Computers/Technology | Duke Research Blog

Students Create Multimedia Ocean Conservation Text

April 16th, 2013

By Ashley Yeager

This screenshot shows one of the opening page of of Johnston's new iBook. Image courtesy of Dave Johnston, Duke.

This screenshot shows one of the opening pages of a chapter in Johnston’s new iBook. Image courtesy of Dave Johnston, Duke.

Duke marine biologist Dave Johnston and his students are back in business on iTunes.

They’ve just released The View From Below, a free iBook for middle school students and teachers that uses multimedia and classroom exercises to discuss overfishing, marine debris, climate change, invasive species and other issues related to marine conservation.

This is Johnston’s second digital textbook. His first was Cachalot, an iPad textbook covering the latest science of marine mammals like whales, dolphins and seals. Experts contributed the text, images and open-access papers.

The View From Below, however, is a bit different.

Undergraduate students in Johnston’s Marine Conservation Service Learning class wrote the book using Apple’s iBooks authoring tool. Johnston and Tom Schultz, Director of the Marine Conservation Molecular Facility at Duke’s Marine Lab, edited it.

“There are a lot of people exploring the use of the iBooks platform for student-generated content, among other development platforms,” Johnston says. “I don’t think we’ve seen many that focus on marine science yet though, and I’m pretty sure it’s the first marine conservation textbook written by students on the iTunes store.”

Johnston says the class chose to use the iBooks software because the technology is free, easy to use and provides “great templates to get things going quickly.” The software also works well because Duke’s Marine Lab has an iPad loaner program, making the tablet the platform of choice for developing and testing the textbook.

The middle school that the service learning class works with also has access to iPads for students and instructors, so the audience was there for the iPad format, Johnston adds.

His students chose to write the book as the class project to spur learning and discussion about some of the most serious problems facing Earth’s oceans.

“As the text indicates, all life on earth is ultimately supported by the ocean, so we need to take care of it,” he says.

Film Presents Alan Turing In Full; Duke Preview Monday

October 24th, 2012

Guest post by Pender M. McCarter, Trinity College (1968), Senior Public Relations Counselor, IEEE-USA/Washington

A scene from the movie “Codebreaker” about the life of Alan Turing.

Alan Turing has been hailed as a digital Darwin, an Einstein and a Newton who helped to “catapult civilization in to the digital age.” The British mathematician laid the groundwork for everything we do with computers today, according to Apple co-founder Steve Wozniak. The Turing Machine incorporated all the basic aspects of computer input and output. His 1950 paper, “Computing Machinery and Intelligence,” posited that computers can be programmed to mimic human behavior. And at the end of his life, Turing wrote about pattern formation in biology, what he called morphogenesis, that could be observed in animal stripes and spirals and even exist in ecosystems and galaxies. Turing is best known for leading the British Bletchley Park code breakers team that cracked Germany’s Naval Enigma Code, helped end World War II, and saved perhaps millions of lives.

Yet until recently Turing’s contributions have been little known or appreciated outside of the sci-tech community. And his personal life as a gay man has generally been glossed over. In 2012, the centenary of Alan Turing’s birth, hundreds of events have been held worldwide. A new film, Codebreaker, presents Turing’s personal and professional life without flinching, including how his sexual nature contributed to his extraordinary achievements and tragic downfall.

The drama documentary emphasizes that the support and encouragement Turing enjoyed with other eccentric and brilliant technologists at Bletchley Park motivated and sustained him. When he lost this community after World War II, at a time when there was a craving for normalcy and scant tolerance for non-conformists, Turing learned how unforgiving the world could be.

The drama scenes in Codebreaker center on the psychotherapy sessions Turing participated in during the last 18 months of his life. In these final months, Turing faced persecution as a gay man under the same 19^th century British laws that were used to prosecute Oscar Wilde. In 1954, at the age of 41, Turing committed suicide leaving us to wonder about potential future accomplishments in a more accepting and tolerant time. In 2009, former British Prime Minister Gordon Brown apologized posthumously to Turing: “We’re sorry; you deserved so much better.”

