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In it to win it
Sometimes it seems like competition has become a dirty word, with kids in sports sometimes getting trophies no matter where their team falls in the rankings. There may or may not be good reasons for decreasing competitive pressure on kids, but at least one study has found that we grown-ups could definitely stand some competition, particularly in the life-science realm.
Specifically, new research published in the journal GigaScience indicates that dynamic and open contests may be a good tool for driving innovation and developing new tools for life-science research, further noting that using a dynamic leaderboard to monitor progress in a competition actively stimulates participants to strive harder for success. These conclusions come by way of work done by Eagle, a bioinformatics service solutions specialist, and the Pistoia Alliance, which describes itself as "a not- for-profit, precompetitive alliance of companies and organizations engaged in lowering the barriers to innovation in life-science R&D."
In 2012, the Pistoia Alliance launched its "Sequence Squeeze" competition to encourage the development of novel and enhanced data compression algorithms to improve the management of the large volumes of gene sequence data coming from next-generation sequencing machines, working with Eagle to organize the event, set up the supporting infrastructure and manage the process of receiving and judging entries.
The end result of the contest, Pistoia and Eagle say, was a set of new compression algorithms for next-gen sequencing data that are fully open-source and available for the community to use and build upon with their own ideas. The research partners says the open-source requirement was a key factor for them, ensuring that everyone has a chance to benefit from the innovation and everyone can share in the data compression lessons learned in the process.
According to Nick Lynch from Pistoia Alliance, a co-author of the GigaScience paper, "We were very pleased not only with the output from the Sequence Squeeze competition itself, but also how the leaderboard worked to foster constructive competition between our contributors. We hope that this model can be adopted more widely as this experiment clearly shows the benefits of such an approach."
"While the life-science industry has made huge steps in sequencing many new genomes, the sheer amount of data we are now producing has created incredible challenges," adds Richard Holland, chief business officer of Eagle and first author of the paper. "We were very pleased to be involved in the Sequence Squeeze competition. However, through initiatives such as this, we can develop effective tools to help manage the flood of data we are now creating."
Such news about the value of competitive efforts is probably good news for many right now, with a number of competitions large and small dotting the life-science landscape these days, whether open or closed.
One of those competitive efforts, Industrial Methodology for Process Verification in Research (IMPROVER), was launched in 2009 by tobacco industry giant Philip Morris International (PMI) and computing giant IBM, building on the idea of the ongoing Dialogue on Reverse Engineering Assessment and Methods (DREAM) challenge project IBM had previously played a key role in launching. Both DREAM and IMPROVER are focused on systems biology issues, with DREAM attempting to figure out how to fairly compare the strengths and weaknesses of various systems biology methods and gain a clear sense of the reliability of the models that researchers create and IMPROVER looking to create an industry standard—a product to help make systems biology-related work more efficient and useful. Both challenges combine themes of competitiveness and crowdsourcing.
"Peer review isn't coming to an end, but it does have its limitations, especially when it comes to big data, because most people just can't deal with that complexity on their own or with just a few other people," notes Dr. Jörg Sprengel, an IBM senior managing consultant. "What we are doing is applicable to a lot of industries, including environmental, animal health and food safety, but we think it's particularly relevant to pharma and biotech."
DREAM is up to DREAM8 now, in conjunction with Sage Bionetworks, looking this time to run four "big data" open science challenges between now and fall to tackle problems from toxicology to cancer. Buoyed by the successful outcomes of DREAM challenges so far, Dr. Gustavo Stolovitzky, manager of functional genomics and systems biology at the IBM Computational Biology Center, sees great potential that "IMPROVER could significantly influence how systems biology can be verified in industrial contexts in the years to come."
IMPROVER launched its first effort, the Diagnostic Signature Challenge, in March 2012 and completed that in late 2012. This spring, it moved on to the second phase with the Species Translation Challenge, aimed at determining translatability of data from model systems—rodent models in particular—to human cell lines.
Of course, there are risks, concerns and downsides at times with competitions and challenges if some parties have vested interests. A May 13 article on the Action on Smoking & Health website characterizes the PMI and IBM effort as being designed to "award three $20,000 grants to scientists who can best poke holes in translating disease lab results in rodents to humans" in an attempt to play down the risks of smoking.
PMI's scientific communications director, Hugh Brown, has maintained that "Our no. 1 objective is to do something about our dangerous products" and that his company is investing in systems biology because it wants to sort out the environmental and genetic factors leading to diseases like emphysema and cancer and better understand how smoking and chewing tobacco leads to complex interactions in a user's biological systems.
But whether there are hidden agendas at times or not, competitive efforts abound, and the Eagle-Pistoia research indicates they may have great value as more companies—life- science ones and those who dabble in the realm like IBM—decide to pit researchers against problems and sometimes against each other.
For example, Sanofi at the end of 2012 announced the winner of its Collaborate Activate Innovation Challenge: Registries for All Diseases, which received $300,000 for the creation of a crowd-sourced, cross-disease registry to aid in accelerating translational research in more than a thousand diseases.
More recently, in May of this year, the Epilepsy Therapy Project's "Shark Tank" competition announced as its $100,000 winner a novel point-of-care disposable microfluidic chip which can immediately detect the levels of antiepileptic drugs based on a finger-prick sample of blood, designed by researchers at Brigham and Women's Hospital, Harvard Medical School and the Harvard-MIT Division of Health Sciences and Technology.
On a smaller scale, May also saw the Office of the National Coordinator for Health Information Technology launch a challenge in conjunction with the National Cancer Institute that will award as many as three $5,000 prizes in the first phase for the development of innovative information management tools and applications that help cancer survivors manage their transition from specialty to primary care.