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Two Challenges in Genomics That Can Benefit from Petascale Platforms [chapter]

Catherine Putonti, Meizhuo Zhang, Lennart Johnsson, Yuriy Fofanov
Euro-Par 2006: Parallel Processing  
While there are many challenges in genomics that can greatly benefit from the development of more expedient machines, herein we will focus on just two projects which have direct clinical applications.  ...  The rate in which new data is becoming available, however, far exceeds the rate in which one can perform analysis.  ...  While there are many challenges in genomics that can greatly benefit from the development of more expedient machines, herein we will focus on just two projects having direct clinical applications.  ... 
doi:10.1007/978-3-540-72337-0_31 dblp:conf/europar/PutontiZJF06 fatcat:5jnsvtizabhwvpzjix3apocf5y

Reconfigurable Computing Cluster (RCC) Project: Investigating the Feasibility of FPGA-Based Petascale Computing

Ron Sass, William V. Kritikos, Andrew G. Schmidt, Srinivas Beeravolu, Parag Beeraka
2007 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2007)  
These results characterize key subsystems -including the system software, network performance, memory bandwidth, power consumption of nodes in the cluster. Results suggest that the approach is sound.  ...  The Reconfigurable Computing Cluster (RCC) project is a multi-institution, multi-disciplinary project investigating the use of FPGAs to build cost-effective petascale computers.  ...  This paper has argued that petascale computer designer will face challenges that are quite different from those of the last 15 years and put forth the hypothesis that FPGA-based clusters offer a competitive  ... 
doi:10.1109/fccm.2007.62 dblp:conf/fccm/SassKSBB07 fatcat:umj4bfkikzhinj6cnydv232q3m

Identification Of Applications Associated With Socio-Economic Challenges

Maciej Szpindler
2013 Zenodo  
This White Paper reports on the identification of major socio-economic challenges and associated key community application codes as a part of application support within PRACE Third Implementation Phase  ...  Acknowledgements This work was financially supported by the PRACE-3IP project funded in part by the EUs 7th  ...  Focus of the project coordinated by University of Oslo from Norway is to design scalable workflow that will scale from 1 genome to 1000 genomes and be applicable to computing genomic variety based on short  ... 
doi:10.5281/zenodo.810598 fatcat:dtlovvsjlzfztgmj4x2vyiuniq

Named Data Networking for Genomics Data Management and Integrated Workflows

Cameron Ogle, David Reddick, Coleman McKnight, Tyler Biggs, Rini Pauly, Stephen P. Ficklin, F. Alex Feltus, Susmit Shannigrahi
2021 Frontiers in Big Data  
The reader should note that the goal of this paper is to introduce NDN to the genomics community and discuss NDN's properties that can benefit the genomics community.  ...  Our contributions in this work are as follows 1) we enumerate the cyberinfrastructure challenges of the genomics community that NDN can alleviate, and 2) we describe our efforts in applying NDN for a contemporary  ...  Reference genomes are used by many researchers across the world that can benefit from efficient data delivery mechanisms.  ... 
doi:10.3389/fdata.2021.582468 pmid:33748749 pmcid:PMC7968724 fatcat:4uojbvni65grjnc2nccy2kdqua

The International Exascale Software Project: a Call To Cooperative Action By the Global High-Performance Community

Jack Dongarra, Pete Beckman, Patrick Aerts, Frank Cappello, Thomas Lippert, Satoshi Matsuoka, Paul Messina, Terry Moore, Rick Stevens, Anne Trefethen, Mateo Valero
2009 The international journal of high performance computing applications  
We believe the community must work together to prepare for the challenges of exascale computing, ultimately combing their efforts in a coordinated International Exascale Software Project.  ...  of technologies necessary to make them work together smoothly and efficiently, both within individual petascale systems and between different systems.  ...  In order to be able to move from one platform to another it would be beneficial to have underlying libraries that "do the right thing" for any given platform.  ... 
doi:10.1177/1094342009347714 fatcat:4pjbmkhzfrhhtnvk53esiuriyq

Report from the 3rd Workshop on Extremely Large Databases

Jacek Becla, Kian-Tat Lim, Daniel Liwei Wang
2010 Data Science Journal  
Frequent checkpointing of MR limits performance but is critical for handling failures that can wreak havoc with RDBMSes' optimistic assumptions.  ...  The science benchmark that emerged from the 2 nd workshop in this series was also debated. This paper is the final report of the discussions and activities at this workshop.  ...  However, two notable exceptions exist: (a) microscopic and other forms of imaging and (b) protein and genomic sequencing. Both are now approaching the petascale.  ... 
doi:10.2481/dsj.xldb09 fatcat:574dpairjbb6zh2l5qywipgm4m

Many-Task Computing and Blue Waters [article]

Daniel S. Katz, Timothy G. Armstrong, Zhao Zhang, Michael Wilde, Justin M. Wozniak
2012 arXiv   pre-print
Hence, additional software support is likely to be required to gain full benefit from the HPC hardware.  ...  However, MTC applications have significant features that distinguish them from typical HTC applications.  ...  Acknowledgments This research is part of the Blue Waters sustained-petascale computing project, which is supported by the National Science Foundation (award number OCI 0725070) and the state of Illinois  ... 
arXiv:1202.3943v1 fatcat:c4ou6svp25bzdgcnjc23nqgwiu

