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Trends in life science grid: from computing grid to knowledge grid

Akihiko Konagaya
2006 BMC Bioinformatics  
Computing grid technologies have been matured enough to solve high-throughput real-world life scientific problems.  ...  Grid computing has great potential to become a standard cyberinfrastructure for life sciences which often require high-performance computing and large data handling which exceeds the computing capacity  ...  Acknowledgements The authors express special thanks for the member of the Open Bioinformatics Grid project and anonymous reviewers for their valuable discussion and useful comments for this manuscript.  ... 
doi:10.1186/1471-2105-7-s5-s10 pmid:17254294 pmcid:PMC1764466 fatcat:tlemqfzeljfdbaxa6gw5mid7f4

International Workshop on Applications of Workflows in Computational Science (AWCS 08) [chapter]

Adam Belloum, Zhiming Zhao, Marian Bubak
2008 Lecture Notes in Computer Science  
The goal of the Workshop on Applications of Workflows in Computational Sciences (WACS) is to provide a forum for sharing knowledge and experience on developing workflow applications, and to highlight important  ...  This short paper gives an overview on scientific workflow management systems and their application in e-Science, and introduces the topics of the Workshop.  ...  Acknowledgement We would like to express our great appreciation for all PC members, referees and colleagues who have supported AWCS 08.  ... 
doi:10.1007/978-3-540-69389-5_52 fatcat:d57q7xoqknb7leeg4xwkuhjvq4

Distributed Data Mining in the Grid Environment [chapter]

C. B. SelvaLakshmi, S. Murali, P. Chanthiya, P. N. Karthikayan
2013 Advances in Intelligent Systems and Computing  
Grid computing has emerged as an important new branch of distributed computing focused on large-scale resource sharing and high-performance orientation.  ...  In these area grid technologies provides effective computational support for applications such as knowledge discovery.  ...  The Knowledge Grid framework The Knowledge Grid framework is a system implemented to support the development of distributed KDD processes in a Grid [2] .  ... 
doi:10.1007/978-81-322-1299-7_15 fatcat:zzbbsq72zjfurcwyxdrjb66hba

An Open Job Scheduling Service for Large-Scale Data Processing

Zhenghua Xue, Jianhui Li, Yuanchun Zhou, Yang Zhang, Geng Shen
2011 2011 Sixth Open Cirrus Summit  
Scientific Data Grid (SDG) of Chinese Academy of Sciences aims at integrating distributed scientific data, providing transparent data access mechanism and efficient data analysis, processing and visualization  ...  SDGJS has successfully served for some data grid applications.  ...  Based on the scientific data and advanced computing and storage facilities, SDG can provide convenient application services for analysis, processing and visualization of scientific data and forms the framework  ... 
doi:10.1109/ocs.2011.11 fatcat:lm3rfvst6jgsfiqxvluxyyu4aq

Accelerating the scientific exploration process with scientific workflows

Ilkay Altintas, Oscar Barney, Zhengang Cheng, Terence Critchlow, Bertram Ludaescher, Steve Parker, Arie Shoshani, Mladen Vouk
2006 Journal of Physics, Conference Series  
A scientific workflow is the process of combining data and processes into a configurable, structured set of steps that implement semi-automated computational solutions of a scientific problem.  ...  Currently deployed workflows range from local analytical pipelines to distributed, high-performance and high-throughput applications, which can be both data-and compute-intensive.  ...  the Kepler team for their excellent collaboration.  ... 
doi:10.1088/1742-6596/46/1/065 fatcat:z5ltbncglnhvrgt6rscnzhjubq

Ontological framework for a free-form query based grid search engine

Chaitali Gupta, Rajdeep Bhowmik, Madhusudhan Govindaraju
2008 Proceedings of the 17th international symposium on High performance distributed computing - HPDC '08  
Current implementations of XML-based Grid service descriptions require end users to have intimate knowledge of service descriptions, related toolkits, and query languages.  ...  If the model of free-form queries, which has proved successful for HTML based search on the Web, is made available for Grid services, it will serve as a powerful tool for scientists to retrieve information  ...  SPARQL Query Query in the Proposed Framework ARCHITECTURE OF THE SEMANTIC QUERY BASED FRAMEWORK FOR GRID WEB SERVICES The architecture of our Semantic Free-Form Query framework comprises of WSDL Processor  ... 
doi:10.1145/1383422.1383449 dblp:conf/hpdc/GuptaBG08 fatcat:whynidvrgfaztfbimxrpseal6a

A Framework for the Design and Reuse of Grid Workflows [chapter]

Ilkay Altintas, Adam Birnbaum, Kim K. Baldridge, Wibke Sudholt, Mark Miller, Celine Amoreira, Yohann Potier, Bertram Ludaescher
2005 Lecture Notes in Computer Science  
Grid workflows can be seen as special scientific workflows involving high performance and/or high throughput computational tasks.  ...  As high-end computing resources are becoming more of a commodity that is available to new scientific communities, there is an increasing need to also improve the design and reusability "performance" of  ...  Grid Workflows can be seen as special scientific workflows that exhibit features of high-performance computing (HPC) workflows and/or high-throughput computing (HTC) workflows.  ... 
doi:10.1007/11423287_11 fatcat:fgxytu53wbbprgkhnff6mp3ep4

A Pattern Specification and Optimizations Framework for Accelerating Scientific Computations on Heterogeneous Clusters

