title: The NIH BD2K center for big data in translational genomics.
abstract: The world's genomics data will never be stored in a single repository - rather, it will be distributed among many sites in many countries. No one site will have enough data to explain genotype to phenotype relationships in rare diseases; therefore, sites must share data. To accomplish this, the genetics community must forge common standards and protocols to make sharing and computing data among many sites a seamless activity. Through the Global Alliance for Genomics and Health, we are pioneering the development of shared application programming interfaces (APIs) to connect the world's genome repositories. In parallel, we are developing an open source software stack (ADAM) that uses these APIs. This combination will create a cohesive genome informatics ecosystem. Using containers, we are facilitating the deployment of this software in a diverse array of environments. Through benchmarking efforts and big data driver projects, we are ensuring ADAM's performance and utility.
authors.affiliation: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA benedict@soe.ucsc.edu haussler@soe.ucsc.edu.
authors.forename: Benedict
authors.initials: B
authors.lastname: Paten
authors.affiliation: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Diekhans
authors.affiliation: Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Druker
authors.affiliation: Sage Bionetworks, Fairview Ave North, Seattle 98109, WA, USA.
authors.forename: Stephen
authors.initials: S
authors.lastname: Friend
authors.affiliation: Sage Bionetworks, Fairview Ave North, Seattle 98109, WA, USA.
authors.forename: Justin
authors.initials: J
authors.lastname: Guinney
authors.affiliation: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
authors.forename: Nadine
authors.initials: N
authors.lastname: Gassner
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
authors.forename: Mitchell
authors.initials: M
authors.lastname: Guttman
authors.affiliation: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
authors.forename: W James
authors.initials: WJ
authors.lastname: Kent
authors.affiliation: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA Jack Baskin School of Engineering, University of California, Santa Cruz, CA, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Mantey
authors.affiliation: Computational Biology Program, Oregon Health & Science University, Portland, OR, USA.
authors.forename: Adam A
authors.initials: AA
authors.lastname: Margolin
authors.affiliation: Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, USA.
authors.forename: Matt
authors.initials: M
authors.lastname: Massie
authors.affiliation: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
authors.forename: Adam M
authors.initials: AM
authors.lastname: Novak
authors.affiliation: Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, USA.
authors.forename: Frank
authors.initials: F
authors.lastname: Nothaft
authors.affiliation: Department of Mathematics, University of California Berkeley, Berkeley, CA, USA Department of Molecular & Cellular Biology, University of California Berkeley, Berkeley, CA, USA.
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
authors.affiliation: Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, USA.
authors.forename: David
authors.initials: D
authors.lastname: Patterson
authors.affiliation: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
authors.forename: Maciej
authors.initials: M
authors.lastname: Smuga-Otto
authors.affiliation: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Stuart
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
authors.forename: Laura
authors.initials: L
authors.lastname: Van't Veer
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA benedict@soe.ucsc.edu haussler@soe.ucsc.edu.
authors.forename: Barbara
authors.initials: B
authors.lastname: Wold
authors.affiliation: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA Howard Hughes Medical Institute, Bethesda, MD, USA benedict@soe.ucsc.edu haussler@soe.ucsc.edu.
authors.forename: David
authors.initials: D
authors.lastname: Haussler
mesh_terms: D019295:Computational Biology; D066264:Datasets as Topic; D023281:Genomics; D006801:Humans; D051188:Knowledge Bases; D009316:National Institutes of Health (U.S.); D057170:Translational Research, Biomedical; D014481:United States
keywords: APIs; big data; computational genomics; genome informatics; genomics