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Welcome to the July 23, 2012 edition of ACM TechNews, providing timely information for IT professionals three times a week.

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Stanford Researchers Produce First Complete Computer Model of an Organism
Stanford Report (CA) (07/19/12) Max McClure

Stanford University researchers recently used data from more than 900 scientific papers to account for every molecular interaction that takes place in the life cycle of the world's smallest free-living bacterium to create the world's first complete computer model of an organism. The researchers say the model enables scientists to answer questions that have not been practical to examine in the past. They also note the model represents a stepping-stone toward the use of computer-aided design in bioengineering and medicine. "Comprehensive computer models of entire cells have the potential to advance our understanding of cellular function and, ultimately, to inform new approaches for the diagnosis and treatment of disease," says the U.S. National Institutes of Health's James M. Anderson. The final model used more than 1,900 experimentally determined parameters, which were integrated into a unified machine by being separated into 20 modules, each governed by its own algorithm. The modules communicated to each other after every step, resulting in a unified whole that closely matched the bacterium's real-world behavior. The completely computational cell allows for procedures that would be difficult to perform in an actual organism, as well as opportunities to reexamine experimental data.

Researchers Squeeze GPU Performance From 11 Big Science Apps
HPC Wire (07/18/12) Michael Feldman

The Oak Ridge Leadership Computing Facility published a report in which researchers documented that graphical processing unit (GPU)-equipped supercomputers increased application speeds by a factor of between 1.4 and 6.1 across a range of science applications. The performance gains using GPU-based supercomputers indicate the technology is generating good results across a range of applications. The 11 simulation programs, which include S3D, Denovo, LAMMPS, WL-LSMS, CAM-SE, NAMD, Chroma, QMCPACK, SPECFEM-3D, GTC, and CP2K are used by tens of thousands of researchers around the world. The report was written by researchers from Oak Ridge National Laboratory, the National Center for Supercomputing Applications, and the Swiss National Supercomputing Center (CSCS). The researchers ran the programs on CSCS' Monte Rosa, which has two AMD Interlagos central processing units (CPUs) per node, and TitanDev, which consists of hybrid nodes that each contain one NVIDIA Fermi GPU and one Interlagos CPU. The researchers found that only Chroma fully exploited the performance advantage of GPU-based processing. Meanwhile, another factor to consider in comparing application performance is power usage, since GPU accelerators use about twice as much power as high-end X86-based systems.

NaCl to Give Way to RockSalt
Harvard University (07/20/12) Mureji Fatunde

Harvard University researchers have developed RockSalt, software that can boost the security and enhance the performance of Web and mobile applications. RockSalt can verify that native computer programming languages comply with a certain security policy. “When a user opens an external application, such as Gmail or Angry Birds, Web browsers such as Google Chrome typically run the program’s code in an intermediate and safer language such as JavaScript,” says Harvard professor Greg Morrisett. “In many cases it would be preferable to run native machine code directly.” Morrisett previously developed a way to implement the decade-old software fault isolation solution developed by University of California, Berkeley on CISC-based chips. Google then modified the routine for Google Chrome, developing it into Google Native Client. However, bugs and different vulnerabilities were eventually discovered within the checker for NaCl, so Morrisett had his undergraduate students develop a solution. RockSalt consists of just 80 lines of code, and is faster and has no known vulnerabilities. Morrisett says it enables programmers to code in any language, compile it to native executable code, and secure it without going through intermediate languages such as JavaScript.

Computer Analysis Predicted Rises, Ebbs in Afghanistan Violence
Los Angeles Times (07/17/12) Jon Bardin

A team of international researchers has developed a model based on recently published WikiLeaks data that can predict which provinces in Afghanistan will experience the most violence in the future. The researchers used written reports of violence from 2004 to 2009 to predict a pattern of violence in 2010. The combination of widely available data and steady increases in computing power has prompted experts to utilize objective quantitative analysis in fields that previously were considered fundamentally subjective, such as literature and the study of social groups. "For the first time, we have large data sets from places like Facebook and Twitter that we can analyze with high-powered computers and get meaningful results," says U.S. Military Academy at West Point researcher Paulo Shakarian. The model "doesn't take in any knowledge of military operations or political events, and it treats all types of violence exactly the same, whether it's a stop-and-search or a big battle," says University of Edinburgh researcher Guido Sanguinetti. The researchers were surprised that the model could predict activity even in Afghanistan's less violent northern provinces. "This shows that the escalation we see isn't just attributed to the noise in the data," says Edinburgh researcher Andrew Zammit Mangion.

