In it to win it

Research indicates that open competition can be used to drive innovation

Jeffrey Bouley
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Sometimes it seems like competition has become a dirty word,with kids in sports sometimes getting trophies no matter where their team fallsin the rankings. There may or may not be good reasons for decreasingcompetitive pressure on kids, but at least one study has found that wegrown-ups could definitely stand some competition, particularly in thelife-science realm.
Specifically, new research published in the journal GigaScience indicates that dynamic andopen contests may be a good tool for driving innovation and developing newtools for life-science research, further noting that using a dynamicleaderboard to monitor progress in a competition actively stimulates participantsto strive harder for success. These conclusions come by way of work done byEagle, a bioinformatics service solutions specialist, and the Pistoia Alliance,which describes itself as "a not-for-profit, precompetitive alliance ofcompanies and organizations engaged in lowering the barriers to innovation inlife-science R&D."
In 2012, the Pistoia Alliance launched its "SequenceSqueeze" competition to encourage the development of novel and enhanced datacompression algorithms to improve the management of the large volumes of genesequence data coming from next-generation sequencing machines, working withEagle to organize the event, set up the supporting infrastructure and managethe process of receiving and judging entries.
The end result of the contest, Pistoia and Eagle say, was aset of new compression algorithms for next-gen sequencing data that are fullyopen-source and available for the community to use and build upon with theirown ideas. The research partners says the open-source requirement was a keyfactor for them, ensuring that everyone has a chance to benefit from theinnovation and everyone can share in the data compression lessons learned inthe process.
According to Nick Lynch from Pistoia Alliance, a co-authorof the GigaScience paper, "We werevery pleased not only with the output from the Sequence Squeeze competitionitself, but also how the leaderboard worked to foster constructive competitionbetween our contributors. We hope that this model can be adopted more widely asthis experiment clearly shows the benefits of such an approach."
"While the life-science industry has made huge steps insequencing many new genomes, the sheer amount of data we are now producing hascreated incredible challenges," adds Richard Holland, chief business officer ofEagle and first author of the paper. "We were very pleased to be involved inthe Sequence Squeeze competition. However, through initiatives such as this, wecan develop effective tools to help manage the flood of data we are now creating."
Such news about the value of competitive efforts is probablygood news for many right now, with a number of competitions large and smalldotting the life-science landscape these days, whether open or closed.
One of those competitive efforts, Industrial Methodology forProcess Verification in Research (IMPROVER), was launched in 2009 by tobaccoindustry giant Philip Morris International (PMI) and computing giant IBM,building on the idea of the ongoing Dialogue on Reverse Engineering Assessmentand Methods (DREAM) challenge project IBM had previously played a key role inlaunching. Both DREAM and IMPROVER are focused on systems biology issues, withDREAM attempting to figure out how to fairly compare the strengths andweaknesses of various systems biology methods and gain a clear sense of thereliability of the models that researchers create and IMPROVER looking tocreate an industry standard—a product to help make systems biology-related workmore efficient and useful. Both challenges combine themes of competitivenessand crowdsourcing.
"Peer review isn't coming to an end, but it does have itslimitations, especially when it comes to big data, because most people justcan'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 doingis applicable to a lot of industries, including environmental, animal healthand food safety, but we think it's particularly relevant to pharma andbiotech."
DREAM is up to DREAM8 now, in conjunction with SageBionetworks, looking this time to run four "big data" open science challengesbetween now and fall to tackle problems from toxicology to cancer. Buoyed bythe successful outcomes of DREAM challenges so far, Dr. Gustavo Stolovitzky,manager of functional genomics and systems biology at the IBM ComputationalBiology Center, sees great potential that "IMPROVER could significantlyinfluence how systems biology can be verified in industrial contexts in theyears to come."
IMPROVER launched its first effort, the Diagnostic SignatureChallenge, in March 2012 and completed that in late 2012. This spring, it movedon to the second phase with the Species Translation Challenge, aimed atdetermining translatability of data from model systems—rodent models inparticular—to human cell lines.
Of course, there are risks, concerns and downsides at timeswith competitions and challenges if some parties have vested interests. A May13 article on the Action on Smoking & Health website characterizes the PMIand IBM effort as being designed to "award three $20,000 grants to scientistswho can best poke holes in translating disease lab results in rodents tohumans" in an attempt to play down the risks of smoking.
PMI's scientific communications director, Hugh Brown, hasmaintained that "Our no. 1 objective is to do something about our dangerousproducts" and that his company is investing in systems biology because it wantsto sort out the environmental and genetic factors leading to diseases likeemphysema and cancer and better understand how smoking and chewing tobaccoleads 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 mayhave great value as more companies—life-science ones and those who dabble inthe realm like IBM—decide to pit researchers against problems and sometimesagainst each other.
For example, Sanofi at the end of 2012 announced the winnerof its Collaborate Activate Innovation Challenge: Registries for All Diseases,which received $300,000 for the creation of a crowd-sourced, cross-diseaseregistry to aid in accelerating translational research in more than a thousanddiseases.
More recently, in May of this year, the Epilepsy TherapyProject's "Shark Tank" competition announced as its $100,000 winner a novelpoint-of-care disposable microfluidic chip which can immediately detect thelevels of antiepileptic drugs based on a finger-prick sample of blood, designedby researchers at Brigham and Women's Hospital, Harvard Medical School and theHarvard-MIT Division of Health Sciences and Technology.
On a smaller scale, May also saw the Office of the NationalCoordinator for Health Information Technology launch a challenge in conjunctionwith the National Cancer Institute that will award as many as three $5,000prizes in the first phase for the development of innovative informationmanagement tools and applications that help cancer survivors manage theirtransition from specialty to primary care.


Jeffrey Bouley

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