Codebreaker will be screened at the Duke Center for LGBT Life (02 West Union Building) on Monday, Oct. 29, from 7-8:30 p.m., with underwriting from IEEE-USA, the Washington-based office of the IEEE, the world’s largest professional association for the advancement of technology. The drama documentary will be introduced by Executive Producer Patrick Sammon, who will also answer questions about the film.

Here’s a link to the trailer: http://www.turingfilm.com/

Refereed physics for Twitter and Facebook, maybe

October 19th, 2012

By Ashley Yeager

These library stacks of science journals are going out of style as more publishers opt for online-only, open access formats. Credit: UCSF.

When journal publishers send peer-reviewed tweets, they’ll have truly entered the digital age. They’re not there yet, but that doesn’t mean they’re not trying, said Gene Sprouse, editor-and-chief of the American Physical Society(APS) and a physics professor at Stony Brook University.

Sprouse, speaking at an Oct. 17 physics colloquium, described how the Internet is changing the way scientists share their research. They used to submit papers to journals, have their ideas vetted by other scientists, and then see their arguments and data in print — or not. He said it has been this way since the 1660s when the first journal, Philosophical Transactions, was first published.

But with online journals available right on researchers’ desktop and open-access digital archives, such as arXiv.org, journal editors, like those at the helm of magazines and newspapers, are trying to figure out how to shift print publications online while still making a profit.

“Eventually print journals will disappear,” Sprouse said, explaining that sans paper, authors and publishers could include new types of content like movies and active graphics in their articles. But even with new media features, “what physicists want is rapid acceptance of their paper into a prestigious journal with no hassles during peer review. They want attention for their work, and they want it widely distributed.”

To meet those demands in the new media landscape, APS has developed a Creative Commons license for authors to share their articles on their personal web sites and encourages them to publish pre-prints in online digital archives, such as arXiv.org.

Hoping to merge the prestige of the “baby Nature” journals – Nature Photonics, Nature Optics, Nature Physics, etc. – with the open-access model of the Public Library of Science, or PLOS, journals, the society has also created Physical Review X.

It’s the society’s first online-only, fully open-access journal. The one-year-old publication, which charges authors $1,500 per accepted article, is already comparable in prestige to APS’s other leading journal, Physical Review Letters. The difference is that now authors have an open-access journal to submit to at APS, which is important as more funders push researchers to submit to that type of publication, Sprouse said.

The society isn’t ignoring Twitter and Facebook either. When asked when the society would post the first refereed physics tweet, Sprouse said he couldn’t really say because he personally doesn’t use social media. But, APS, he added quickly, is working on its social media strategy and would “welcome any advice from those of you exploring that realm.”

A second crack at the nature of glass

August 13th, 2012

By Ashley Yeager

Glassblowers shape molten silica before the glass transitions from liquid to a more solid structure. Credit: handblownglass.com.

Patrick Charbonneau and his collaborators have taken another crack at understanding the nature of glass. Their latest simulations show that a key assumption of theoretical chemists and physicists to explain the molecular structure of glass is wrong.

Glass forms when liquids are slowly compressed or super-cooled, but don’t crystallize the way cooled water turns to ice. The liquidy pre-cursors to glass, like molten silica, do become hard like a solid, but the atoms in the material don’t organize themselves into a perfect crystal pattern.

The result is a substance that is as hard as a solid but has the molecular arrangement of a liquid — a phenomenon that scientists can’t quite explain, yet.

Previous theories assumed that at the transition point between a liquid and glass, the material’s atoms become caged by each other in a “simple” Gaussian shape. This same shape describes the distribution of people’s height in the U.S. and is known as a bell-shaped curve.

But new simulations, described online Aug. 13 in PNAS, suggest this assumption is wrong. The simulations model the interactions of glass particles in multiple dimensions and show the shape of the particle cage is much more complex than a Gaussian distribution.