A Texas Hold 'Em Tournament for AIs
IEEE Spectrum (07/17/12) Richard Gibson

The University of Alberta's Computer Poker Research Group has been competing in the Annual Computer Poker Competition (ACPC) since the contest was launched in 2006. ACPC's first contest had just four entrants that played one of two poker games. However, ACPC has grown quickly. Last year's contest had 21 poker-playing programs for heads-up limit, eight programs for heads-up no limit, and 10 programs for three-player limit. This year's competition includes three poker games, including heads-up limit, heads-up no limit, and three-player limit Texas Hold 'Em. In the future, more games will likely be introduced as recommended by competitors and the competition's officials. After playing millions of hands of poker, two criteria are used to determine the winner in each of the three games. In the total bankroll mechanism, the winner is simply the program that wins the most chips against all of its opponents combined. In contrast, the bankroll instant-runoff mechanism for determining winners sequentially eliminates the player that earned the fewest chips against the remaining non-eliminated players, and the last player remaining is declared the winner.

The UI Computer Science and Psychology Dept's Create Bike Simulators
Daily Iowan (07/20/12) Tom Clos

University of Iowa researchers have developed two bike simulators that are used to study aspects of child safety behavior. "In order to understand what risks are involved with children and how to protect them, we need to know how their behavior differs from adults," which is the main focus of this study, says Iowa professor Joe Kearney. The simulator involves a child subject riding the bike down a street for several blocks before stopping at a busy intersection. When the subjects restart the bike in an attempt to cross the street, their timing is measured in comparison to adult subjects. "Unlike most virtual experiences, this runs on self-initiated motion," Kearney notes. The data is transmitted directly from the bike to a computer where software is used to complete the experiment. "We'll also create computer programs to identify where you were in the simulation and extract information out of it," Kearney says. The second bike simulator, which is nearing completion, enables people to ride with each other, and provides researchers with another variable for the study. Each subject sees an avatar of the other rider on the screen riding next to them during the simulation.

Research Update: Chips With Self-Assembling Rectangles
MIT News (07/17/12) Caroline McCall

Massachusetts Institute of Technology (MIT) researchers have developed an approach to creating the array of wires on microchips that uses a system of self-assembling polymers. The process produces arrays of wires that meet at right angles, forming squares and rectangles, which are traditionally very difficult to produce through self-assembly. When molecules self-assemble, they have a natural tendency to create hexagonal shapes, such as in a honeycomb or an array of soap bubbles between sheets of glass, notes MIT professor Caroline Ross. The MIT researchers' approach creates an array of tiny posts on the surface that guides the patterning of the self-assembling polymer molecules. The system also creates a variety of shapes of the material itself, including cylinders, spheres, ellipsoids, and double cylinders. These shapes are possible because "the template, which is coated so as to repel one of the polymer components, causes a lot of local strain on the pattern," says MIT professor Karl Berggren. The technique also can make "complex patterns, which is an objective for nanodevice fabrication," with fewer steps than current processes, says MIT's Amir Tavakkoli.

NSF Announces New SAVI at Intersection of IT, Disasters
CCC Blog (07/19/12) Erwin Gianchandani

U.S. and Japanese researchers will collaborate on developing fundamental advances in information technology (IT) to support disaster management under a new Science Across Virtual Institutes project. The U.S. National Science Foundation (NSF) says the project, called the Global Research on Applying Information Technology to Support Effective Disaster Management (GRAIT-DM), will foster collaboration on improving the resilience and responsiveness of IT to enable real-time data sensing and analysis, which is critical for time-sensitive decision-making. GRAIT-DM also will focus on advancing fundamental knowledge and innovation for resilient and sustainable civil infrastructure and distributed infrastructure networks, and acquiring big data and improving broad knowledge of preparedness and response at human, societal, and global scales. NSF, Japan's National Institute of Informatics, and the Japan Society for the Promotion of Science will support the research team. Georgia Tech's Carlton Pu and the University of Tokyo's Masuru Kitsuregawa will co-lead the team. GRAIT-DM also should address some challenges highlighted in a recent Computing Community Consortium report on the outcomes of visioning activity on computing for disaster management.

