Following the people and events that make up the research community at Duke

Students exploring the Innovation Co-Lab

Author: Becca Bayham

Solving problems with iPad (or Android) apps

eCLIP iPad applicationBy Becca Bayham

When a patient comes into the E.R. with a lung problem, doctors usually put them on a ventilator. Unfortunately, this procedure helps some patients, but hurts others. Doctors have difficulty predicting which will be the case, due to a lack of data on risk factors. A predictive model was recently developed to solve this problem, but the calculations require more time and information than E.R. doctors usually have.

Enter Raquel Bartz, an emergency room doctor at Duke Hospital. She envisioned an iPad application where doctors and family members could input the necessary medical information, and the app would spit out the treatment protocol for a particular patient. Bartz turned to Richard Lucic and Robert Duvall’s Software for Mobile Devices class (COMPSCI 196) to make her idea a reality.

The result? An application called eCLIP, developed by students last Fall and available now in iTunes’ App Store. (See photos at left)

eCLIP is one of five applications created by students during the two semesters COMPSCI 196 has been offered. Lucic and Duvall described the course — and its various student-produced applications — at last week’s Visualization Friday Forum, sponsored by the Visualization Studies Initiative ( and Duke’s computer science department.

“We’re trying to teach students about the mobile app world,” Lucic said. “In addition, we’re trying to teach students about the software development process, from conception of an idea to delivering a product to a client.”

Lucic emphasized the importance of teamwork, as well as the value of visual design skills for increasing a product’s appeal. Furthermore, user testing is a critical step for identifying problems.

This semester, nine clients pitched their application ideas. Students voted for their favorite projects, and three were ultimately chosen:

  • Ajay Patel, IT Manager in the Duke Cancer Center, wanted a way to track medical samples during processing and reduce human error
  • Allison Besch, educational curator for the North Carolina Maritime Museum, wanted a fun, educational tool for teaching marine resource conservation to 4th graders
  • Rachel Cook, Duke alumna and former futures trader, wanted an app to encourage microlending and bridge the gap between lenders and borrowers

Each client worked with a team of 3-4 students, and met with them every other week to discuss the team’s progress.

“A lot of students are learning how to code mobile apps for the first time, so there’s only 6-7 weeks of actual coding time,” Duvall said.

Despite the time crunch, students try to present a finished product to their clients by the end of the semester. But who keeps the app going after the course’s conclusion?

“What we’re trying to do is have the students provide enough documentation and write their code well enough that the app can be maintained by the client’s organization,” Lucic said. “Clients have been thrilled with the experience. I think we’ve done a superb job of meeting their needs, as much as you can in a one-semester course.”

Sharing is caring, when it comes to scientific data

By Becca Bayham

Worms don’t typically evoke a sense of awe. But C. elegans nematode worms — all 558 cells of them — played an important role in how scientific data is shared today.

Scientists Robert Waterston and Sir John Sulston described this connection during the James B. Wyngaarden Distinguished Lecture on Nov. 14, sponsored by the Institute for Genome Sciences and Policy. [Watch the whole lecture – 1 hour, 9 minutes)

During the 80s, Waterston and Sulston were unraveling the nematode genome at their University of Cambridge lab. Worms make good subjects for study because they are finite, transparent and genetically manipulatable.

The Worm Breeder's Gazette - Volume 8, Issue 2When Waterston moved from Cambridge to Washington University in St. Louis, he felt isolated from the research community he’d left. However, an informal and creatively-covered publication — the Worm Breeder’s Gazette (see photo at left) — helped bridge that physical divide. Researchers used the Gazette to share short summaries of their discoveries.

“Through this very informal means, the community was made aware of what was going on, and invited to share in it,” Waterston said. “Indeed, it worked spectacularly. Now we knew not just these anonymous pieces of DNA, but where they belonged. And that made [the data] much more useful for us and the community.”

Waterston and Sulston were the first to sequence a multi-cellular organism’s genome. Following their success with worms, the two moved on to the holy grail of science at the time: the human genome.

In terms of data sharing, “human genetics was the polar opposite of the worm field. Human geneticists held things very close to their chests,” Waterston said.

In 1996, the two scientists joined other researchers at a conference in Bermuda to discuss how human genome data should be handled. Should it be stored in proprietary databases, with limited access? Or shared freely with the world? Waterston and Sulston advocated for the latter, and this opinion ultimately prevailed. If it hadn’t, the humane genome story might have ended differently — or not at all. Data sharing “kept the lines of communication open” between researchers, Waterston said, and greatly facilitated the sequencing process.

