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The virtual kidney: an eResearch interface and grid portal

CollectionsAustralian Partnership for Sustainable Repositories (APSR)
Title: The virtual kidney: an eResearch interface and grid portal
Author(s): Harris, Peter
Keywords: APSR
Australian Partnership for Sustainable Repositories
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.


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