9 results on '"Bonazzi, Vivien R."'
Search Results
2. FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources
- Author
-
Clarke, Daniel JB, Wang, Lily, Jones, Alex, Wojciechowicz, Megan L, Torre, Denis, Jagodnik, Kathleen M, Jenkins, Sherry L, McQuilton, Peter, Flamholz, Zachary, Silverstein, Moshe C, Schilder, Brian M, Robasky, Kimberly, Castillo, Claris, Idaszak, Ray, Ahalt, Stanley C, Williams, Jason, Schurer, Stephan, Cooper, Daniel J, de Miranda Azevedo, Ricardo, Klenk, Juergen A, Haendel, Melissa A, Nedzel, Jared, Avillach, Paul, Shimoyama, Mary E, Harris, Rayna M, Gamble, Meredith, Poten, Rudy, Charbonneau, Amanda L, Larkin, Jennie, Brown, C Titus, Bonazzi, Vivien R, Dumontier, Michel J, Sansone, Susanna-Assunta, and Ma'ayan, Avi
- Subjects
Generic health relevance ,Health Resources ,Humans ,Information Dissemination ,Internet ,Online Systems ,Biochemistry and Cell Biology - Abstract
As more digital resources are produced by the research community, it is becoming increasingly important to harmonize and organize them for synergistic utilization. The findable, accessible, interoperable, and reusable (FAIR) guiding principles have prompted many stakeholders to consider strategies for tackling this challenge. The FAIRshake toolkit was developed to enable the establishment of community-driven FAIR metrics and rubrics paired with manual and automated FAIR assessments. FAIR assessments are visualized as an insignia that can be embedded within digital-resources-hosting websites. Using FAIRshake, a variety of biomedical digital resources were manually and automatically evaluated for their level of FAIRness.
- Published
- 2019
3. From biomedical cloud platforms to microservices: next steps in FAIR data and analysis
- Author
-
Sheffield, Nathan C., Bonazzi, Vivien R., Bourne, Philip E., Burdett, Tony, Clark, Timothy, Grossman, Robert L., Spjuth, Ola, and Yates, Andrew D.
- Published
- 2022
- Full Text
- View/download PDF
4. Additional file 1 of Accelerating genomic workflows using NVIDIA Parabricks
- Author
-
O’Connell, Kyle A., Yosufzai, Zelaikha B., Campbell, Ross A., Lobb, Collin J., Engelken, Haley T., Gorrell, Laura M., Carlson, Thad B., Catana, Josh J., Mikdadi, Dina, Bonazzi, Vivien R., and Klenk, Juergen A.
- Abstract
Additional file 1. Additional results of benchmarking on AWS. Table S1 shows NVIDIA A100 GPU machine benchmarking results, and figures show benchmarking the NVIDIA V100 GPU machine.
- Published
- 2023
- Full Text
- View/download PDF
5. Accelerating genomic workflows using NVIDIA Parabricks
- Author
-
O’Connell, Kyle A., primary, Yosufzai, Zelaikha B., additional, Campbell, Ross A., additional, Lobb, Collin J., additional, Engelken, Haley T., additional, Gorrell, Laura M., additional, Carlson, Thad B., additional, Catana, Josh J., additional, Mikdadi, Dina, additional, Bonazzi, Vivien R., additional, and Klenk, Juergen A., additional
- Published
- 2022
- Full Text
- View/download PDF
6. Accelerating genomic workflows using NVIDIA Parabricks.
- Author
-
O'Connell, Kyle A., Yosufzai, Zelaikha B., Campbell, Ross A., Lobb, Collin J., Engelken, Haley T., Gorrell, Laura M., Carlson, Thad B., Catana, Josh J., Mikdadi, Dina, Bonazzi, Vivien R., and Klenk, Juergen A.
- Subjects
WEB services ,CLOUD computing ,WORKFLOW ,GRAPHICS processing units ,INDIVIDUALIZED medicine ,WORKFLOW management ,COMPUTING platforms ,NUCLEOTIDE sequencing ,CENTRAL processing units - Abstract
Background: As genome sequencing becomes better integrated into scientific research, government policy, and personalized medicine, the primary challenge for researchers is shifting from generating raw data to analyzing these vast datasets. Although much work has been done to reduce compute times using various configurations of traditional CPU computing infrastructures, Graphics Processing Units (GPUs) offer opportunities to accelerate genomic workflows by orders of magnitude. Here we benchmark one GPU-accelerated software suite called NVIDIA Parabricks on Amazon Web Services (AWS), Google Cloud Platform (GCP), and an NVIDIA DGX cluster. We benchmarked six variant calling pipelines, including two germline callers (HaplotypeCaller and DeepVariant) and four somatic callers (Mutect2, Muse, LoFreq, SomaticSniper). Results: We achieved up to 65 × acceleration with germline variant callers, bringing HaplotypeCaller runtimes down from 36 h to 33 min on AWS, 35 min on GCP, and 24 min on the NVIDIA DGX. Somatic callers exhibited more variation between the number of GPUs and computing platforms. On cloud platforms, GPU-accelerated germline callers resulted in cost savings compared with CPU runs, whereas some somatic callers were more expensive than CPU runs because their GPU acceleration was not sufficient to overcome the increased GPU cost. Conclusions: Germline variant callers scaled well with the number of GPUs across platforms, whereas somatic variant callers exhibited more variation in the number of GPUs with the fastest runtimes, suggesting that, at least with the version of Parabricks used here, these workflows are less GPU optimized and require benchmarking on the platform of choice before being deployed at production scales. Our study demonstrates that GPUs can be used to greatly accelerate genomic workflows, thus bringing closer to grasp urgent societal advances in the areas of biosurveillance and personalized medicine. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
7. A framework for human microbiome research
- Author
-
Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Huttenhower, Curtis, Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien R., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Michael W., Jr, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Chris S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., Wilson, Richard K., and White, Owen
- Published
- 2012
- Full Text
- View/download PDF
8. FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources
- Author
-
Clarke, Daniel J. B., primary, Wang, Lily, additional, Jones, Alex, additional, Wojciechowicz, Megan L., additional, Torre, Denis, additional, Jagodnik, Kathleen M., additional, Jenkins, Sherry L., additional, McQuilton, Peter, additional, Flamholz, Zachary, additional, Silverstein, Moshe C., additional, Schilder, Brian M., additional, Robasky, Kimberly, additional, Castillo, Claris, additional, Idaszak, Ray, additional, Ahalt, Stanley C., additional, Williams, Jason, additional, Schurer, Stephan, additional, Cooper, Daniel J., additional, de Miranda Azevedo, Ricardo, additional, Klenk, Juergen A., additional, Haendel, Melissa A., additional, Nedzel, Jared, additional, Avillach, Paul, additional, Shimoyama, Mary E., additional, Harris, Rayna M., additional, Gamble, Meredith, additional, Poten, Rudy, additional, Charbonneau, Amanda L., additional, Larkin, Jennie, additional, Brown, C. Titus, additional, Bonazzi, Vivien R., additional, Dumontier, Michel J., additional, Sansone, Susanna-Assunta, additional, and Ma’ayan, Avi, additional
- Published
- 2019
- Full Text
- View/download PDF
9. Should biomedical research be like Airbnb?
- Author
-
Bonazzi, Vivien R., primary and Bourne, Philip E., additional
- Published
- 2017
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.