Sure enough, following the human genome’s completion in 2000, the entire sequence was released into the public domain. Public data sharing has become standard practice for other animal genomes and other areas of science. However, even though Waterston and Sulston’s efforts encouraged data sharing on a massive scale, the tendency towards secrecy still exists.

“Pushing for more open science continues to be important,” Waterston said. “The nature of science is that private initiatives continue to push on public domain. If we don’t push back, we’re going to be the poorer for it.”

Greening a classroom, student-style

By Becca Bayham

When students sit down in a classroom, their minds are (usually) on the course material. However, in the case of classroom A158 in the LSRC, the paint on the walls might be just as interesting as the writing on the blackboard.

The Duke Environmental Leadership Program (DEL) provides environmental education for business and community leaders. When the program decided to renovate one of its classrooms, it took a somewhat different approach.

Rather than opting for Duke’s usual vendors, the program sought recommendations from a team of students taking professor Deb Gallagher’s Sustainable Business Strategy class, offered jointly by the Nicholas School and the Fuqua School of Business.

“[DEL’s] vision was two-fold – to provide a green classroom that reflects the spirit of the Nicholas School, as well as to provide an executive atmosphere,” team member Debbie Breisblatt says.

The student team — composed of Breisblatt, Kealy Devoy, Stephen Hiser and Jennifer Weiss — researched sustainable options on DEL’s behalf, with each group member tackling one of four categories: technology, furniture, lighting and miscellaneous (storage solutions and floor/wall coverings). The team produced a final recommendation with three levels: green, greener and greenest.

The lowest level (green) included low-hanging fruit such as low- or no-VOC paint and furniture that fulfilled some environmental criteria. Higher levels were more expensive, largely because they incorporated more technology (such as a telepresence system that would reduce the need for travel). Presented with these options, DEL administrators were able to choose a mix that worked best for their sustainability goals and their budget.

“I think it’s great that [DEL] realized how important it is for it to walk the walk and incorporate sustainability into its operations as well as it is able. A lot of companies are in that position right now… they realize that they should do X, for environmental and ethical reasons, but they don’t know how to get there,” Devoy says.

The team finalized its recommendations last spring, and the classroom renovation took place over the summer. DEL incorporated a number of the team’s suggestions, such as zero-VOC paint and furniture made with recycled material. The cost was not substantially higher than a regular classroom remodel, Devoy says.

“One of the other objectives for this renovation was to showcase what a green classroom could look like at Duke and hopefully to inspire other departments to take environmental factors into consideration when they renovate,” Breisblatt says.

Devoy says she wishes that more on-campus departments and organizations would take advantage of grad students’ abilities.

“I think the value of student labor is a lot higher than people think it is. We have skills. There are tons of grad programs with students that could do things we currently hire consultants for,” she says.

Do we judge ourselves by our covers?

By Becca Bayham

After giving a lecture at a major women’s magazine, Dan Ariely was faced with a dilemma — in the shape of a huge Prada duffel bag.

As the behavioral economist walked down the street with the bag (a gift from the magazine), he wondered whether he should display the large Prada logo to passersby or hide it against his side.

He decided to hide the logo, but “I was surprised that I still felt like I was walking around with a Prada bag,” Ariely said. “What if I had Ferrari underwear… would I walk a little faster?”

How do the things we wear affect how we think about ourselves? Ariely explored this question (among others) at a Chautauqua lecture on Oct. 18.

In one of Ariely’s experiments, subjects wore shirts emblazoned with the word “stingy” or “generous.” After wearing the shirts around for awhile, participants completed tasks that evaluated their generosity. Strangely enough, “generous” t-shirt wearers gave more during these tasks than those with the “stingy” shirt on.

The word on a participant’s shirt “kind of penetrated their personality,” Ariely said. Notably, the effect was just as strong when participants wore shirts with the writing on the inside.

“Telling ourselves who we are seems to be a crucial element,” Ariely said.

It’s like giving money to a beggar. Giving money doesn’t instantly make you a better person, but it points out certain qualities in yourself. We learn about ourselves the same way that we learn about other people — by observing our actions.

In another study, women were given designer purses, but some were told that their purses were fake. Then participants played a game where cheating was advantageous.

Everyone started fairly enough, but eventually began to cheat. And once they’d cheated a little bit, they just cheated the rest of the time.

“We call this the ‘what the hell’ effect. Everyone who’s been dieting knows this feeling… I’m not good, so I might as well enjoy,” Ariely said.

