Computer scientists develop new way to study molecular networks

Jan. 24, 2013 — In biology, molecules can have multi-way interactions within cells, and until recently, computational analysis of these links has been "incomplete," according to T. M. Murali, associate professor of computer science in the College of Engineering at Virginia Tech.

His group authored an article on their new approach to address these shortcomings, titled "Reverse Engineering Molecular Hypergraphs," that received the Best Paper Award at the recent 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine.

Intricate networks of connections among molecules control the processes that occur within cells. The "analysis of these interaction networks has relied almost entirely on graphs for modeling the information. Since a link in a graph connects at most two molecules (e.g., genes or proteins), such edges cannot accurately represent interactions among multiple molecules. These interactions occur very often within cells," the computer scientists wrote in their paper.

To overcome the limitations in the use of the graphs, Murali and his students used hypergraphs, a generalization of a graph in which an hyperedge can connect multiple molecules.

"We used hypergraphs to capture the uncertainty that is inherent in reverse engineering gene to gene networks from systems biology datasets," explained Ahsanur Rahman, the lead author on the paper. "We believe hypergraphs are powerful representations for capturing the uncertainty in a network's structure."

They developed reliable algorithms that can discover hyperedges supported by sets of networks. In ongoing research, the scientists seek to use hyperedges to suggest new experiments. By capturing uncertainty in network structure, hyperedges can directly suggest groups of genes for which further experiments may be required in order to precisely discover interaction patterns. Incorporating the data from these experiments might help to refine hyperedges and resolve the interactions among molecules, resulting in fruitful interplay and feedback between computation and experiment.

Murali, and his students Ahsanur Rahman and Christopher L. Poirel, both doctoral candidates, and David L. Badger, a software engineer in Murali's group, all of Blacksburg, Va., and all in the computer science department, used funding from the National Institutes of Health and the National Science Foundation to better understand this uncertainty in these various forms of interactions.

Murali is also the co-director of the Institute for Critical Technology and Applied Science's Center for Systems Biology of Engineered Tissues and the associate program director for the computational tissue engineering interdisciplinary graduate education program at Virginia Tech.

Share this story on Facebook, Twitter, and Google:

Other social bookmarking and sharing tools:

Story Source:

The above story is reprinted from materials provided by Virginia Tech, via EurekAlert!, a service of AAAS.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Study reveals impact of public DNS services; Researchers develop tool to help

Oct. 25, 2012 — A new study by Northwestern University researchers has revealed that public DNS services could actually slow down users' web-surfing experience. As a result, researchers have developed a solution to help avoid such an impact: a tool called namehelp that could speed web performance by 40 percent.

Through a large-scale study involving more than 10,000 hosts across nearly 100 countries, Fabián Bustamante, associate professor of electrical engineering and computer science at Northwestern's McCormick School of Engineering and Applied Science, and his team found that one cause of slow web performance is a growing trend toward public Domain Name Systems (DNS), a form of database that translates Internet domain and host names into Internet Protocol (IP) addresses.

DNS services play a vital role in the Internet: every time a user visits a website, chats with friends, or sends email, his computer performs DNS look-ups before setting up a connection. Complex web pages often require multiple DNS look-ups before they start loading, so users' computers may perform hundreds of DNS look-ups a day. Most users are unaware of DNS, since Internet Service Providers (ISP) typically offer the service transparently.

Over the last few years, companies such as Google, OpenDNS, and Norton DNS have begun offering "public" DNS services. While "private" DNS services, such as those offered by ISPs, may be misconfigured, respond slowly to queries, and go down more often, public DNS services offer increased security and privacy, and quicker resolution time. The arrangement is also beneficial for public DNS providers, who gain access to information about users' web habits.

Bustamante and his team found that while using public DNS services may provide many benefits, users' web performance can suffer due to the hidden interaction of DNS with Content Delivery Networks (CDNs), another useful and equally transparent service in the web.

CDNs help performance by offering exact replicas of website content in hundreds or thousands of computer servers around the world; when a user types in a web address, he is directed to the copy geographically closest to him. Most popular websites -- more than 70 percent of the top 1,000 most popular sites, according to the Northwestern study -- rely on CDNs to deliver their content quickly to users around the world.

But researchers found that using public DNS services can result in bad redirections, sending users to content from CDN replicas that are three times farther away than necessary.

Public DNS and CDN services are working to address the problem, but current users are left with two mediocre options -- bad web performance through public DNS services or bad security and privacy support through private DNS services.

Now Bustamante and his group have developed a tool called namehelp that may let users have their cake and eat it, too -- by using public DNS services without compromising on web performance.

namehelp runs personalized benchmarks in the background, from within users' computers, to determine their optimal DNS configuration and improve their web experience by helping sites load faster. If it finds that a user is receiving less than optimal web performance, namehelp automatically fixes it by cleverly interacting with DNS services and CDNs to ensure the user gets his content from the nearest possible copy.

You can download namehelp today from: http://aqualab.cs.northwestern.edu/projects/namehelp.

The paper describing the research is titled "Content Delivery and the Natural Evolution of DNS: Remote DNS Trends, Performance Issues and Alternative Solutions." The team's findings will be presented at the Internet Measurement Conference (IMC 2012) in Boston this November. In addition to Bustamante, authors on the paper are lead author John S. Otto, Mario A. Sanchez, and John P. Rula, all of Northwestern.

