HPC in the Cloud: On Your Mark, Get Set, Squeeze

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December 12, 2011

On Your Mark, Get Set, Squeeze

Tiffany Trader

DNA sequencing approaches hold tremendous promise for society. The research of today will become the powerful diagnostic and therapeutic tools of tomorrow. In an era where researchers are increasingly looking to DNA to unlock the secrets of disease, many DNA sequencing centers are looking to cloud computing as a way to handle the data-intensive workloads. Indeed, data volumes are so large that current compression techniques are falling short. That's where the Sequence Squeeze contest comes in. The Pistoia Alliance is offering $15,000 for the best novel open-source NGS compression algorithm submitted before the closing date of March 15, 2012.

Pistoia Alliance The contest itself is a good demonstration of the way cloud computing resources can support the field of DNA research. In an email, Competition Coordinator Richard Holland explained that the contest is hosted on Amazon servers and requires participants to enter their solutions packaged up as Amazon S3 buckets. This means that you need an Amazon account to enter, but Amazon Web Services offers a trial period free tier, which Holland says should be sufficient for most solutions. Entries will then be unpackaged and run on a testing machine hosted inside Amazon. The first 40 entries to the event will receive $20 AWS vouchers.

The distinguished panel of judges draws from the most-renowned sequencing centers in the world: the Wellcome Trust Sanger Institute in Cambridge, England; the Beijing Genomics Institute in China; and the Broad Institute in the United States.

For more information, visit the Sequence Squeeze Competition website.

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