Interestingly, women wearing counterfeit goods started cheating a lot earlier. Did having fake bags “penetrate their personality,” just as in the t-shirt experiment?

“What if fashion’s not just about telling other people who we are, but also about telling ourselves who we are?” Ariely said.

A few small steps for mankind

By Becca Bayham

Eureka Symposium“There are the thermometers who passively record social injustices, and then there are the thermostats that actively do something about it,” Dr. Sunny Kishore said during the Eureka Symposium last Saturday, a dPS-sponsored event that brought together 120 students and a number of Duke alums for some deep thinking about social change.

The main lecturers were followed by break-out sessions, which ranged in topic from global health to human rights. The four-hour symposium packed a philosophical punch, outlining a few actions that could save millions or even billions of lives in the developing world. It’s probably the most inspired I’ve felt on a Saturday afternoon.

Representatives from the Enough Project made the case for using conflict-free minerals on campus (similar to the idea behind conflict-free diamonds). Tin, tantalum, coltan and gold — used in cell phones and other electronics — currently fuel war in eastern Congo, where various armed groups mine them for profit; more than five million people are thought to have died from the conflict so far. (Following a rather pointed editorial in the Chronicle by two Symposium organizers, Duke Procurement stated on its website that it would “[give] preference to vendors who have made a commitment to conflict-free supply chains when quality and cost performance are equal or superior.”)

Drs. Anthony So, Robert Johnston and Kishore discussed strategies that could provide people in developing nations with access to life-saving treatments and vaccines — at a price they can afford. Triple therapy for AIDS used to cost $10-15,000, “too high a price for hope,” So said. But thanks to ‘bootstrap philanthropy’ — free licenses and free production, supported by grant money — that same treatment costs less than $100 now.

Royalty fees and license exclusivity have usually put vaccines out of reach for the developing world, unless the drug is off-patent. Johnston (of Global Vaccines, Inc.) proposed one solution: commercial sub-licenses, which allow low-cost manufacturers to produce affordable vaccines without violating companies’ intellectual property rights.

“You have the ability to have a drug at first-world prices in developed countries and can now provide lower-cost medicines in developing countries,” Kishore said.

Research universities could play a pivotal role by allowing “humanitarian licenses” of their technologies, according to Kishore. Several universities — Duke among them — have signed a statement supporting dissemination of medical technologies, but not much progress has been made.

“Are we engaged in rhetoric or are we engaged in actually doing something?” Kishore said. “These are our labs, our drugs, and this is our responsibility.”

Open source science

By Becca Bayham

In 2009, mathematician Timothy Gowers posed this question to the blogosphere: “Is massively collaborative mathematics possible?” He described an unsolved math problem and asked for help figuring it out. Over the next few hours and days, commenters began to pick at the problem together. They brought up incomplete ideas, which were expanded and incorporated into other peoples’ ideas, until Gowers posted 37 days later that the problem had (probably) been solved.

Which raises the question — Can open source principles be applied to scientific problems? Michael Nielsen explored this idea during a lecture last Tuesday, sponsored by the Duke University Libraries.

When a non-profit needed a technology that didn’t exist (an affordable solar-powered wireless router), they turned to InnoCentive, a website that allows organizations to post descriptions of scientific problems they’d like solved. Rewards range from a couple thousand dollars (for designing a better beverage container) to a cool million (for finding the biomarker for ALS).

The challenge was solved by a man who’d made a hobby of building his own low-cost radio networks and solar power systems. The moral of the story — if a problem requires an unusual combination of expertise, someone somewhere might have it. Or a collaboration of people might generate the “conversational critical mass” to make easy work of the problem.

Open source science can be difficult to achieve, however. Nielsen said that numerous wikis and online communities have tried to facilitate idea sharing, but failed for a lack of incentives.

“Imagine you’re a young scientist who wants to get a job at some point,” Nielsen said. “You know that from the point of view of some hiring committee, a long slew of brilliant contributions to a wiki doesn’t count as much as a single mediocre scientific paper that no one is going to read.”

Nielsen advocated creating incentives for scientists to share in new ways. For example, including blog posts in Google Scholar searches, or publishing data sets instead of just papers.

“The payoff is to develop new methods for the construction of knowledge … and to expand the range of scientific problems that we can attack,” Nielsen said.

