[CAnet - news] Steering bio-medical applications over grids and high speed networks

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[Some excerpts from an exciting cyber-infrastructure application reported on
Science Grid-- BSA]

http://www.interactions.org/sgtw/2005/1102/spice_more.html


Scientists in the UK combine grid computing, high-speed networks,
supercomputers and three-dimensional visualization technology to study how
biomolecules move through cell and nuclear membranes. Translocation, the
process through which a DNA or mRNA fragment moves from the outside of a
membrane to the inside through a pore, is important for several scientific
disciplines and technological applications.

"Geneticists, biologists and physicists all study this problem," said
Shantenu Jha, a physicist from University College London (UCL). "Geneticists
are interested in how the DNA unravels, and physicists are interested in
translocation as an energy problem. It has technical applications as
well-nanotechnology and materials science researchers want to use artificial
pores very similar to the natural pore we're investigating to screen
thousands of DNA fragments against a test fragment and see what matches."

Jha collaborates in the SPICE-Simulated Pore Interactive Computing
Environment-project, which uses the RealityGrid Steering Library and
associated middleware to run interactive simulations on the UK's National
Grid Service and TeraGrid in the U.S. The simulations are unique; instead of
a one-way flow of simulation data from supercomputer to remote visualization
resource, the scientist also uses the visualization to steer the simulation.
The bi-directional data flow is made more challenging when the simulation
and visualization resources are located hundreds, or even thousands, of
miles away.

With SPICE, a scientist at UCL uses a visualizer to apply forces to
individual atoms in the DNA molecule, "dragging" the DNA through the pore.
Information about his actions is sent across high-speed networks to
supercomputers connected to the NGS or TeraGrid, where the response is
simulated and sent back to UCL. He physically feels the response through a
haptic device, and views it in 3D through the use of goggles and a tiled
display. The RealityGrid steering framework permits the integration of
numerical simulations and instruments to the same grid middleware. 

View a SPICE demonstration video at http://www.realitygrid.org/SPICE/.


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