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Archive for the ‘Genomics’ Category

cancer-classifiers-web

Finding a better way to fight cancer doesn’t always mean discovering a new drug or surgical technique. Sometimes just defining the disease in greater detail can make a big difference. A more specific diagnosis may allow a physician to better tailor a patient’s treatment, using available therapies proven to work better on a specific subtype of disease or avoiding unnecessary complications for less aggressive cases.

“Finding better ways to stratify kids when they present and decide who needs more therapy and who needs less therapy is one of the ways in which we’ve gotten much better at treating pediatric cancer,” said Samuel Volchenboum, Computation Institute Fellow, Assistant Professor of Pediatrics at Comer Children’s Hospital and Director of the UChicago Center for Research Informatics. “For example, kids can be put in one of several different groups for leukemia, and each group has its own treatment course.”

Classically, patients have been sorted into risk or treatment groups based on demographic factors such as age or gender, and relatively simple results from laboratory tests or biopsies. Because cancer is a genetic disease, physicians hope that genetic factors will point the way to even more precise classifications. Yet despite this promise, many of the “genetic signatures” found to correlate with different subtypes of cancer are too complex – involving dozens or hundreds of genes – for clinical use and difficult to validate across patient populations.

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Graphic by Ana Marija Sokovic

Graphic by Ana Marija Sokovic

When Charles Darwin took his historic voyage aboard the HMS Beagle from 1831 to 1836, “big data” was measured in pages. On his travels, the young naturalist produced at least 20 field notebooks, zoological and geological diaries, a catalogue of the thousands of specimens he brought back and a personal journal that would later be turned into The Voyage of the Beagle. But it took more than two decades for Darwin to process all of that information and into his theory of natural selection and the publication of On the Origin of Species.

While biological data may have since transitioned from analog pages to digital bits, extracting knowledge from data has only become more difficult as datasets have grown larger and larger. To wedge open this bottleneck, the University of Chicago Biological Sciences Division and the Computation Institute launched their very own Beagle — a 150-teraflop Cray XE6 supercomputer that ranks among the most powerful machines dedicated to biomedical research. Since the Beagle’s debut in 2010, over 300 researchers from across the University have run more than 80 projects on the system, yielding over 30 publications.

“We haven’t had to beat the bushes for users; we went up to 100 percent usage on day one, and have held pretty steady since that time,” said CI director Ian Foster in his opening remarks. “Supercomputers have a reputation as being hard to use, but  because of the Beagle team’s efforts, because the machine is well engineered, and because the community was ready for it, we’ve really seen rapid uptake of the computer.”

A sampler of those projects was on display last week as part of the first Day of the Beagle symposium, an exploration of scientific discovery on the supercomputer. The projects on display covered the very big — networks of genes, regulators and diseases built by UIC’s Yves Lussier — to the very small — atomic models of molecular motion in immunological factors, cell structures and cancer drugs. Beagle’s flexibility in handling projects from across the landscape of biology and medicine ably demonstrated how computation has solidified into a key branch of research in these disciplines alongside traditional theory and experimentation.

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image descriptionPeople who work in laboratories take a lot of things for granted. When they come into work in the morning, they expect the equipment to have power, the sink to produce hot and cold water, and the internet and e-mail to be functional. Because these routine services are taken care of “behind the scenes” by facilities and IT staff, scientists can get started right away on their research.

But increasingly, scientists are hitting a new speed bump in their day-to-day activities: the storage, movement and analysis of data. As datasets grow far beyond what can easily be handled on a single desktop computer and long-distance collaborations become increasingly common, frustrated researchers find themselves spending more and more time and money on data management. To get the march of science back up to top speed, new services must be provided that make handling data as simple as switching on the lights.

That mission was the common thread through the second day of the GlobusWorld conference, an annual meeting for the makers and users of the data management service, held this year at Argonne National Laboratory. As Globus software has evolved from enabling the grids that connect computing centers around the world to a cloud-based service for moving and sharing data, the focus has shifted from large, Big Science collaborations to individual researchers. Easing the headache for those smaller laboratories with little to no IT budget can make a big impact on the pace of their science, said Ian Foster, Computation Institute Director and Globus co-founder, in his keynote address.

“We are sometimes described as plumbers,” Foster said. “We are trying to build software and services that automate activities that get in the way of discovery and innovation in research labs, that no one wants to be an expert in, that people find time-consuming and painful to do themselves, and that can be done more effectively when automated. By providing the right services, we believe we can accelerate discovery and reduce costs, which are often two sides of the same coin.”

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Dna-splitThe original Human Genome Project needed 13 years, hundreds of scientists and billions of dollars to produce the first complete human DNA sequence. Only ten years after that achievement  genome sequencing is a routine activity in laboratories around the world, creating a new demand for analytics tools that can grapple with the large datasets these methods produce. Large projects like the HGP could assemble their own expensive cyberinfrastructure to handle these tasks, but even as sequencing gets cheaper, data storage, transfer and analysis remains a time and financial burden for smaller labs.

Today at the Bio-IT World conference in Boston, the CI’s Globus Online officially unveiled their solution for these scientists: Globus Genomics. Per the news release, “integrates the data transfer capabilities of Globus Online, the workflow tools of Galaxy, and the elastic computational infrastructure of Amazon Web Services. The result is a powerful platform for simplifying and streamlining sequencing analysis, ensuring that IT expertise is not a requirement for advanced genomics research.”

In the release, positive feedback is provided by researchers including William Dobyns, who studies the genetics and neuroscience of developmental disorders at the University of Washington, and Kenan Onel, a pediatric oncologist who directs the Familial Cancer Clinic at The University of Chicago Medicine. Nancy Cox, section chief for genetic medicine at UChicago Medicine, said the service enabled her laboratory to meet the big data challenges of modern genomic research.

“We needed a solution that would give us flexibility to extend our analysis pipelines and apply them to very large data sets,” says Dr. Cox. “Globus Genomics has provided us with a key set of tools and scalable infrastructure to support our research needs.”

If you’re at the Bio-IT World conference, you can visit the Globus Online team at Booth 100 and get a tutorial on the new Globus Genomics service.

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“We know more about the movement of celestial bodies than about the soil underfoot.”

Leonardo da Vinci never gave a TED talk, but if he did, that quote from around the beginning of the 16th century might have been a good tweetable soundbite. Five centuries later, da Vinci’s statement still holds true, and it was there for CI Senior Fellow Rick Stevens to pluck as the epigraph for his talk in November 2012 at the TEDxNaperville conference. Stevens used his 18 minutes on the TED stage to talk about the Earth Microbiome Project, an international effort “to systematically study the smallest life forms on earth to build a comprehensive database to capture everything we can learn about these organisms.”

Stevens talks about how little we know about the estimated 1 billion species of microbes on Earth (“In one kilogram of soil there are more microbes than there are stars in our galaxy,” he says), and how citizen science, high-throughput genomics and supercomputing are coming together to finally reveal this vast ecosystem — a process he likens to reconstructing the front page of the newspaper using only the firehose of Twitter and Facebook posts. In 5-10 years, Stevens says, microbiology will finally exceed astronomy, with enormous implications for our understanding of the world around us.

You can watch video of Stevens’ talk below:

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