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to make formats compatible with their instrument. Usually the person doing this is a biologist, who doesn’t have training in computer science or math. So the researcher fumbles around looking for someone, often a graduate student, who knows enough about computer science to help. “They are completely at a loss,” Sundquist says.
This whole model, Sundquist says, ought to be turned around. DNAnexus has built a system that takes all that genomic data running off the instruments, keeps it stored on a cloud computing platform run by Amazon Web Services, and displays the results in a Web 2.0-style web-based interface.
This system requires the researcher to have access to an expensive instrument and the chemicals to run it. But using the cloud computing service from Amazon means that researchers don’t need to spend money on servers or use resources of their own server cluster on campus, which may or may not have enough horsepower to store and process the genomic data over time. And DNAnexus is set up so that researchers pay for the Web-based program and storage on a pay-as-you-go basis, instead of locking them into monthly recurring fees or annual software licenses.
“We want people to start using the technology at such a low cost that it’s a no-brainer. We want next-generation sequence analysis accessible to everyone,” Sundquist says. “You shouldn’t have to invest a lot of money to get access to it. Nor should you need to have a bioinformatics PhD to start using these technologies.”
The DNAnexus interface was designed to look a little like Gmail, Sundquist says. A user logs in, and can see the sample data. If the user is running a centralized core sequencing facility shared by many researchers on a campus, then the user can get a quick look at quality stats that look at how well the sequencing runs were performed, or to what extent there may have been errors in sample preparation, Sundquist says.
Sharing is one of the key pieces of the puzzle. Researchers are able, Web 2.0-style, able to click and drag on what they want to, and zoom in or zoom out for the degree of resolution they want on their sequencing run. If you zoom all the way in, you can see individual letters of A, C, G, or T, the chemical units of DNA, Sundquist says.
I wondered if all this genomic data—given that each genome has 6 billion data points—might clog up the broadband at some campuses that aren’t really equipped … Next Page »