Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space

The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, management, and analysis. In this perspective, we present AnVIL, des...

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Published in:	Cell genomics Vol. 2; no. 1; p. 100085
Main Authors:	Schatz, Michael C., Philippakis, Anthony A., Afgan, Enis, Banks, Eric, Carey, Vincent J., Carroll, Robert J., Culotti, Alessandro, Ellrott, Kyle, Goecks, Jeremy, Grossman, Robert L., Hall, Ira M., Hansen, Kasper D., Lawson, Jonathan, Leek, Jeffrey T., Luria, Anne O’Donnell, Mosher, Stephen, Morgan, Martin, Nekrutenko, Anton, O’Connor, Brian D., Osborn, Kevin, Paten, Benedict, Patterson, Candace, Tan, Frederick J., Taylor, Casey Overby, Vessio, Jennifer, Waldron, Levi, Wang, Ting, Wuichet, Kristin, Baumann, Alexander, Rula, Andrew, Kovalsy, Anton, Bernard, Clare, Caetano-Anollés, Derek, Van der Auwera, Geraldine A., Canas, Justin, Yuksel, Kaan, Herman, Kate, Taylor, M. Morgan, Simeon, Marianie, Baumann, Michael, Wang, Qi, Title, Robert, Munshi, Ruchi, Chaluvadi, Sushma, Reeves, Valerie, Disman, William, Thomas, Salin, Hajian, Allie, Kiernan, Elizabeth, Gupta, Namrata, Vosburg, Trish, Geistlinger, Ludwig, Ramos, Marcel, Oh, Sehyun, Rogers, Dave, McDade, Frances, Hastie, Mim, Turaga, Nitesh, Ostrovsky, Alexander, Mahmoud, Alexandru, Baker, Dannon, Clements, Dave, Cox, Katherine E.L., Suderman, Keith, Kucher, Nataliya, Golitsynskiy, Sergey, Zarate, Samantha, Wheelan, Sarah J., Kammers, Kai, Stevens, Ana, Hutter, Carolyn, Wellington, Christopher, Ghanaim, Elena M., Wiley, Ken L., Sen, Shurjo K., Di Francesco, Valentina, s Yuen, Deni, Walsh, Brian, Sargent, Luke, Jalili, Vahid, Chilton, John, Shepherd, Lori, Stubbs, B.J., O’Farrell, Ash, Vizzier, Benton A., Overbeck, Charles, Reid, Charles, Steinberg, David Charles, Sheets, Elizabeth A., Lucas, Julian, Blauvelt, Lon, Cabansay, Louise, Warren, Noah, Hannafious, Brian, Harris, Tim, Reddy, Radhika, Torstenson, Eric, Banasiewicz, M. Katie, Abel, Haley J., Walker, Jason
Format:	Journal Article
Language:	English
Published:	United States Elsevier Inc 12-01-2022 Elsevier
Online Access:	Get full text
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Summary:	The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) was developed to address a widespread community need for a unified computing environment for genomics data storage, management, and analysis. In this perspective, we present AnVIL, describe its ecosystem and interoperability with other platforms, and highlight how this platform and associated initiatives contribute to improved genomic data sharing efforts. The AnVIL is a federated cloud platform designed to manage and store genomics and related data, enable population-scale analysis, and facilitate collaboration through the sharing of data, code, and analysis results. By inverting the traditional model of data sharing, the AnVIL eliminates the need for data movement while also adding security measures for active threat detection and monitoring and provides scalable, shared computing resources for any researcher. We describe the core data management and analysis components of the AnVIL, which currently consists of Terra, Gen3, Galaxy, RStudio/Bioconductor, Dockstore, and Jupyter, and describe several flagship genomics datasets available within the AnVIL. We continue to extend and innovate the AnVIL ecosystem by implementing new capabilities, including mechanisms for interoperability and responsible data sharing, while streamlining access management. The AnVIL opens many new opportunities for analysis, collaboration, and data sharing that are needed to drive research and to make discoveries through the joint analysis of hundreds of thousands to millions of genomes along with associated clinical and molecular data types. [Display omitted] The NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL; https://anvilproject.org) inverts the traditional model of genomic data analysis by providing a unified cloud-computing environment for data storage, management, and analysis. The AnVIL platform eliminates the need for data movement, allows for active threat detection and monitoring, and provides scalable, shared computing resources that can be acquired by researchers as needed.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 The members of the AnVIL team are Anne O’Donnell Luria, Alessandro Culotti, Alexander Baumann, Andrew Rula, Anthony A. Philippakis, Anton Kovalsy, Brian D. O’Connor, Clare Bernard, Derek Caetano-Anollés, Eric Banks, Geraldine A. Van der Auwera, Jonathan Lawson, Justin Canas, Kaan Yuksel, Kate Herman, M. Morgan Taylor, Marianie Simeon, Michael Baumann, Qi Wang, Robert Title, Ruchi Munshi, Sushma Chaluvadi, Valerie Reeves, William Disman, Salin Thomas, Allie Hajian, Elizabeth Kiernan, Candace Patterson, Namrata Gupta, Trish Vosburg, Frederick J. Tan, Ludwig Geistlinger, Levi Waldron, Marcel Ramos, Sehyun Oh, Dave Rogers, Frances McDade, Mim Hastie, Nitesh Turaga, Jeffrey T. Leek, Kasper D. Hansen, Alexander Ostrovsky, Alexandru Mahmoud, Dannon Baker, Dave Clements, Enis Afgan, Jennifer Vessio, Katherine E.L. Cox, Keith Suderman, Nataliya Kucher, Sergey Golitsynskiy, Stephen Mosher, Samantha Zarate, Casey Overby Taylor, Michael C. Schatz, Sarah J. Wheelan, Kai Kammers, Vincent J. Carey, Ana Stevens, Carolyn Hutter, Christopher Wellington, Elena M. Ghanaim, Ken L. Wiley, Jr., Shurjo K. Sen, Valentina Di Francesco, Denis Yuen, Jeremy Goecks, Kyle Ellrott, Brian Walsh, Luke Sargent, Vahid Jalili, Anton Nekrutenko, John Chilton, Lori Shepherd, Martin Morgan, B.J. Stubbs, Ash O’Farrell, Benedict Paten, Benton A. Vizzier, Jr., Charles Overbeck, Charles Reid, David Charles Steinberg, Elizabeth A. Sheets, Julian Lucas, Kevin Osborn, Lon Blauvelt, Louise Cabansay, Noah Warren, Brian Hannafious, Tim Harris, Robert L. Grossman, Radhika Reddy, Eric Torstenson, Kristin Wuichet, Robert J Carroll, M. Katie Banasiewicz, Ting Wang, Haley J. Abel, Jason Walker, and Ira M. Hall. CONSORTIA
ISSN:	2666-979X 2666-979X
DOI:	10.1016/j.xgen.2021.100085