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PacBio Teams with Cycle Computing to Create Cloud Version of SMRT Analysis Software Suite

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By Uduak Grace Thomas

Pacific Biosciences has tapped Cycle Computing to cloud-enable an open source software suite it launched earlier this year to provide secondary analysis for its PacBio RS single-molecule sequencing system (BI 4/8/2011).

Cycle will help PacBio set up a supported cluster environment for the Single Molecule Real Time Analysis software on the Amazon Elastic Compute Cloud infrastructure that it can offer to its customers as a service, Jason Stowe, Cycle Computing's CEO, told BioInform. He added that the offering will also include data storage for users.

Cycle demonstrated an early version of the solution this week at the Bio-IT World Cloud Computing conference held in La Jolla, Calif., and the Amazon Web Services Genomics event in Seattle.

PacBio decided to move the SMRT Analysis software suite to the cloud to "offer customers more flexibility" without requiring them to "maintain complex and expensive hardware and software," Edwin Hauw, PacBio's director of software product management, said in a statement.

The company said in a statement that the cloud-based infrastructure would be a key component of a sequencing workflow "that includes sample preparation, sequencing, and completed data analysis in less than one day."

The move is in line with similar strategies that other sequencing vendors have followed in an effort to lower the informatics barrier to purchasing their instruments. In May, Life Technologies offered a cloud-based option as one of three configurations for the LifeScope Genomic Analysis software for its 5500 SOLiD sequencer (BI 5/27/2011).

Illumina has also said that it is developing a cloud-based analysis platform for its sequencing technology that it plans to release by the end of the year (BI 05/06/2011).

Complete Genomics, meantime, is partnering with DNAnexus to allow customers to store and visualize their human genome sequencing data in the company's cloud-based platform (BI 3/18/2011).

A Direct Sale

DNAnexus is also a member of PacBio's partner program and is one of several partners that offer some form of cloud-based bioinformatics services, such as GenomeQuest and Perkin Elmer subsidiary Geospiza. But Hauw told BioInform that the arrangement with Cycle differs from these partnerships because PacBio will offer the resource directly to customers of its sequencing platform.

Additionally, PacBio didn't want to "prefer one third-party vendor to another" in terms of software, he said.

He added that PacBio chose Cycle because of its "extensive experience with pharma ... and financial services companies," which has prepared the firm to handle security concerns that customers might have.

Last year, Cycle Computing launched CycleCloud for Life Sciences to offer researchers access to cloud-based CPU clusters along with a suite of preconfigured life science algorithms such as Blast, GMAP, and HMMer, in the Amazon EC2 environment (BI 3/19/2010).

Cycle serves as "a general purpose contract shop to figure out ways to deploy software in the cloud," Hauw explained.

The companies plan to link the sequencer to the cloud-based infrastructure in such a way that "as the [PacBio RS] system is sequencing, we are going to stream the data up to the cloud ... so that ... [the] analysis is seamless to the customer," he said.

PacBio plans to launch a beta version of the cloud-based software alongside the next major release of its sequencing system, which is currently scheduled for the end of this year.

Hauw said PacBio has targeted some of its existing customers as candidates for the beta run but he declined to mention specific names.

The company is planning a full commercial release of the solution for mid-2012 at which time it will disclose the pricing for the offering.

Hauw wouldn't provide specific details about the cost but he did say that it would be "competitive" compared to similar offerings on the market.

Pricing models for cloud-based bioinformatics offerings vary. For example, Life Technologies' LifeScopeCloud.com offering is available under a subscription model that charges $1,500 for 3,000 node hours per month and 3 TB of permanent disk storage. The company also offers several pay-as-you-go models, including one for $199 a month that provides access to one core of a Xeon 2.4GHz processor with 4 GB of RAM, and another that allows users to pay $0.35 per core hour.

DNAnexus, meantime, bases its pricing on volume, charging academic customers a rate of $20 per gigabase of raw sequence, which includes analysis and storage for two years.

And India's Geschickten offers a mix of up-front and subscription fees for its cloud-based iOmics platform, charging users a one-time setup fee of $1,000 and then $199 per month.


Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com

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