Linchuan Chen, Xin Huo, Gagan Agrawal
2015 2015 IEEE International Parallel and Distributed Processing Symposium  
In this paper, we focus on the following question: "can simple APIs be developed for several classes of popular scientific applications, to ease application development and yet maintain parallel efficiency  ...  We enable a number of optimizations that are normally implemented by hand by scientific programmers.  ...  More specifically, we focus on the question "can high-level APIs be developed for several classes of popular scientific applications, to ease application development, while achieving high performance on  ... 
doi:10.1109/ipdps.2015.13 dblp:conf/ipps/ChenHA15 fatcat:w6nxwycib5byhhaybm76ntdy44

A Framework for Building Scientific Knowledge Grids Applied to Thermochemical Tables

Gregor von Laszewski, Branko Ruscic, Kaizar Amin, Patrick Wagstrom, Sriram Krishnan, Sandeep Nijsure
2003 The international journal of high performance computing applications  
This application demonstrates a number of interesting and future-oriented uses, such as the need for batch processing, interactive and collaborative steering, use of multiple platforms, visualization through  ...  We have designed a variety of access environments including a shell, a Grid desktop and a portal for accessing the set of services provided, which include the display of network dependencies between the  ...  Open Grid Service Architecture Our framework for knowledge Grids is based on standards under development by the Grid computing community to provide a solid foundation for our current and future work.  ... 
doi:10.1177/10943420030174007 fatcat:h23l2h3fqnar5mxcintj6gp6ve

Optimisation of component-based applications within a grid environment

Nathalie Furmento, Anthony Mayer, Stephen McGough, Steven Newhouse, Tony Field, John Darlington
2001 Proceedings of the 2001 ACM/IEEE conference on Supercomputing (CDROM) - Supercomputing '01  
We match a high-level application specification, defined as a network of components, to an optimal combination of the currently available component implementations within our grid environment.  ...  We demonstrate the effectiveness of this architecture through high-level specification and solution of a set of linear equations by automatic and optimal resource and implementation selection.  ...  Introduction The emergence of computational grids presents a number of challenges for the future of high performance computing.  ... 
doi:10.1145/582034.582064 dblp:conf/sc/FurmentoMMNFD01 fatcat:f663al7xwnbabi4rux6jsiptqa

A note on new trends in data-aware scheduling and resource provisioning in modern HPC systems

Jie Tao, Joanna Kolodziej, Rajiv Ranjan, Prem Prakash Jayaraman, Rajkumar Buyya
2015 Future generations computer systems  
The paper ''ParSA: High-throughput Scientific-data Analysis Framework with Distributed File System'' [8] presents a software framework (ParSA) for high performance analysis on scientific data.  ...  based model of the learning monitoring Grid system for supporting the security awareness of evolutionary driven Grid schedulers.  ... 
doi:10.1016/j.future.2015.04.016 fatcat:z2254f74bjdhtgoxus44ogqkyq

Knowledge Grid: An Intelligent System for Collaboration and Knowledge Management in Nigerian Universities

Boluwaji A. Akinnuwesi, Adedoyin Odumabo, Benjamin S. Aribisala
2020 Data Science Journal  
Also we did a systematic review and analysis of knowledge grid (KG) technology vis-à-vis its use for knowledge management in Nigerian universities.  ...  We focused on identifying the strengths and challenges of knowledge grid development and implementation vis-à-vis the technological, economic and social implications involved in the process.  ...  KG is built on the use of high-bandwidth communication networks and high-performance parallel computers for the purpose of mining data.  ... 
doi:10.5334/dsj-2020-002 fatcat:ifjrz4oypvfs5ns3adtlk65tsi

The Observational-Inductive Framework for Science

Timothy E. Eastman
2006 AIP Conference Proceedings  
A new observational-inductive framework for science is emerging due to recent developments in sensors, data systems, computers and knowledge discovery techniques.  ...  The hypotheticaldeductive/inductive schemas were developed before the massive growth (by orders of magnitude) in the volume of observational data and power of high performance computing.  ...  Brown of the Library of Congress for invaluable discussions, and Dr. Farzad Mahootian for critical insights and references in philosophy of science.  ... 
doi:10.1063/1.2189133 fatcat:z63y66cdsbcullhmbmof2dg6pe

Semantic-Based Workflow Composition for Video Processing in the Grid

Gayathri Nadarajan, Yun-heh Chen-Burger
2006 2006 IEEE/WIC/ACM International Conference on Web Intelligence (WI 2006 Main Conference Proceedings)(WI'06)  
The requirements for such a system are presented, whereby we aim for a solution that best satisfies these requirements and that overcomes the limitations of existing Grid workflow composition systems.  ...  We outline the problem of automatic video processing for the EcoGrid [1]. This poses many challenges as there is a vast amount of raw data that need to be analysed effectively and efficiently.  ...  Active and notable efforts in the development of Grid workflow systems could benefit from the semantic-and performance-based emphases that our framework proposes.  ... 
doi:10.1109/wi.2006.156 fatcat:lixclthvxzawhh6fnw6fqepxqq

Using GPU's to accelerate stencil-based computation kernels for the development of large scale scientific applications on heterogeneous systems

Jian Tao, Marek Blazewicz, Steven R. Brandt
2012 Proceedings of the 17th ACM SIGPLAN symposium on Principles and Practice of Parallel Programming - PPoPP '12  
We present CaCUDA -a GPGPU kernel abstraction and a parallel programming framework for developing highly efficient large scale scientific applications using stencil computations on hybrid CPU/GPU architectures  ...  CaCUDA was tested and benchmarked using a 3D CFD code based on a finite difference discretization of Navier-Stokes equations.  ...  This work was performed using the computational resources of LSU/LONI and was supported by the Center for Computation and Technology at LSU. This work was also supported by  ... 
doi:10.1145/2145816.2145857 dblp:conf/ppopp/TaoBB12 fatcat:btvpqjgi6rakpef2yv5l2rx27y
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