation results (eg solute concentrations or local flow rates) are visible on the virtual kidney structures as scaled colour gradients, thus allowing a visual and quantitative appreciation of the effects of simulated parameter changes. A separate panel shows x-y plots of the results. The underlying models are implemented via CellML descriptions and are consistent, as far as possible, with standards and ontologies being developed for other organs under the Physiome initiative.

Work done in collaboration with S Randall Thomas, Andrew Lonie, Bill Appelbe, Belinda May, Peter Hunter, Raj Buyya and Xingchen Chu.

About the speaker

Peter Harris has been a subject teacher and course convener in Departments of Physiology and now has faculty and university-wide involvement in curriculum evaluation, design and delivery, particularly in relation to educational technology. He has been a pioneer in the introduction of problem-based learning in physiology, and an early adopter and developer of novel interactive computer-aided learning programs. As a laboratory researcher, he led a team of scientists and students in a range of projects related to basic science in the areas of kidney and cardiovascular function. Peter has published over 100 articles and chapters in refereed journals and books.

Within the Department of Physiology and as Associate Dean in the Faculty of Medicine, Dentistry and Health Sciences, Peter initiated and led the development and introduction of multimedia programs for teaching and learning. He established a successful and growing organisation within the Faculty for development, delivery and evaluation of computer-aided learning resources in the new medical and health sciences curricula.

Current research activities include leadership roles with the University of Melbourne Health Informatics Network, Melbourne University Virtual Environments for Simulation (MUVES) and e-research developments for the renal physiome project.