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Rethinking Databases for an Avalanche of Genetic Data

human os iconIn a lab on the ground floor of deCODE Genetics’ building in Reykjavik, Iceland, robots quietly go about chip-typing or “SNP-typing” the latest of 155,000 or so Icelanders. SNPs are single-nucleotide polymorphisms, or small variations in genetic code that can represent the basis for disease or health, presence or absence of a condition of some type or other. A floor up, Illumina HiSeq X machines, worth millions of dollars each, take a few days to come up with a complete human genome. They’ve done so for about 3,600 Icelanders at latest count.

All that sequencing means an enormous amount of data. The As, Ts, Cs, and Gs add up, and of course, the idea here is to actually make use of those letters. Across the building from the sequencing labs, I spoke with Hakon Gudbjartsson, deCODE’s VP for informatics, on the challenges and methods for dealing with mountains of data. Each individual person sequenced accounts for around 100 gigabytes of data, and it’s data, he says, “that requires a lot of organization.”

The primary means to organize the genetic information is a database the company developed that is known as GOR, or genomically ordered relations. Traditional databases, like Oracle or MySQL, organize data in tables that don’t quite make sense for genetic information; Gudbjartsson says using such methods creates bottlenecks when trying to retrieve the data. The GOR database organizes genetic code according to a “reference build,” essentially placing the data in sequential order.

“It’s a database that organizes the downstream data according to the position in the genome,” Gudbjartsson says. All the specific variations observed also fit in based on their physical place. “Whether its a SNP or… a copy number variation, anything. All the tables are basically ordered according to the genome.”

That ordering allows the design of algorithms to query the information in a much more efficient fashion. Researchers can even “stream” the genomic information, instead of calling up one specific spot.

The goal at deCODE (now owned by Amgen) is to take this impressive collection of genetic data and match it up with rich clinical and genealogical data as well. Iceland is home to only 320,000 people or so, and all Icelanders can trace their lineages to 1650, and often further back. Along with good recent medical records, that means the ability to take a genotype and match it up with a phenotype; they have produced some impressive results, perhaps most famously the discovery of a gene in 2012 that confers almost complete protection against development of Alzheimers disease.

This rich data set has created some controversy. Some critics have expressed discomfort with aggressive DNA collection methods (all participants do sign consent forms) and the apparent ability to make “data inferences” based on available data and those rich genealogical and clinical records. (Essentially, even if an individual doesn’t give consent for sequencing, but enough others do, the close genetic connections in Iceland could allow the researchers to fill in the gaps.) However, Gudbjartsson points out that everyone at deCODE signs an agreement to never actually use such inferences.

Gudbjartsson says that GOR can run on several hundred computers simultaneously already. “GOR should be elastic,” he adds, noting that, “we foresee growth.” It is already a challenge to efficiently transpose the full sequencing data from the 3600 or so completed genomes onto the chip data for the 155,000 Icelanders in the database (a way to find common variations, and match with phenotypes). But sequencing will inevitably get even faster and cheaper. The full genome for all Icelanders, or other populations around the world, will present an even greater challenge for data manipulation.

Rocky Road Ahead for Space Tourism

Last Friday, Virgin Galactic’s SpaceShipTwo, a rocket-powered craft designed to take passengers to the outer edge of Earth’s atmosphere, crashed to Earth, killing one pilot and critically injuring another.

A lot has happened in the week since. After initial rumors of an explosion, the U.S. National Transportation Safety Board (NTSB), which is investigating the accident, determined that co-pilot Mike Alsbury prematurely released the spaceship’s feathered tails, which boost stability and drag during reentry, at a particularly dangerous point in the flight.

The NTSB has since expanded the scope of their investigation to include potential human factors, such as cockpit design and pilot training. At the same time, there’s been buzz about Virgin Galactic’s safety culture. Doug Messier, a writer who witnessed the accident, said in a vivid recent account for Outside magazine that safety experts told him Virgin’s testing schedule, with just a few test flights before taking paying passengers, was overly aggressive.

We may be months or even a year away from a definitive conclusion on the cause or causes of the accident. But regardless of how the investigation plays out, this is a setback for Virgin Galactic. And it invites new scrutiny of the suborbital space industry.

The U.S. government has actually held back from detailed oversight of the space tourism industry. In 2004, the U.S. Congress passed the Commercial Space Launch Amendments Act, which barred the Federal Aviation Administration from instituting spacecraft design or operational regulations (except in case of serious or fatal injury or a serious accident). Advocates say the intent of the provision is to protect a fledgling industry. It was extended in 2012 and is now set to expire in October 2015.

George Nield, who heads up the FAA’s Office of Commercial Space Transportation, came out months ago against another extension. And he might get his wish. “I think when the end of the moratorium comes in 2015, Congress will not renew it,” says space law attorney Michael Listner.

It will be a tough balancing act. So far, Virgin Galactic is the only private firm to have started an ongoing program of piloted suborbital flights, and they’re still just experimental ones. It’s unclear how much data the government will be able to feed into regulations. Chances are the results of the NTSB investigation will help inform new rules. But Listner says there is the danger that the government could swing too far in the pursuit of better safety, and that the same goes for the space tourism industry itself: “if they go out and just go crazy on this, they’re going to kill the industry on their own.” 

Virgin Galactic has big plans for its business; it has talked about the possiblity of moving beyond space tourism to zippy, point-to-point travel that could take passengers halfway around the Earth in just a few hours. But for now, there are big open questions about its future. 

“The real issue for Virgin Galactic is do they have sufficient resources to respond to whatever the investigation turns up,” says Scott Pace, director of the Space Policy Institute at George Washington University in Washington, DC. “Do they have the manufacturing resources to do a safe return to flight and complete the rest of their test program?”