The discovery is a “paradigm shift in the sense that so many people have been having the same, wrong, conception for so long, and they should now revisit that basic assumption,” says Charbonneau, a theoretical chemist at Duke. “The assumption was actually constraining how they thought about the problem.”

Even with a new shine on the way scientists think about glass, it is not clear how close or far the theorists are from writing an accurate description of what happens at the liquid-glass transition. But “the path to get there seems clearer than it has been in a long time,” Charbonneau says.

The next step in the research is to understand the relationship between glassy states of matter and those that are jammed, like pieces of cereal wedged in a grain hopper. Charbonneau and collaborators are already at work about how to study the connections between the two forms of matter.

Citation:
“Dimensional study of the caging order parameter at the glass transition.” 2012. Charbonneau, P., et al. PNAS Early Edition. DOI: 10.1073/pnas.1211825109

Reading between the lines of light

August 10th, 2012

By Ashley Yeager

Harry Potter's invisibility cloak is not exactly what scientists have in mind for their light tricks. Credit: Warner Brothers.

The way we understand light is largely based on how we see it. To our eyes, light is like a stream of particles.

Scientists usually study these particle streams by measuring their wavelengths and how they interact with objects. But over the last decade, researchers have begun to realize that light particles can interact with objects within wavelengths too.

Now, scientists are looking inside wavelengths to control and manipulate light, which is transforming the traditional field of optics, according to Duke engineer David Smith and his colleagues.

They describe the changes to the field of optics in a review article appearing online Aug. 2 in Science, and they describe how, at a tenth or even a hundredth of the wavelength of visible light, the classic picture of how we see breaks down.

In this regime, streams of light particles can bend away from an object, essentially tricking the eye into thinking the object is not there. As a result, scientists can no longer think of light in terms of particle streams. Instead, they must think of it as a manipulation of electric and magnetic field lines.

Thinking of light this way, Smith and other scientists are beginning to understand how they can hide one object within another and even harvest energy. The new understanding “will be the design tool of choice” as scientists continue to play with the forces between electrically charged particles, the authors argue.

Citation:

“Transformation Optics and Subwavelength Control of Light.” Pendry, J., et. al. 2012. Science 337: 549-552.
DOI: 10.1126/science.1220600

‘Chicken’ Logic Secures Planes, Trains and Ports

July 13th, 2012

By Ashley Yeager

U.S. goalkeeper Hope Solo deflects a penalty kick. Credit: AP

Soccer penalty kicks, ‘Chicken’ and other games may thwart terrorist attacks, drug smugglers and even freeloaders trying to board trains without tickets.

It’s not so much the intensity and adrenaline of the games that lead to better security, but the logic the players use, says Vincent Conitzer, a professor of computer science and economics at Duke.

This logic is called game theory and now scientists are using it to compute solutions for security issues, Conitzer explained at a July 11 talk with undergraduates completing summer research projects on campus.

During the talk, Conitzer gave a brief overview of game theory using real-world examples, such as penalty kicks in soccer and a set of drivers playing chicken. In the soccer example, he described a “zero-sum game” between the goalie and the kicker, where no matter the outcome, one player wins and the other loses.

But in the case of chicken, in which two cars drive straight at each other until one of the drivers “chickens out” and diverts course, the stakes of each choice are a bit higher. If both drivers stay straight, they crash. It’s no longer a zero-sum game.

When it comes to preventing security problems, there are more angles of attack, smuggler entry points and ways to board a train than the simple left, right or straight of these game examples.

Cars and buses wait to clear a security checkpoint at LAX. Credit: cardatabase.net

To make predictions about what the bad guys will do in the security scenarios, Conitzer is working with Milind Tambe and his group at USC. The team has designed game theory algorithms to set the schedule of security checkpoints and canine rounds at LAX airport, smuggler-scouting in Boston Harbor and even methods for preventing terrorist attacks in Mumbai.

Tambe “treats the problem of Mumbai personally” since that is his home city, Conitzer said, adding that he is only directly involved in this project with the USC group.

