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Information overload
Culling useful information from the huge amounts of data available is a daunting task. DNA-sequence data can be found in hundreds of public and proprietary databases. With so many databases created on different platforms in different formats, there's a dire need to integrate this information in a way that makes it useful and easily accessible to scientists.
Data integration is one of the major bottlenecks in biotech's ability to move from the sequencing stage of genome research to the next stage of converting those sequences into information about gene function.
One company that's stepped up to the challenge is Incyte Genomics (INCY) in Palo Alto, Calif. The result of its efforts is the Genomics Knowledge Platform, which is based on a biology-object model -- a virtual representation of how data stored in different databases are related.
For example, DNA sequences comprise genes. Genes code for chains of amino acids. Chains of amino acids make up proteins. Proteins are the basis of cell structure and participate in chemical reactions in cells. In a biology-object model, all the pieces of information in databases about DNA sequences, genes and proteins are placed in relation to one another as we would, in our mind's eye, see them. A biology-object model is able to pull together data that are scattered across different databases and computers and put them in an easy-to-use format for researchers.
The search for an integration platform began with Incyte's need to process its own collected data. When it found it could not purchase an existing integration platform, Incyte thought about hiring a company to build one for it. This, too, proved unsuccessful.
Incyte's vice president of software development, Lee Grover, says, "We had service organizations come in and make presentations on what they could and couldn't do. We concluded that it would not be accomplished in the time frame we had to accomplish this."
Incyte needed specialized help to build the integration platform, and it chose application-server provider Secant Technologies in Cleveland, Ohio. A small, relatively young private company, Secant was not the obvious choice, but it turned out to be the best one.
Incyte was looking to build an integration platform based on a biology-object model, and it needed a company that knew a lot about object-modeling technology. Secant's technology and experience with object-modeling technology were far superior to those offered by every other company Incyte had explored.
Secant's experience as a service provider also made the company stand out from its competitors. Secant's founder and CTO, John Pompeii, says, "We went out to see Incyte and really talked to them in depth about what they were doing. They were looking for a great deal of guidance on how it is that they could put this together. They were on a very short schedule and needed to do this right the first time."
Grover at Incyte applauds Secant's proactive approach: "I wanted the lead engineers to be part of the project. Secant, right up to the CTO, has been highly involved and has really overseen a lot of the exploitation of the technology."
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