Detecting disease with sound

By Becca Bayham

Most people experience ultrasound technology either as a pregnant woman or a fetus. Ultrasound is also employed for cardiac imaging and for guiding semi-invasive surgeries, largely because of its ability to produce real-time images. And Kathy Nightingale, associate professor of biomedical engineering, is pushing the technology even further.

“We use high-frequency sound (higher than audible range) to send out echoes. Then we analyze the received echoes to create a picture,” Nightingale said at a Chautauqua Series lecture last Tuesday.

According to Nightingale, ultrasound maps differences in the acoustic properties of tissue. Muscles, blood vessels and fatty tissue have different densities and sound passes through them at different speeds. As a result, they show up as different colors on the ultrasound. Blood is more difficult to image, but researchers have found an interesting way around that problem.

“The signal from blood is really weak compared to the signal coming from tissue. But what you can do is inject microbubbles, and that makes the signal brighter,” Nightingale said.

Microbubbles are small enough to travel freely throughout the circulatory system — anywhere blood flows. Because fast-growing tumors require a large blood supply, microbubbles can be particularly helpful for disease detection.

Like most other electronics, ultrasound scanners have gotten smaller and smaller over the years. Hand-held ultrasounds “are not as fully capable as one of those larger scanners, just as with an iPad you don’t have as many options as your computer or laptop,” Nightingale said. However, the devices’ portability has earned them a place both on the battlefield and in the emergency room.

Nightingale’s research explores another aspect of ultrasonic sound — its ability to “push” on tissue at a microscopic scale. The amount of movement reveals how stiff a tissue is (which, in turn, can indicate whether tissue is healthy or not). It’s the same concept as breast, prostate and lymph node exams, but allows analysis of interior organs too.

“We can use an imaging system to identify regions in organs that are stiffer than surrounding tissue,” Nightingale said. “That would allow doctors to look at regions of pathology (cancer or scarring) rather than having to do a biopsy or cut someone open to look at something.”

Visualizing the past

Duke Academic Quad from Duke Chapel, c.1932

Duke Academic Quad, circa 1932 (Duke University Archives)

By Becca Bayham

Perkins Library didn’t always look the way it does now. Since the sanctum of scholarly thought was built in 1928, it has been expanded and renovated several times — so if you looked at a blueprint from 1928, you’d only be getting part of the story. The same applies to historical structures, according to Caroline Bruzelius, professor of art, art history & visual studies.

“Buildings are constantly changing, and a [building] plan represents one part of the process … of course it is useful in many ways, but it’s very frozen,” Bruzelius said during the Sept. 16 Visualization Friday Forum, a recurring lecture series sponsored by the Research Computing Center. Bruzelius was joined by fellow art, art history and visual studies professors Sheila Dillon and Mark Olson for a discussion of how digital representational technologies — such as animation, 3D modeling and virtual reality — can benefit the humanities.

Unlike static drawings or building plans, digital technologies can illustrate how forms change over time, something “no one’s really thought about showing,” Bruzelius said. Structural changes often reflect changing social, religious, political and ideological concerns, as was the case with the church of San Francesco in Folloni, Italy. See below: a student project about the church’s transformation over several centuries.

See Video:
San Francesco a Folloni on Vimeo.

Dillon has also used visualization technologies to show change — but for ancient sculpture bases, instead of buildings.

“We’ve been really good about representing the buildings of an ancient site. But for the most part, the bases on which statues stood tend to be ‘edited out’ of ground plans,” Dillon said, either because of uncertainty about the bases’ original location or because they make a site seem impossibly cluttered. The reality is that statues were abundant, and constantly vying with each other for the attention of passerby.

“When you set up your statue monument, you wanted it to be visible. You wanted it to be in the most prestigious location,” Dillon said. “I tell my students that the best way to imagine these spaces is to imagine the most open part of East campus and fill it up with 3,000 statues of Benjamin Duke.”

The accumulation of statues over time (courtesy Sheila Dillon)

According to Dillon, some archeologists have qualms with digital representation as a research tool, claiming that it is misleading and hypothetical. Dillon argued that ground plans can be misleading too, because they represent 3D objects in 2D space. 3D representation can offer a more true-to-life view, especially in the case of ancient statues.

“When you open up that elevation, [the space] becomes much less crowded,” Dillon said.

Olson acknowledged a few challenges with digital representation: disseminating and preserving large amounts of data, conveying uncertainty and allowing annotation from other scholars. For the most part, digital representational technologies can help humanities researchers ask and answer new questions.

“Visualization becomes a way of doing our research– not just [something we do] at the end,” Olson said.

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