The Virtual Kidney: an eScience interface and Grid portal

Abstract

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.

Modeling transport in the kidney: investigating function and dysfunction

“…Thus an important challenge for modelers is how to make their work more accessible, their hypotheses and suggestions more widely read, and their tools more useful to experimental researchers. The Renal Physiome Project seeks to make a major effort to facilitate access to quantitative kidney data (http://physiome.ibisc.fr/qkdb/) and to make mathematical models of the kidney part of the normal toolbox of renal research laboratories (21,88,89). Whether through this interface or another, greater feedback between modelers and experimentalists should increase the pace of progress toward a common goal, an improved understanding and treatment of kidney diseases.…”

From digital hype to analogue reality: Universal simulation beyond the quantum and exascale eras

“…There are multiscale models of the skeletal and musculoskeletal systems [ 66 ]. Efforts are also under way to develop virtual livers [ 67 ], lungs [ 68 ] and kidneys [ 69 ]. In particular, great progress has been made since the 1960s in modelling the heart [ 70 ], flows in the aorta [ 71 ] and to integrate knowledge at the tissue, cellular, and molecular levels.…”

Current Trends and New Challenges of Databases and Web Applications for Systems Driven Biological Research

“…This endeavor will continue till an acceptable end result is accomplished. Many projects have tried to solve the interoperability problems by developing specialized platforms called grids (e.g., caGRID, Saltz et al, 2006 ; PathGrid, Arbona et al, 2007 ; Walton et al, 2010 ; The Virtual Kidney, Harris et al, 2009 ; Abramson et al, 2010 ; GEMSS, Benkner et al, 2005 ). At its conception the “Grid” was envisioned as a distributed and cost-effective solution to boost computational power to solve large-scale mathematical and data-bound problems.…”