Virgin also faces competition. XCOR Aerospace, for example, is hard at work on its Lynx rocket plane, also under construction at the Mojave Air and Space Port, where SpaceShipTwo was tested. Lynx is designed to take off from the ground and, as of the beginning of last month, slated to begin test flights next year. Virgin says it has a second ship that is 65% complete and could potentially start test flights in 2015 as well.

This article was updated on 7 November, 2014. 

Swedish Researchers Report Record Wireless Data Transmission Rate

4K (or ultra high definition) television technology requires high-speed TV cameras that produce data streams of 12 to 20 gigabytes per second. Such data rates can only be transmitted from the cameras by optical fiber links. In live reporting of sporting events such as soccer games—often requiring slow motion instant replay—these optical cables have to be dug in under the grass, severely limiting the mobility of the cameramen. Up to now, there have been no wireless links capable of handling these torrents of data.

A new advance may change this. Researchers from Chalmers University of Technology in Göteborg, Sweden, and from Ericsson Research, also in Göteborg, announced in late October at the Compound Semiconductor Integrated Circuits Symposium in San Diego that they have built wireless transmitter and receiver chips that achieved a transmission rate of 40 gigabits per second. That’s twice as fast as the previous record, which was reported in 2012 by Hiroyuki Takahashi and colleagues from Osaka University, Toyonaka, in Japan. The Göteborg researchers demonstrated a wireless link operating in the D-band, the 110- to 170-GHz frequency range, and using a bandwidth of 40 GHz. In the laboratory experiment, the transmitter and receiver were linked by a two meter dielectric waveguide, but the researchers expect that in an outdoor point-to-point experiment they will be able to bridge one kilometer.

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Alaska's Online Voting Leaves Cybersecurity Experts Worried

Some Americans who lined up at the ballot boxes on Tuesday may have wished for the convenience of online voting. But cybersecurity experts continue to argue that such systems would be vulnerable to vote tampering — warnings that did not stop Alaska from allowing voters to cast electronic ballots in a major election that had both a Senate seat and the governorship up for grabs.

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Body Sensors Help Dogs 'Talk' to Humans

Throughout history, dogs have learned to obey the hand signals and voice commands of people. Now a new two-way communication system could give man’s best friend a new way to talk back to his or her human handler.

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Technologists Hatch "Turtle Sense" System With Ecology and Economy in Mind

A group of volunteer technologists that goes by the name Nerds Without Borders has made some recent progress addressing an interesting environmental problem: protecting sea turtle nests at Cape Hatteras National Seashore on North Carolina’s Outer Banks. The National Park Service puts quite a bit of effort into ensuring that sea turtle nests there are not disturbed, but it’s a thorny problem.

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Biomedical Entrepreneur Jonathan Rothberg Is Up to Something Again

It ususally doesn’t count for much when entrepreneurs declare that their new company will change the world—although they can’t tell you how, or when, or actually any details at all. But Jonathan Rothberg has two things going for him that make his vague proclamations about his new company, Butterfly Network, noteworthy: money and a track record. 

Rothberg announced yesterday that Butterfly Network has raised $100 million to create a device/system/something-or-other that will “transform medical imaging and non-invasive surgery by leveraging advances in semiconductors, deep learning, and cloud computing.” That’s not chump change. 

And then there’s Rothberg’s backstory. The serial entrepreneur first founded a company called 454 Life Sciences and invented a new technique for cheap and fast genome sequencing, which made it practical to scan the entire genome of an individual. He sold the company to Roche for $155 million. Then Rothberg founded Ion Torrent and invented an even cheaper and faster sequencing machine that IEEE Spectrum covered a few years ago. He sold that company to Life Technologies for $725 million. 

So Butterfly Network might be worth watching. In a conversation with Spectrum, Rothberg said that the company’s mysterious device will offer fast, cheap, and high-resolution medical images. The images will be stored on the cloud, where the company’s mysterious artificial intelligence program will go through them and begin to learn all about radiology.

“There are AI techniques that can keep up with the information without getting bottlenecked,” Rothberg says. “So you have services that make humans more efficient, whether they’re radiologists or genetic counselors.” Over time, Rothberg says, the system could grow proficient enough to do much of the doctor’s work. “There are only 38 radiologists in Uganda,” he says. “Nobody will complain if we make them 1000 times as efficient.”  

Butterfly Network is one of four companies that Rothberg is nurturing at his new incubator, 4Combinator. Rothberg is speaking to the press, apparently, because he’s on a hiring spree and wants to spread the word. “I need the best and the brightest,” Rothberg said, adding that he hopes to steal talent not only from tech companies like Google, Baidu, Facebook, and Netflix (!), but also from finance firms. “I want to get the smartest people in Goldman Sachs to come do something else with their lives,” he says. 

First Terahertz Amplifier "Goes to 11"

The world’s first radio amplifier operating at terahertz frequencies could lead to communications systems with much higher data rates, better radar, high-resolution imaging that could penetrate smoke and fog, and better ways of identifying dangerous substances, say the researchers who built it.

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Tiny Cancer-Killing Death Rays: Spaser Therapy Proposed

Encircling tumors with a phalanx of miniature lasers could offer a new way to battle cancer, a team of Australian researchers is proposing.

Technically, the proposed device isn’t really a laser at all, but a spaser, with surface plasmons rather than light undergoing amplification. Plasmons are oscillations in electron density created in the surface of a small metal object when photons strike it. It’s possible to design a device so that the plasmons feed back on themselves, amplifying in much the same way photons bouncing around a laser cavity stimulate the emission of other photons, creating laser light.

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