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NGS Leaders Blog

Call for Entries: The Sequence Squeeze Competition

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Editor’s Note: Richard Holland is chief business officer and co-founder of Eagle Genomics Ltd, a UK-based bioinformatics services company that is partnering with the Pistoia Alliance to administer the Sequence Squeeze competition. 

January 6, 2012

Richard Holland :
Capitalizing on next-generation sequencing requires as much attention to technology and computer science as life science. The biggest players in the life sciences have also realized that no one will get ahead by “going it alone.” Instead, they are working together pre-competitively to develop open solutions that will benefit the entire industry. The Pistoia Alliance has succeeded in building a unique coalition of industry players - the world’s top pharma companies, life science information, services, and technology suppliers, and academic researchers - to resolve common barriers to R&D innovation, such as the handling of “big data”.

An exciting example of a Pistoia Alliance-led project of particular interest to the NGS community is the Pistoia Alliance Sequence Squeeze Competition, which will award a $15,000 cash prize to the developer of the best new, open-source algorithm for compressing NGS data.

Currently available compression technologies, which enable labs to store data from sequencing runs, are faltering under the data volumes produced by NGS. Pistoia Alliance members recognize that compression solutions may well come from computer scientists or mathematicians - hence the Alliance’s willingness to put forward a generous monetary incentive to encourage anyone to develop a better algorithm.

The judging panel further highlights the importance of this issue to the sequencing community: BGI, the Broad Institute, and the Wellcome Trust Sanger Institute have all put forward staff to judge the competition.

The competition is open to ANYONE, because it recognizes that life scientists may not necessarily have the expertise to resolve this “big data” problem. The answer may lie in statistics, mathematics, computer science, physics, or other non-biological disciplines, so the Alliance is spreading the word as widely as possible in order to encourage entries from previously untapped sources.

Entries can be submitted via the contest website at http://www.sequencesqueeze.org, which also contains details of the functional requirements for entries and some sample code to use as a starting point. Judging of entries takes place within the Amazon EC2 cloud and so we require entries to be submitted using Amazon's S3 file system.

As an incentive to have a go and enter the contest, Amazon is generously offering the first 40 entrants a $20 voucher for use with their cloud services. The competition closes to new entries at 5:00 pm GMT on March 15, 2012. Winners will be announced at the Pistoia Alliance Conference in Boston on April 24, 2012 (held in conjunction with this year’s Bio-IT World Conference & Expo).

The Sequence Squeeze Competition is just one of the projects the Pistoia Alliance is sponsoring. We also have an active effort underway to develop shared cloud services for storing and analyzing NGS data, which we call Sequence Services. The Alliance website at http://www.pistoiaalliance.org has full details of this and other ongoing projects.

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