Robot Swarms Aim to Bring Buildings to Life
BBC News (07/18/12) Christopher Mims

Engineer Akira Mita seeks to create "living" buildings occupied by swarms of robotic sensors that track and understand virtually everything about human residents, including their emotional state. The sensors will learn from their errors, self-regulate through the use of digital "hormones," and record information over the course of years, accumulating an experiential archive to be used to program future sensors or even other buildings. Mita aims to replace conventional sensor networks used in contemporary smart homes with sensor swarms, and his research has yielded a prototype device called the e-bio that can precisely pinpoint sounds and build a three-dimensional model of its environment 10 times a second with a laser eye. Mita's team is focused on making these machines hyper-sensitive to signals emitted by humans, such as body language or words that indicate discomfort. In response, the robots would communicate a hormonal signal that would change the network's behavior to adjust temperature, illumination, or other environmental controls to increase occupants' comfort levels. Mita's vision is for the robots to make consensus decisions for changing a building's environment.

College Degrees, Designed by the Numbers
Chronicle of Higher Education (07/18/12) Marc Parry

Colleges are starting to tap opportunities inherent in big data, using insights mined from information about students' performance to tailor courses and degrees. Arizona State University is at the forefront of this trend with applications such as eAdvisor, a degree-monitoring system that tracks students' performance in their majors, and flags them as "off-track" if they do not sign up for a key course or do well enough. Meanwhile, Austin Peay State University has a robot adviser evaluate student profiles and direct students toward courses in which they are likely to succeed, before they register for classes. Underlying this system is software that merges each student's transcript with thousands of past students' grades and standardized test scores to generate suggestions. When students log into the online portal, they see 10 personalized course suggestions ranked on a five-star scale. "We're steering students toward the classes where they are predicted to make better grades," says provost and software programmer Tristan Denley. Analysts expect that colleges will use data-mining technology to gain knowledge about all aspects of student life, including social situations, which have been shown to influence academic performance.

UT Computer Science Professor Develops New Software to Aid in Disease Treatment
Daily Texan (07/18/12) David Maly

University of Texas (UT) researchers have developed software that can determine which compounds will best treat diseases using less information than was previously required. The software relies on the 3D quasi-atomistic model of a virus' protein cells to identify possible cures. The researchers, led by UT professor Chandrajit Bajaj, developed algorithms to study the necessary detail on the 3D quasi-atomistic cell model needed to determine which drugs are most likely to prevent or treat a disease. UT researcher Qin Zhang says the software will greatly help with future drug research by enabling scientists to research viruses without using the 3D atomistic model. Although the software has been used mostly for HIV research, other scientists have approached the UT team about using it for work on other viruses. "Each one is where they don’t have an atomistic model to begin with, and there is not any solution available other than ours," Bajaj says.

Clemson Researcher: Humanizing Computer Aids Affects Trust, Dependence
Clemson University (SC) (07/17/12) Brian Mullen

Clemson University professor Richard Pak has found that computerized decision-support aids that include person-like characteristics can influence trust and dependence among adults. Pak's research examined how decision-making would be affected by a human-like aid, focusing on adults' trust, dependence, and performance while using a computerized decision-making aid for persons with diabetes. "Just as trust is an important factor in how humans deal with other humans, it also can determine how users interact with computerized systems," Pak says. When automation is only reliable part of the time, a user's trust level becomes an important factor that can determine how often the aid will be used. "Figuring out how trust is affected by the design of computerized aids is important because we want people to trust and use only reliable aids," Pak says. His research demonstrates that the inclusion of a person's image can substantially change perceptions of a computerized aid when there is no distinction in the aid's reliability or presentation of information. "Human-like computer aids provide a reduced decision-making reaction time for adults," Pak says.

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