The Virtual Kidney: an eScience interface and Grid portal.

The Virtual Kidney uses a web interface and distributed computing to provide experimental scientists and analysts with access to computational simulations and knowledge databases hosted in geographically separated laboratories. Users can explore a variety of complex models without requiring the specific programming environment in which applications have been developed. This initiative exploits high-bandwidth communication networks for collaborative research and for shared access to knowledge resources. The Virtual Kidney has been developed within a specialist community of renal scientists but is transferable to other areas of research requiring interaction between published literature and databases, theoretical models and simulations and the formulation of effective experimental designs. A web-based three-dimensional interface provides access to experimental data, a parameter database and mathematical models. A multi-scale kidney reconstruction includes blood vessels and serially sectioned nephrons. Selection of structures provides links to the database, returning parameter values and extracts from the literature. Models are run locally or remotely with a Grid resource broker managing scheduling, monitoring and visualization of simulation results and application, credential and resource allocation. Simulation results are viewed graphically or as scaled colour gradients on the Virtual Kidney structures, allowing visual and quantitative appreciation of the effects of simulated parameter changes.

Recommendations of the 2006 Human Variome Project meeting.

Lists of variations in genomic DNA and their effects have been kept for some time and have been used in diagnostics and research. Although these lists have been carefully gathered and curated, there has been little standardization and coordination, complicating their use. Given the myriad possible variations in the estimated 24,000 genes in the human genome, it would be useful to have standard criteria for databases of variation. Incomplete collection and ascertainment of variants demonstrates a need for a universally accessible system. These and other problems led to the World Heath Organization-cosponsored meeting on June 20-23, 2006 in Melbourne, Australia, which launched the Human Variome Project. This meeting addressed all areas of human genetics relevant to collection of information on variation and its effects. Members of each of eight sessions (the clinic and phenotype, the diagnostic laboratory, the research laboratory, curation and collection, informatics, relevance to the emerging world, integration and federation and funding and sustainability) developed a number of recommendations that were then organized into a total of 96 recommendations to act as a foundation for future work worldwide. Here we summarize the background of the project, the meeting and its recommendations.