The NIH BD2K center for big data in translational genomics

Benedict Paten; Mark Diekhans; Brian J Druker; Stephen Friend; Justin Guinney; Nadine Gassner; Mitchell Guttman; W James Kent; Patrick Mantey; Adam A Margolin; Matt Massie; Adam M Novak; Frank Nothaft; Lior Pachter; David Patterson; Maciej Smuga-Otto; Joshua M Stuart; Laura Van't Veer; Barbara Wold; David Haussler

doi:10.1093/jamia/ocv047

The NIH BD2K center for big data in translational genomics

J Am Med Inform Assoc. 2015 Nov;22(6):1143-7. doi: 10.1093/jamia/ocv047. Epub 2015 Jul 13.

Authors

Benedict Paten¹, Mark Diekhans², Brian J Druker³, Stephen Friend⁴, Justin Guinney⁴, Nadine Gassner², Mitchell Guttman⁵, W James Kent², Patrick Mantey⁶, Adam A Margolin⁷, Matt Massie⁸, Adam M Novak², Frank Nothaft⁸, Lior Pachter⁹, David Patterson⁸, Maciej Smuga-Otto², Joshua M Stuart², Laura Van't Veer¹⁰, Barbara Wold¹¹, David Haussler¹²

Affiliations

¹ UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA benedict@soe.ucsc.edu haussler@soe.ucsc.edu.
² UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
³ Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
⁴ Sage Bionetworks, Fairview Ave North, Seattle 98109, WA, USA.
⁵ Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
⁶ UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA Jack Baskin School of Engineering, University of California, Santa Cruz, CA, USA.
⁷ Computational Biology Program, Oregon Health & Science University, Portland, OR, USA.
⁸ Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, USA.
⁹ Department of Mathematics, University of California Berkeley, Berkeley, CA, USA Department of Molecular & Cellular Biology, University of California Berkeley, Berkeley, CA, USA.
¹⁰ Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
¹¹ Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA benedict@soe.ucsc.edu haussler@soe.ucsc.edu.
¹² 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.

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.

Keywords: APIs; big data; computational genomics; genome informatics; genomics.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Computational Biology
Datasets as Topic*
Genomics*
Humans
Knowledge Bases
National Institutes of Health (U.S.)
Translational Research, Biomedical*
United States

Abstract

Publication types

MeSH terms

Grants and funding