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Workload characterization for MG-RAST metagenomic data analytics service in the cloud

Wei Tang, Jared Bischof, Narayan Desai, Kanak Mahadik, Wolfgang Gerlach, Travis Harrison, Andreas Wilke, Folker Meyer
2014 2014 IEEE International Conference on Big Data (Big Data)  
In this paper, we characterize the MG-RAST workloads running in the cloud, from the perspectives of computation, I/O, and data transfer.  ...  For example, MG-RAST, a production open-public metagenome annotation service, has experienced increasingly large amount of data submission and has demanded scalable resources for the computational needs  ...  ACKNOWLEDGMENTS This work was supported in part by the NIH award U01HG006537 "OSDF: Support infrastructure for NextGen sequence storage, analysis, and management", and U.S.  ... 
doi:10.1109/bigdata.2014.7004394 dblp:conf/bigdataconf/TangBDMGHWM14 fatcat:4qcliocqhbfyxam2ch26dmst2u

A Case Study in Using Discrete-Event Simulation to Improve the Scalability of MG-RAST

Caitlin Ross, Misbah Mubarak, John Jenkins, Philip Carns, Christopher D. Carothers, Robert Ross, Wei Tang, Wolfgang Gerlach, Folker Meyer
2016 Proceedings of the 2016 annual ACM Conference on SIGSIM Principles of Advanced Discrete Simulation - SIGSIM-PADS '16  
The metagenomics analysis server MG-RAST at Argonne National Laboratory, a computational biology data processing platform, is receiving several terabytes of data submissions per month.  ...  Discrete-event simulation provides a way to evaluate the performance of MG-RAST with increased workloads without disrupting the production system.  ...  Acknowledgments This material was based upon work supported by the U.S.  ... 
doi:10.1145/2901378.2901387 dblp:conf/pads/RossMJCCRTGM16 fatcat:4gyxkpbznbarlgmznr2kg72e6e

Vision Paper: Grand Challenges in Resilience: Autonomous System Resilience through Design and Runtime Measures

Saurabh Bagchi, Vaneet Aggarwal, Somali Chaterji, Fred Douglis, Aly El Gamal, Jiawei Han, Brian Henz, Henry Hoffmann, Suman Jana, Milind Kulkarni, Felix Xiaozhu Lin, Karen Marais (+3 others)
2020 IEEE Open Journal of the Computer Society  
For resilience-by-design, we focus on design methods in software that are needed for our cyber systems to be resilient.  ...  For each of the two themes, we survey the current state, and the desired state and ways to get there.  ...  However, for global-scale, multi-tenant execution pipelines and data repositories, such as the metagenomics repository MG-RAST [26] , [149] , the workloads may be more dynamic and unpredictable, making  ... 
doi:10.1109/ojcs.2020.3006807 fatcat:sngt6fii3rhi7hiovtbjj5ptuy

Grand Challenges in Resilience: Autonomous System Resilience through Design and Runtime Measures [article]

Saurabh Bagchi, Vaneet Aggarwal, Somali Chaterji, Fred Douglis, Aly El Gamal, Jiawei Han, Brian J. Henz, Hank Hoffmann, Suman Jana, Milind Kulkarni, Felix Xiaozhu Lin, Karen Marais (+4 others)
2020 arXiv   pre-print
For resilience-by-design, we focus on design methods in software that are needed for our cyber systems to be resilient.  ...  For each of the two themes, we survey the current state, and the desired state and ways to get there.  ...  However, for global-scale, multi-tenant execution pipelines and data repositories, such as the metagenomics repository MG-RAST [24] , [122] , the workloads may be more dynamic and unpredictable, making  ... 
arXiv:1912.11598v3 fatcat:d4lf2vs4yjbbrnrg7hk65qtbbm

Dagstuhl Reports, Volume 6, Issue 8, August 2016, Complete Issue [article]

2017
Resources include EBI, NCBI's SRA, HMP DACC, CAMI, MetaHIT, iMicrobe, MG-RAST, etc.  ...  recognition (much harder than recognising a single activity), combining historical data with recently collected data for analytics (short-term vs. longterm)).  ...  statistical models for organism identification, or requiring substantial computational resources in order to process the large volumes of data necessary to ensure sufficient coverage.  ... 
doi:10.4230/dagrep.6.8 fatcat:jhbruchpmvdthoe45w75w35wpe

DGHM Lecture 2015

2015 International Journal of Medical Microbiology  
Due to the limited data output the actual used system is not suitable for in-depth-investigation of 16S amplicon sequencing of metagenomes.  ...  For use in remote areas further improvements are needed to unbind the base-calling from "the cloud".  ...  Our data support the need for systematic analyses regarding the development of resistance against echinocandins in Candida spp.  ... 
doi:10.1016/j.ijmm.2015.09.002 fatcat:yuxjcmjr4ffapmmbe54v2jofxy