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Invitrogen Eyes FPGAs to Aid Its Push into Compute-Hungry Second-Gen Sequencing

Invitrogen this week said that it has begun a joint project with Active Motif’s TimeLogic biocomputing unit to “explore” the use of field-programmable gate array technology to speed the analysis of next-generation sequencing data.
The announcement is in step with a number of aggressive moves the reagent giant has made recently to capture a share of the rapidly growing sequencing market.
Invitrogen wasn’t the only company to expand its footprint in the next-gen sequence-analysis field this week. Applied Biosystems announced that it had expanded the Software Development Community Program for its SOLiD second-generation sequencer to include four new commercial partners and five new internally developed software tools.
In May, Invitrogen released its first product targeted at the second-gen sequencing sector: its SequalPrep Long PCR kits for sample preparation. A month later, it announced its plans to acquire ABI for $6.7 billion and disclosed that it has been developing its own “third-generation” sequencer internally. The firm has not yet provided any details on the technology or its commercialization timeline.
This week, Invitrogen said that it is now taking steps to address the IT challenges associated with next-gen sequencing by teaming with Active Motif to evaluate its TimeLogic line of FPGA-based technology for accelerating bioinformatics searches.
Active Motif CEO Joe Fernandez said in a statement that the companies are working together to “explore ways in which our technology can speed the processing of data directly from next-generation sequencing instruments, and to assess the physical requirements — such as power consumption, cooling, data transfer, and space constraints — that an optimal computational solution for research and clinical teams would require.”
This week at the Intelligent Systems for Molecular Biology conference in Toronto, Christopher Hoover, who handles business development for the TimeLogic division at Active Motif, told BioInform that partnering with a large company like Invitrogen could help TimeLogic “reach this big emerging market through different channels.”
Invitrogen is “a very well-recognized name in life sciences,” Hoover noted, while TimeLogic has a “market-leading“ presence in bioinformatics but is not as well known to the broad range of biologists who are starting to use next-generation sequencing technology.
As a result, the partnership could “help us reach people and help us get better feedback on what people see are their real needs,” he said.
Though the companies are "at an early stage in this exploration, the partnership could help us communicate with a wider range of researchers utilizing next-generation sequencing data," he said.
Hoover declined to provide financial details of the arrangement.
The first step in the exploration process, Hoover said, is “identifying customer needs and seeing which applications, which algorithms … we are going to explore.” These include algorithms for SNP-mapping and calling, de novo sequencing, visualization, and a range of emerging applications that next-generation has enabled to date.
Hoover estimated that it will take “at least six months of hardcore engineering time” to develop an FPGA-based system geared toward next-gen sequencing, “so we want to ensure that we are providing an optimal solution for researchers’ needs."

The open source licensing is expected to “help catapult the development efforts of all parties interested in developing algorithms or software for our SOLiD System.”

TimeLogic has already begun making inroads into the informatics market for next-gen sequencing. In March, it released a new FPGA accelerator called SeqCruncher that it said was “designed to handle the explosion of data from next-generation sequencing endeavors.”
SeqCruncher is based on larger Xilinx FPGA chips and a faster PCIe interface to improve the performance of TimeLogic’s DeCypher and CodeQuest accelerators by up to 20-fold, depending on the algorithm, the company said.
For example, the company said the new card can accelerate Smith-Waterman searches for oligo-sized sequences by up to 15-fold over the company's prior-generation accelerator — an application that should be of interest to customers for short-read sequencing technologies such as the Illumina Genome Analyzer or the ABI SOLiD.
Hoover said that TimeLogic has signed on four customers for the SeqCruncher to date: the University of North Carolina, Hiram College in Ohio, California-based Perlegen, and Korea’s National Institutes of Health.
He said that in benchmarks, a single SeqCruncher card has been delivering the equivalent computational power of up to 500 3-GHz Xeon cores.
"We’re pleased with the scalability. Adding a second SeqCruncher card to a 2-CPU server nearly doubles the throughput of a single-card system," he said. In addition, the cards draw only 15 watts of power, which is about 10 percent of a CPU, he said.
Invitrogen officials declined to comment on the agreement. In a conference call to discuss the company’s quarterly financial results this week, Invitrogen CEO Greg Lucier noted that even before the ABI transaction the firm has been “committed to playing a significant role in the next-generation sequencing market.”
Lucier said that the third-generation sequencing product that Invitrogen is developing will “sequence a genome at the lowest possible cost in the shortest amount of time,” and noted that the company will “continue to make investments in engaging collaborations to enhance that capability, such as the deal announced with Active Motif this week.”
However, he added, “this is the most detail we will provide on this program until we are closer to providing a commercially viable product.”
Building on a SOLiD Base
For its part, ABI this week dramatically expanded the set of tools available for users of its SOLiD system by releasing five new analysis packages through its Software Development Community website: the Small RNA Analysis Tool; the SRF Conversion Tool; the Color Space Mapping Tool; the GFF Conversion Tool; and the Analysis Pipeline Tool.  
All five packages are available under the GPL open-source license, Roger Canales, senior manager of ABI’s SOLiD Software Development Community, told BioInform via e-mail. 
Canales said that the company expects that the “transparency” of the open source licensing “will help catapult the development efforts of all parties interested in developing algorithms or software for our SOLiD System.”
While Canales said the open-source software is “unsupported by Applied Biosystems,” he noted that the company plans to continue to develop the software “as part of our own internal software-development efforts.” He said ABI will release updates through the website.
In addition to the five internally developed packages, ABI also added four new commercial partners to the Software Development Community program: InteRNA Genomics, Biotique Systems, Genomatix, and the BioTeam. They join Geospiza and GenomeQuest, which in February became the first commercial firms to participate in the program [BioInform 02-08-08]. 
Canales said that ABI is “actively encouraging” other third-party developers to participate in the program, including academic groups and commercial software firms.
For example, he said that Michael Brudno of the University of Toronto has developed a short-read alignment tool called Shrimp that will be available through ABI’s website some time in the next few weeks.
Brudno “has offered to create a project on the community website that contains information about how to access and use his tool and this project is currently under development by his group,” Canales said. In addition, he said that ABI has “spoken to several other third-party software developers and [we] expect them to make their tools available as well.”
Canales explained that the two different sides of the initiative — commercial and open source — represent ABI’s “commitment to providing our customers with a wide spectrum of software solutions for our platform’s applications.”
As a result, he said, “we will continue to develop tools that cannot only be used directly but can also be used to accelerate development efforts of our commercial partners.”
In addition to software partners, Canales said that ABI has had “discussions” with some hardware vendors who are interested in participating in the program, but he did not name the firms.
Hoover declined to comment on whether TimeLogic is in discussions with ABI regarding the Software Development Community. In addition to TimeLogic, Intel has also signaled its interest in developing FPGA-accelerated solutions to handle data analysis for second-gen sequencers [BioInform 05-02-08].  
“Given the sheer magnitude of data generation and the requirements for robust data processing and analytical procedures for next-generation sequencing data, there are some clear synergies between combining software and hardware to tackle some of the analytics and data storage issues,” Canales said. 
— Vivien Marx contributed to this article.

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