Survey for genetics labs: how do you store & manage your data?
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@matthew-keller-2483
Last seen 9.6 years ago
Hello all, I am an asst. professor at CU Boulder and a fellow at the Institute for Behavioral Genetics (IBG). I am writing this email on behalf of my colleagues here at IBG. We are in the process of trying to determine the best way forward for storing large databases (100, 500, and 1000K SNP chip data and sequencing data coming) in a way that a) is easily accessed by researchers here (over an intranet preferably), b) is relational to other databases, and c) can be easily pulled into existing statistical packages like R (and Bioconductor) or SAS. We have a meeting to discuss how to proceed next Friday. For anyone who has the time, we would truly appreciate feedback. How does your lab deal with data distribution and storage of large databases? If you use a relational database, what language (eg, SQL... are there any others?) and specific system (eg., SQLite, Oracle, PostgreSQL etc) does your lab use? Do you find these interact nicely with your statistical programs? Do you hire a full time staff member in charge of database issues? Answers to these questions, as well as any discussion of pluses or minuses of different approaches, or additional words of wisdom, would be greatly appreciated. Best, Matthew Keller -- Matthew C Keller Asst. Professor of Psychology University of Colorado at Boulder www.matthewckeller.com
Sequencing Genetics PROcess Sequencing Genetics PROcess • 548 views
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