Share this story on Facebook, Twitter, and Google:

Other social bookmarking and sharing tools:

Story Source:

The above story is reprinted from materials provided by Northwestern University.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Scientists develop biological computer to encrypt and decipher images

ScienceDaily (Feb. 7, 2012) — Scientists at The Scripps Research Institute in California and the Technion-Israel Institute of Technology have developed a "biological computer" made entirely from biomolecules that is capable of deciphering images encrypted on DNA chips. Although DNA has been used for encryption in the past, this is the first experimental demonstration of a molecular cryptosystem of images based on DNA computing.

The study was published in a recent online-before-print edition of the journal Angewandte Chemie.

Instead of using traditional computer hardware, a group led by Professor Ehud Keinan of Scripps Research and the Technion created a computing system using bio-molecules. When suitable software was applied to the biological computer, it could decrypt, separately, fluorescent images of The Scripps Research Institute and Technion logos.

A Union Between Biology and Computer Science

In explaining the work's union of the often-disparate fields of biology and computer science, Keinan notes that a computer is, by definition, a machine made of four components -- hardware, software, input, and output. Traditional computers have always been electronic, machines in which both input and output are electronic signals. The hardware is a complex composition of metallic and plastic components, wires, and transistors, and the software is a sequence of instructions given to the machine in the form of electronic signals.

"In contrast to electronic computers, there are computing machines in which all four components are nothing but molecules," Keinan said. "For example, all biological systems and even entire living organisms are such computers. Every one of us is a biomolecular computer, a machine in which all four components are molecules that 'talk' to one another logically."

The hardware and software in these devices, Keinan notes, are complex biological molecules that activate one another to carry out some predetermined chemical work. The input is a molecule that undergoes specific, predetermined changes, following a specific set of rules (software), and the output of this chemical computation process is another well-defined molecule.

"Building" a Biological Computer

When asked what a biological computer looks like, Keinan laughs.

"Well," he said, "it's not exactly photogenic." This computer is "built" by combining chemical components into a solution in a tube. Various small DNA molecules are mixed in solution with selected DNA enzymes and ATP. The latter is used as the energy source of the device.

"It's a clear solution -- you don't really see anything," Keinan said. "The molecules start interacting upon one another, and we step back and watch what happens." And by tinkering with the type of DNA and enzymes in the mix, scientists can fine-tune the process to a desired result.

"Our biological computing device is based on the 75-year-old design by the English mathematician, cryptanalyst, and computer scientist Alan Turing," Keinan said. "He was highly influential in the development of computer science, providing a formalization of the concepts of algorithm and computation, and he played a significant role in the creation of the modern computer. Turing showed convincingly that using this model you can do all the calculations in the world. The input of the Turing machine is a long tape containing a series of symbols and letters, which is reminiscent of a DNA string. A reading head runs from one letter to another, and on each station it does four actions: 1) reading the letter; 2) replacing that letter with another letter; 3) changing its internal state; and 4) moving to next position. A table of instructions, known as the transitional rules, or software, dictates these actions. Our device is based on the model of a finite state automaton, which is a simplified version of the Turing machine. "

Unique Biological Properties

Now that he has shown the viability of a biological computer, does Keinan hope that this model will compete with its electronic counterpart?

"The ever-increasing interest in biomolecular computing devices has not arisen from the hope that such machines could ever compete with electronic computers, which offer greater speed, fidelity, and power in traditional computing tasks," Keinan said. "The main advantages of biomolecular computing devices over electronic computers have to do with other properties."

As shown in this work, he continues, a wealth of information can be stored and encrypted in DNA molecules. Although each computing step is slower than the flow of electrons in an electronic computer, the fact that trillions of such chemical steps are done in parallel makes the entire computing process fast. "Considering the fact that current microarray technology allows for printing millions of pixels on a single chip, the numbers of possible images that can be encrypted on such chips is astronomically large," he said.

"Also, as shown in our previous work and other projects carried out in our lab, these devices can interact directly with biological systems and even with living organisms," Keinan explained. "No interface is required since all components of molecular computers, including hardware, software, input, and output, are molecules that interact in solution along a cascade of programmable chemical events." He adds that because of DNA's ability to store information, major computer companies have been extremely interested in the development of DNA-based computing systems.

The first author of the study, "A Molecular Cryptosystem for Images by DNA Computing," is graduate student Sivan Shoshani of Technion. In addition to Keinan and Shoshani, authors include postdoctoral fellow Ron Piran of Scripps Research and Yoav Arava of the Technion.

This work was supported by the National Science Foundation, the Israel-US Binational Science Foundation, and the Skaggs Institute for Chemical Biology, as well as graduate fellowships from the Irwin and Joan Jacobs Foundation, the Fine Foundation, the Russell Berrie Nanotechnology Institute, and the Israel Ministry of Science and Technology.

Share this story on Facebook, Twitter, and Google:

Other social bookmarking and sharing tools:

Story Source:

The above story is reprinted from materials provided by Scripps Research Institute.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Sivan Shoshani, Ron Piran, Yoav Arava, Ehud Keinan. A Molecular Cryptosystem for Images by DNA Computing. Angewandte Chemie International Edition, 2012; DOI: 10.1002/anie.201107156

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here