While the talk focused mainly on security applications, Conitzer also thinks that some “surprising new applications have yet to emerge” from the work. The new uses won’t necessarily help win a game of chicken or score a penalty kick.

But they could help scientists understand how to better use incentives to designgames with only good outcomes, such as encouraging smart energy use.

Citation: “Computing Game-Theoretic Solutions and Applications to Security.” Conitzer, V. In Proceedings of the 26th National Conference on Artificial Intelligence (AAAI-12), Toronto, ON, Canada, 2011.

CSI-House teams could make better medical diagnoses

June 28th, 2012

By Ashley Yeager

Comparing a child's DNA to his parents' could help with identification of hard-to-diagnose genetic diseases. Credit: Henrik Jonsson/iStockphoto

Dr. Gregory House, star of House, M.D., and the lab techs on CSI never fail at their jobs. But that’s Hollywood. In real life, diagnosing illnesses and sequencing DNA isn’t so straightforward. It doesn’t always lead to a happy ending either, especially for children who are sick but can’t be diagnosed, even by gifted, real-life doctors.

That’s exactly why geneticist David Goldstein has teamed with pediatrician Vandana Shashi to combine a little House and CSI to identify apparent genetic diseases and quickly end some families’ diagnostic odysseys.

So far, the team has provided likely genetic diagnoses in six of 12 children it has worked with, said Goldstein at a Cardiovascular Research Center Seminar Series talk on June 27.

The children were referred to Shashi for a pilot study where she would record their symptoms, or phenotypic behavior, much like House. Then, Goldstein and his team at the Center for Human Genome Variation collected DNA samples from the children and both of their biological parents.

Using next-generation genetic sequencers, as well as traditional DNA scanners, Goldstein and his team looked for genetic variations between the children’s and parents’ complete genome. Like looking at DNA to identify a criminal, Goldstein and his genetics team are scouring the sequences for genetic fingerprints of the diseases disrupting the children’s lives.

Once variations were identified, the entire team looked for known diseases with similar gene mutations and symptoms. Goldstein explained that the study not only pinpointed the undiagnosed congenital diseases in some patients but also presented new genes that could also be linked to the illnesses. The study’s success has led to the creation of the Genome Sequencing Clinic.

The clinic will begin to help the families of the 50,000 children (out of the four million) born each year in the US with difficult-to-diagnose genetic diseases. These types of studies will likely be the “earliest drivers for large-scale genetic sequencing,” Goldstein said.

But, he cautioned, “there’s a whole lot of junk,” or variation, in DNA. Every genome has the narrative potential for devastating diseases, and that means that House-CSI teams, like Shashi and Goldstein’s, need to be extremely careful when making diagnoses, especially if the results will influence treatment, he said.

Citation: Clinical application of exome sequencing in undiagnosed genetic conditions. Need, A. et. al. 2012. J. Med Genet. 49:6 353-361. doi:10.1136/jmedgenet-2012-100819

Lab “cloud” goes global

June 15th, 2012

By Ashley Yeager

A network of individual computers are linked through a server. Credit: TAS Software

The National Science Foundation has awarded computer scientist Jeff Chase $300,000 to move a computer cloud he now has in his lab to the university’s campus network, and beyond.

Chase has been building the cloud to improve server networks. In his new model, servers, the computers that process requests and deliver data over a local network or the Internet, have become critical, public infrastructures with open, flexible, secure, robust and decentralized control.

The work, once reproduced outside of the lab, will let Duke scientists across campus and throughout the world to more easily connect to one another through existing networks and to share computational services and access data, according to Tracy Futhey, Duke’s vice president for information technology and chief information officer.

Based on software-defined networking and other technologies, the new, on-demand cloud services will be launched through a distinct network that connects science resources, such as the large datasets generated in physics and genomics experiments.

The project is part of the NSF-funded Global Environment for Networking Innovation, or GENI.

Chase’s work was also recognized on June 14 when the White House launched an initiative, US Ignite, to develop a publicly available system of advanced networks based on important contributions from GENI scientists. Duke is among more than 60 universities across the country that has participated in the project.