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Florida's Farmerie Tries Out External Data Management Systems for Sequencing Data


Core lab facilities have to offer value-added products, says William Farmerie, the associate director of emerging science at the University of Florida's Interdisciplinary Center for Biotechnology Research. It's not enough to just hand off a batch of raw short reads to researchers — analysis needs to be part of the package. For that, some sort of data management platform needs to be in place, he says.

When ICBR was doing mostly Sanger sequencing, Farmerie says that the researchers coming into the center would ask for help on running those sequences through Blast to make some sense of the information. To better handle all the data, ICBR develop an in-house database to support sequencing and microarray studies. But when the center acquired a 454 and then a SOLiD machine, that database was edging close to its limit. "[We are] generating basic information, only now we have a lot more sequence information — we still assemble it, we still annotate it — but our little in-house developed system for holding the basic annotation information on those data sets was becoming rather strained," Farmerie says.

While the center has plenty of PhD-level bioinformaticians and postdocs, Farmerie decided that their time was better spent on other projects rather than database-building and data management, particularly when there are commercially available options. "Rather than spending our time recreating what they've already done, we should just adopt that system and then that way our time is spent doing more higher-end things that we're better suited to do," he says. To that end, ICBR recently acquired both GenomeQuest and Geospiza's data management systems. The Genome-Quest platform is now being used in a metagenomic study of citrus greening, a disease that affects crops in Florida and is caused by an unculturable organism, while the Geospiza system is being put to work on RNA-seq analysis that is part of a large cancer project.

Of course there's a risk. "Everything has a cost," Farmerie says. Here, he says it's whether the upfront cost he has put into these systems will be recouped, and if his perception of his user community — and of the vendors — was correct. "You're calculating based on where the user community seems to be going. 'OK, I think this is important; I want to be ready with this. I [also] want the vendor paying attention to our needs, our community,'" he says.