May 14, 2012
Three teams developed and demonstrated platforms to supply cloud-based, next-generation sequence (NGS) data during the second annual Pistoia Alliance conference. Projects were aimed at assisting research and development in the pharmaceutical industry. The groups consisted of HP and the Swiss Life Science Center; Eagle Genomics and Cycle Computing; and Constellation Technologies and Genestack. BioInform reported on the event.
Each team was responding to a request for proposals [PDF] made by the Pistoia Alliance Sequence Services working group last year, asking for a hosted data services platform that "can solve scientific problems based on DNA/RNA sequence information." Out of ten submissions received, the alliance selected three proposals. Pharmaceutical companies GlaxoSmithKline, AstraZeneca, Roche, Novartis, and Lundbeck provided shared funding for the project.
The platforms are part of a larger plan to build a fully-functional system for NGS storage and analysis to assist the pharmaceutical industry. The first phase, completed last year, resulted in the creation of an infrastructure focused on performance, scalability and availability.
This second phase required open source tools for analysis while accounting for scalability and security concerns. The platform are required to host Ensembl, a genome browser and PlasMapper, an application that builds and annotates plasmid maps.
Each team had its own ideas when it came to implementing the project requirements. For example, Constellation Technologies and Genestack kept flexibility in mind when developing their platform. Rob Gill, Constellations CTO discussed this point: "What we want to do is build a platform that anybody's tool can go on and thus they can do their science...not our science," adding that users would also have their choice of cloud offerings. Constellation plans to work with multiple providers, including Amazon Web Services, Microsoft Azure and others.
Although Gill's group focused on building a versatile platform, he mentioned the other teams as having similar concepts regarding workflow and cloud computing.
Not looking to reinvent the wheel, Cycle Computing and Eagle Genomics focused more on standards. Will Spooner, founder and CTO of Eagle Genomics, spoke with BioInform about their platform: "The way we have put it together is very flexible in terms of tying these different components together using industry standard protocols and web services."
HP, on the other hand, used its foothold in academia to promote a single platform approach. Joel Jankow, Life Science Business Development Manager for HP, seemed confident about the company's offering. He claimed that users could do anything they wanted and followed up by saying "there is a very clear delineation between what we do and what our partners do, [and] that didn't come across as clear with the other [groups]."
All three teams have plans to commercialize their platforms. HP is expecting to integrate its offering into the company's cloud infrastructure in January 2013. Eagle Genomics hopes to launch it product this summer with a pay-as-you-go model, and Constellation Technologies says it will make its platform available in the next six months.
On a related note, the winner of the Pistoia Alliance Sequence Squeeze Competition was announced during the Pistoia Alliance Conference on April 24, 2012. James Bonfield of the Sanger Institute received the $15,000 prize for developing the best new algorithm for compressing next-generation sequencing (NGS) data. The contest was hosted on Amazon servers.
The ever-growing complexity of scientific and engineering problems continues to pose new computational challenges. Thus, we present a novel federation model that enables end-users with the ability to aggregate heterogeneous resource scale problems. The feasibility of this federation model has been proven, in the context of the UberCloud HPC Experiment, by gathering the most comprehensive information to date on the effects of pillars on microfluid channel flow.
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