A new computational tool developed at the U.S. Department of Energy's Pacific Northwest National Laboratory (PNNL) is speeding up our understanding of the machinery of life -- which could bring researchers one step closer to curing diseases, finding safer ways to clean the environment and protecting the country against biological threats.

ScalaBlast is a sophisticated "sequence alignment tool" that can divide the work of analyzing biological data into manageable fragments so that large data sets can run on many processors simultaneously. With this technology, large-scale problems -- such as the analysis of an organism -- can be solved in minutes, rather than weeks.

In order to get answers to complicated biological questions more quickly, researchers at the PNNL "parallelized" the software using the powerful Global Arrays programming tool kit to create algorithms to divvy up the work.

PNNL researchers say ScalaBlast may be used to process complex genomic sequences -- work that's essential to understanding the building blocks of genomes and how they work and fit together. Genomes represent an organism's entire DNA, including its genes.

Before ScalaBlast was available, it took researchers 10 days to analyze one organism. Now, they can analyze 13 organisms in nine hours.

Konrad Zuse

Difference Engines: Get With the Program

In 1941, Konrad Zuse, a German who had already developed a number of calculating machines, released his Z3 machine, which was designed to solve complex engineering equations. The Z3, the first modern programmable computer, was controlled by perforated strips of discarded movie film. It was also the first machine to work on the binary system, as opposed to the more familiar decimal system, making it the true precursor of the modern computers used today.

Binary representation proved important in the future design of computers that took advantage of a multitude of two-state devices such as card readers, electric circuits that could be on or off, and vacuum tubes.

	Munich museum reproduction of the Z3

In 1946, Zuse founded the first pure compute start-up company, Zuse-Ingenieurburo Hopferau. He later founded another company, Zuse KG, which in September 1950 became the first manufacturer in the world to sell a computer, the Z4. Zuse KG's Z22 was the first computer with a memory based on magnetic storage.

Zuse generated ripples in the scientific pond in 1967 when he suggested that the universe itself is running on a grid of computers. His 1969 book Rechnender Raum (translated at MIT as Calculating Space) expanded on the idea and was the obvious precursor to Stephen Wolfram's attention-grabbing 2002 book, A New Kind of Science.

Zuse died in January of 1996.

Groves of Academe

Cell phone usage overlaid on Graz streets

Researchers at MIT have mapped a city in real time by tracking tens of thousands of people traveling about carrying cell phones.

Using anonymous cell phone data provided by Austrian cell phone operator A1/Mobilkom, the researchers developed the Mobile Landscapes project, creating electronic maps of cell phone use in the metropolitan area of Graz, Austria's second-largest city.

The project used three types of data -- the density of cell phone calls, the origins and destinations of the calls, and the positions of users tracked at regular intervals -- to create computer-generated images that can be overlaid on one another and with geographic and street maps to show the peaks and valleys of the landscape as well as peaks in cell phone use.

"For the first time, we are able to visualize the full dynamics of a city in real time," says project leader Carlo Ratti, an architect/engineer and head of MIT's Senseable City Laboratory. "This opens up new possibilities for urban studies and planning. The real-time city is now real."

The research could also have implications for use in large-scale emergencies and for transportation engineers seeking ways to better manage freeway traffic, according to Ratti.