PoPLAR: Portal for Petascale Lifescience Applications and Research

Bhanu Rekapalli, Paul Giblock, Christopher Reardon
2013 BMC Bioinformatics  
This paper will discuss the various developmental stages, challenges, and solutions involved in taking bioinformatics applications from the desktop to petascale with a front-end portal for very-large-scale  ...  We are focusing specifically on fast data analysis and retrieval in bioinformatics that will have a direct impact on the quality of human health and the environment.  ...  This article has been published as part of BMC Bioinformatics Volume 14 Supplement 9, 2013: Selected articles from the 8th International Symposium on Bioinformatics Research and Applications (ISBRA '12  ... 
doi:10.1186/1471-2105-14-s9-s3 pmid:23902523 pmcid:PMC3698029 fatcat:etmnw65kqrenvjetb4ox6n64uq

The International Exascale Software Project roadmap

Jack Dongarra, Pete Beckman, Terry Moore, Patrick Aerts, Giovanni Aloisio, Jean-Claude Andre, David Barkai, Jean-Yves Berthou, Taisuke Boku, Bertrand Braunschweig, Franck Cappello, Barbara Chapman (+53 others)
2011 The international journal of high performance computing applications  
architectures will produce tremendous challenges in the area of education and training.  ...  This version of the roadmap begins that process by including more extensive input from the science application community, international funding agencies, and vendor partners.  ...  application domain, i.e., where we expect the major challenges will be for that domain.  ... 
doi:10.1177/1094342010391989 fatcat:twdszcjfxraijpsdcdacvpp6vm

Software challenges in extreme scale systems

Vivek Sarkar, William Harrod, Allan E Snavely
2009 Journal of Physics, Conference Series  
This has included the world's first true multi-core chip, EXECUBE, that in the early 1990s integrated 4 Mbits of DRAM with over 100K gates of logic to support a complete 8 way binary hypercube parallel  ...  them, and scaling multiple chips to complete systems, for a range of real system applications, from highly scalable deep space exploration to trans-petaflops level supercomputing.  ...  platforms, H, can be simulated by analytical models such as the strawmen Exascale systems introduced in [62] or by extrapolating from current Petascale systems.  ... 
doi:10.1088/1742-6596/180/1/012045 fatcat:iukutry2dvbitfdh6ng7kgz564

Establishing Genome Sequencing Centers, the Thematic Units in the Developing Nations and the Potential Medical, Public Health and Economic Implications

E. William Ebomoyi
2011 Journal of Drug Metabolism & Toxicology  
The knowledge gleaned from interaction with the eclectic post-doctoral scientists investigating each facet of the thematic genomics has prepared us for some of the challenges to be addressed by the international  ...  Jean Creswell who played a major role in ensuring our access to the University Of Illinois, Illinois Institute of Genomic Biology (GB) at Urbana, Illinois. The arrangement made by Ms Jennifer M.  ...  From List 1, there are two centers located in Germany.  ... 
doi:10.4172/2157-7609.1000108 fatcat:7vgpnfggo5a53f7btujojudpqq

Autophagy in Toxicology: Defense against Xenobiotics

Wen Xing Ding
2012 Journal of Drug Metabolism & Toxicology  
The knowledge gleaned from interaction with the eclectic post-doctoral scientists investigating each facet of the thematic genomics has prepared us for some of the challenges to be addressed by the international  ...  Jean Creswell who played a major role in ensuring our access to the University Of Illinois, Illinois Institute of Genomic Biology (GB) at Urbana, Illinois. The arrangement made by Ms Jennifer M.  ...  From List 1, there are two centers located in Germany.  ... 
doi:10.4172/2157-7609.1000e108 fatcat:tz2tu2hp7nhlrhtgcisxb7jevi

Massively parallel genomic sequence search on the Blue Gene/P architecture

Heshan Lin, Pavan Balaji, Ruth Poole, Carlos Sosa, Xiaosong Ma, Wu-chun Feng
2008 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis  
This paper presents our first experiences in mapping and optimizing genomic sequence search onto the massively parallel IBM Blue Gene/P (BG/P) platform.  ...  genes in genomes -in only a few hours on BG/P.  ...  Department of Energy, under Contract DE-AC02-06CH11357; a DOE Early Career PI Award DE-FG02-05ER25685 also from the Office of Advanced Scientific Computing Research; NSF Awards CCF-0621470 and CPA-0702182  ... 
doi:10.1109/sc.2008.5222005 dblp:conf/sc/LinBPSMF08 fatcat:pwjowi5w6ba5vnnbupejeejm4a

Report from the 6th Workshop on Extremely Large Databases

Daniel Liwei Wang, Jacek Becla, Kian-Tat Lim
2013 Data Science Journal  
Petascale data management and analysis remain one of the main unresolved challenges in today's computing.  ...  retrieved from producers) not databases.  ...  While a sequence for a single genome can be described in "only" about 30 GB, sequencing the genomes of 100 million people quickly adds up to 3 exabytes.  ... 
doi:10.2481/dsj.12_023 fatcat:xck6tpf35ncclcca53i3q2qnga

Exascale applications: skin in the game

Francis Alexander, Ann Almgren, John Bell, Amitava Bhattacharjee, Jacqueline Chen, Phil Colella, David Daniel, Jack DeSlippe, Lori Diachin, Erik Draeger, Anshu Dubey, Thom Dunning (+39 others)
2020 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
These solutions will yield high-confidence insights and answers to the most critical problems and challenges for the USA in scientific discovery, national security, energy assurance, economic competitiveness  ...  As noted in Wikipedia, skin in the game refers to having 'incurred risk by being involved in achieving a goal', where 'skin is a synecdoche for the person involved, and game is the metaphor for actions  ...  Without their engagement and commitment, the ECP would not succeed in achieving its aggressive goals and realizing its overall vision.  ... 
doi:10.1098/rsta.2019.0056 pmid:31955678 fatcat:6gijc65k2fa5lirhdkiudbie5q
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