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Geospiza, SAIC Modify LIMS to Handle Genomic Data Deluge from PacBio's Single-Molecule Sequencer

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By Uduak Grace Thomas

As Pacific Biosciences prepares for an early 2011 launch for its single-molecule sequencer, at least one of its early-access customers is taking steps to ramp up its informatics capabilities to keep up with the large quantities of data expected to pour out of this new technology.

Last week, Geospiza said that is partnering with SAIC-Frederick to integrate Geospiza's GeneSifter Lab Edition with the PacBio RS sequencing platform. SAIC-Frederick, a contractor for the National Cancer Institute, is one of 11 early-access customers for the PacBio platform.

Todd Smith, Geospiza's chief technology officer, told BioInform that the company also plans to make its GeneSifter Analysis Edition software compatible with PacBio's sequencers. Gene Sifter Lab Edition serves as a cross-platform laboratory information management system while Analysis Edition includes statistical, visualization, and annotation tools for microarray and sequence analysis. Smith noted that the two packages complement each other.

Aspects of the SAIC project related to Lab Edition will involve "figuring out the details that are important within the PacBio data from a quality control perspective, [such as] how do I know the instrument ran [and] how do I know my samples are good," he explained. "On the analysis side, there are a host of new kinds of experiments that people are going to do with this technology and we want to be able to help them get their science done."

He said that Geospiza's partnership with SAIC grew out of a "working relationship" between the groups. According to Smith, SAIC is already adapting software used in its labs to work with the sequencer and the partnership with Geospiza is "a natural extension of that work."

Geospiza said that SAIC-Frederick will use GeneSifter interfaces already in place in its labs to create custom workflows and data-analysis methods that are "unique" to single-molecule real-time sequencing. SAIC-Frederick will also provide enhancements for systems analysis and automation, resulting in a data-management system that’s tailored to researcher’s needs.

GeneSifter Lab Edition, formerly known as FinchLab, handles sample tracking, data collection, quality control analysis, and data distribution. The system lets users construct and track workflow pipelines for their samples and then performs a quality control check of the resulting data. Since the tool is web based, researchers can install the software in their in-house data centers or Geospiza can host the software in its data centers and users can access it that way.

Currently GeneSifter Lab Edition supports Life Technologies' capillary electrophoresis and SOLiD sequencers, Illumina's Genome Analyzer and BeadArrays, Roche's 454 FLX sequencer and NimbleGene microarrays, Affymetrix GeneChips, and the Helicos Genetic Analysis System.

Geospiza expects that its developers will have to add some features to make it easier for customers to integrate new instruments with its software, but doesn’t expect to have to develop extensive "software adapters" for the system.

Smith said that part of the project involves developing a deeper understanding of the PacBio sequencer to figure out what these additional features will be. For example, as samples are prepared for the PacBio RS, researchers will need to collect laboratory data as recommended by PacBio and develop “various calibration parameters” through experience to ensure that good quality sequence is collected

Smith said that although single-molecule sequencing is a new technology, "one of the things that works to [Geospiza's] advantage is that we have been designing and developing this kind of software for a little over a decade" and the company has developed some "nice ways to build out some general features that can be customized by our clients."

In addition, Smith said that the PacBio team has done "a very good job in building out their application programming interfaces with web services," which he said should make it easier to integrate with GeneSifter Lab Edition since the system is also web-based.

In July, PacBio launched PacBio DevNet, a developers' network intended to help third-party software developers modify their tools to work with its system. The site provides access to data sets, source code, application programming interfaces, conversion tools, and documentation related to SMRT sequencing (BI 7/9/2010).

In addition, Geospiza is one of several informatics firms participating in a partnership program that PacBio kicked off in February intended to help vendors provide software, hardware, IT services, consumables, automation systems, and complementary instruments for the PacBio RS (BI 2/19/201).

Smith said this week that Geospiza GeneSifter Lab Edition can currently support PacBio's sequencer on "some level" for things like setting up laboratory workflows and tracking data. "The next stage of adding the detail [and] the quality control analysis and those kinds of things … will be in the next release," he said noting that the company releases new versions of its software every quarter.

He pointed out that there is a lot of "excitement" in the research community around the upcoming release of the PacBio RS and said that although he doesn’t expect GeneSifter’s sales to increase "significantly” during this early access phase, they could eventually rise as more research groups adopt the novel technology.

PacBio could not be reached to comment directly on the partnership but Eric Schadt, PacBio's chief scientific officer, explained in an e-mail to BioInform that the company "is very encouraged to see these kinds of early collaborations."

Schadt added that PacBio tapped Geospiza as one of its first software partners "because our customers really need the kinds of lab and analysis solutions they build."

SAIC-Frederick and Geospiza "both have very strong teams and I look forward to seeing what they develop," Schadt said.

SAIC-Frederick researchers could not be reached for comment by press time.