Category Archives: Transhuman News

Virginia Polytechnic Institute and State University, more often known as Virginia Tech, is using high-performance computing (HPC) in the Microsoft Azure cloud, together with parallel laptop computing, to support a cancer research programme.

Wu Feng, a professor of computer science at Virginia Tech, said: We looked at trying to empower cancer biologists to tackle problems they would not be able to tackle by unleashing the power of parallel computing to the masses, enabling discoveries to be made faster.

Feng said the computer industry is unable to keep up with the data processing requirements of DNA sequencing. "DNA sequencing has accelerated faster than we can compute. The amount of data coming out of DNA sequencing doubles every six months, while computing power only doubles every 24 months."

The university has used Microsoft Azure to enable Feng and the team of researchers to keep up with DNA sequencing data growth.

When I first started this research, we doubled DNA data every 12 months, then it went to nine months, then to six, said Feng.

From a computational perspective, quadrupling the technology is cost prohibitive, since the requirements of the DNA researchers outpace the economic model based on Moores Law, which the IT industry generally follows.

While it is possible to buy twice as much for the same financial outlay every 18 months to two years, as stipulated by Moores Law, according to Feng the researchers needed four times as much IT every two years.

We needed to look at innovative tools to avoid having to quadruple IT resources every six months, he said.

An exhaustive search on the genome involves a medium-sized dataset, but Feng said processing involves big compute and big output data. He said next-generation DNA sequence analysis will involve big input data, big compute, and the application could output anything from small to very large datasets.

The university tried building a proof-of-concept application using its supercomputer, called HokiSpeed a 400-processor system with 2,400 CPU cores and 400 GPU cards, where each GPU card used 400 cores. This machine made the supercomputer Top500 list a few years ago but, according to Feng, it timed out when the researchers tried to run the proof-of-concept DNA analytics application.

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Virginia Tech powers DNA analysis with PC parallel computing and Azure

IMAGE:This is an artist's impression of shape-complementary DNA components that self-assemble into nanoscale machinery. view more

Credit: C. Hohmann / NIM

The latest DNA nanodevices created at the Technische Universitaet Muenchen (TUM) - including a robot with movable arms, a book that opens and closes, a switchable gear, and an actuator - may be intriguing in their own right, but that's not the point. They demonstrate a breakthrough in the science of using DNA as a programmable building material for nanometer-scale structures and machines. Results published in the journal Science reveal a new approach to joining - and reconfiguring - modular 3D building units, by snapping together complementary shapes instead of zipping together strings of base pairs. This not only opens the way for practical nanomachines with moving parts, but also offers a toolkit that makes it easier to program their self-assembly.

The field popularly known as "DNA origami," in reference to the traditional Japanese art of paper folding, is advancing quickly toward practical applications, according to TUM Prof. Hendrik Dietz. Earlier this month, Dietz was awarded Germany's most important research award, the Gottfried Wilhelm Leibniz Prize, for his role in this progress.

In recent years, Dietz and his team have been responsible for major steps in the direction of applications: experimental devices including a synthetic membrane channel made from DNA; discoveries that cut the time needed for self-assembly processes from a week to a few hours and enable yields approaching 100%; proof that extremely complex structures can be assembled, as designed, with subnanometer precision.

Yet all those advances employed "base-pairing" to determine how individual strands and assemblies of DNA would join up with others in solution. What's new is the "glue."

"Once you build a unit with base pairs," Dietz explains, "it's hard to break apart. So dynamic structures made using that approach tended to be structurally simple." To enable a wider range of DNA nanomachines with moving parts and potentially useful capabilities, the team adapted two more techniques from nature's biomolecular toolkit: the way proteins use shape complementarity to simplify docking with other molecules, and their tendency to form relatively weak bonds that can be readily broken when no longer needed.

Bio-inspired flexibility

For the experiments reported in Science, Dietz and his co-authors - doctoral candidates Thomas Gerling and Klaus Wagenbauer, and bachelor's student Andrea Neuner from TUM's Munich School of Engineering - took inspiration from a mechanism that allows nucleic acid molecules to bond through interactions weaker than base-pairing. In nature, weak bonds can be formed when the RNA-based enzyme RNase P "recognizes" so-called transfer RNA; the molecules are guided into close enough range, like docking spacecraft, by their complementary shapes.

The new technology from Dietz's lab imitates this approach. To create a dynamic DNA nanomachine, the researchers begin by programming the self-assembly of 3D building blocks that are shaped to fit together. A weak, short-ranged binding mechanism called nucleobase stacking can then be activated to snap these units in place. Three different methods are available to control the shape and action of devices made in this way.

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Designer's toolkit for dynamic DNA nanomachines