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Big Data: Computational Biology Opens a New Window on the World’s Challenges for Colby Scientists

  • October 16, 2017

This guest post by Kate Carlisle of Colby Magazine includes observations from genomics expert Andrea Tilden, Ph.D. Tilden is the J. Warren Merrill Associate Professor of Biology at Colby College and a visiting scientist in bioinformatics at the MDI Biological Laboratory. Photo credit: Colby College 

Pick a number, any number. Then multiply that number by, say, a trillion.
You’re getting close; you’re in terabyte territory.

Imagine that the resulting product, that huge number, represents tiny bits of data: information about what makes you human, what gives you brown eyes, and why your hair is curly.

Now, take these data, these trillions of facts, this micro-universe of information, and use them to change the world.

Far-fetched? Not anymore, and not at Colby, where students and faculty are studying clues to the world’s biggest challenges through the use of computational biology, an imposing blend of data and life science and the College’s newest major.

“What makes us ‘us’ and not a plant? Not a bacteria, or a virus,” asks Andrea Tilden, The J. Warren Merrill Associate Professor of Biology and a genomics expert. “Any one genome has six thousand novels’ worth of information. Computational biology is the tool we use to read them.”

Simply put, comp bio (a very short moniker for a very big field) is the study of biological questions through the use of massive data sets, integrating biological, statistical, and computational understanding. Many scientists argue that computation, or the quantitative method, is now absolutely central to biology, imposing order and providing testable concepts on a large scale. They say that someday the “computation” label will disappear, subsumed into the larger label of “biology” as mathematical and statistical tools become as much a part of the science as the agar, Bunsen flame, and microscope were on a 20th-century laboratory bench.

Indeed, the twinning of computing capacity and scientific research is having an effect approaching science fiction, not just on big issues like climate change, but on very personal levels, said Professor and Chair of Computer Science Bruce A. Maxwell. A generation hence, individual health monitors could be as common as the ubiquitous iPhone today. “Imagine if I were standing in my house and a monitor went off and said ‘Bruce, your blood sugar is low. Better eat something,’” he says. “That’s not far-fetched. That is a thing that could happen, and the technology is based in the type of work that is being done right now.”

Maxwell points out, however, that scientists are grappling with big questions right now using computational models that exceed resources available even 10 years ago. He ticks off a long list of applications, including agriculture, social studies, including population and migration, psychology, robotics, and advanced medicine.

The field of computational biology is not brand-new at Colby, Maxwell points out. After arriving in 2007, he guided the first interdisciplinary computation programs here. The official designation of the major (believed to be rare if not unique among small liberal arts colleges in the United States) was a natural evolution of this curriculum development, according to Tilden.

“It started out in a more raw form, where we were just looking at courses we could put together that could combine this growing interest and need to use computational tools to analyze big, biological data,” she said. Tilden, whose work had moved into bioinformatics (using computer tools to look at biological questions), created a ground-breaking Jan Plan genomics course with the education team at Colby partner The Jackson Laboratory (JAX), a biomedical research institution in Bar Harbor, Maine, where more than 1,900 employees search for genomic solutions to human health problems.

Through Tilden’s program, Colby students working at the lab were able to wrangle big data in their search for answers to basic genetic questions. Colby has also benefited tremendously from being part of INBRE—the IDeA Network of Biomedical Research Excellence, a collaborative network led by the MDI Biological Laboratory and sponsored by the National Institutes of Health. Maine INBRE’s goals include creating a technically skilled workforce through biomedical research training for undergraduates, providing research support to faculty to increase their competitiveness for federal grants and improving the research infrastructure through support of a network of core facilities with state of the art equipment.

Since 2004 Colby students and working scientists have had biomedical research funded by INBRE grants, including summer research fellowships at the MDI Biological Laboratory and ongoing research in Colby laboratories. Tilden, a member of the INBRE steering committee, has done her research at the MDI facility for more than two decades, while other Colby scientists have had research funded through the partnership. Additionally, Colby has a bioinformatics relationship set up with the MDI Biological Laboratory, where Tilden will spend the coming year as a visiting scientist in bioinformatics.

Life scientists and medical researchers around the world have begun to use bioinformatics in their approach to every problem, from population ecology to agriculture to cancer.

The field has exploded at a rapid clip, and when current Colby students were born, computational biology was in its infancy, too. “Very recently, around the year 2000, we had just finished sequencing the human genome,” Tilden said. “It had taken 15 years at 20 different labs around the world, a vast project. We now have the tech to accomplish this in a fraction of the time, and while there is still a network of labs and researchers around the world, we can share all this data in virtually no time.”

For example, medical researchers studying a child born with a metabolic condition would have once believed it was a unique genetic problem, but they had no easy means of comparison to help them address or prevent the condition. Through bioinformatics, “you can sequence that child’s genome and compare it to an [international] database to understand what is the one difference,” Tilden said. “Then you begin to have a base to find a solution.” What does it take in 2017 to get this done? “It’s a thousand bucks and one day—we are really close to what we call the thousand-dollar genome.”

Read the full article. 

 

 


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