Stanford University computer scientist Debashis Sahoo and computer science professor David Dill recently completed a study of a program based on Boolean logic that can locate specific genes. Starting with two known B-cell genes, Sahoo searched through databases with thousands of gene products in milliseconds and found 62 genes that matched the patterns he would expect to see for genes that got turned on in between the activation of the two genes he started with. He then examined databases involving 41 strains of laboratory mice that were known to be deficient in one or more of the 62 genes. Of those 41 strains, 26 had defects in B-cell development. “Biologists are really amazed that, with just a computer algorithm, in milliseconds I can find genes that it takes them a really long time to isolate in the lab,” Sahoo says. He is currently using the technique to try to find new genes that contribute to cancer development. “This shows that computational analysis of existing data can provide clues about where researchers should look next,” Sahoo says.
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Howard Hughes Medical Institute (HHMI) computer scientists have developed V3D, a software suite that features tools for visualizing, analyzing, and measuring complex, three-dimensional (3D) biological and biomedical images. The free software promises to greatly accelerate scientists’ ability to assemble and manipulate extremely detailed images. The digital reconstruction tools are 17 times more reliable than those created using commercially available software, according to HHMI computer scientist Hanchuan Peng. The HHMI team wrote algorithms to accelerate the rendering of the images on the screen. V3D allows the user to drag and drop the images to be analyzed, and to pinpoint a location in a 3D image with a mouse click. “Since we have a very fast renderer for 3D images, we were able to design new approaches to manipulate very large images freely in real time,” Peng says.
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Robotics researchers recently have focused on multiple-robot systems that work together and react to each other, with the goal of one day performing dangerous or menial tasks that machines, in combination, might do better than humans. One way researchers are getting robots to work together is by designing all-robotic soccer teams. “When we started this, the main research question was … how do you get multiple robots to coordinate?” says Carnegie Mellon University professor Manuela Veloso. Researchers also are studying insects, such as ants, bees, and termites, that work together to accomplish complex goals such as building an intricate nest. “These collective behaviors are very powerful and arise from very simple individuals,” says Harvard University professor Radhika Nagpal. Nagpal is part of a project to create robotic bees that mimic those in nature. Rice University’s James McLurkin is developing a swarm of robots that can seek out the boundaries of an area, which could be useful in exploration.
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