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共 506 条记录，以下是131-140 订阅

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Kmerind: A Flexible parallel Library for K-mer Indexing of Biological Sequences on distributed Memory Systems 16

Kmerind: A Flexible Parallel Library for K-mer Indexing of B...

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7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)

作者： Pan, Tony Flick, Patrick Jain, Chirag Liu, Yongchao Aluru, Srinivas Georgia Inst Technol Sch Computat Sci & Engn Atlanta GA 30332 USA

ISBN: (纸本)9781450342254

Counting and indexing fixed length substrings, or k-mers, in biological sequences is a key step in many bioinformatics tasks including genome alignment and mapping, genome assembly, and error correction. While advances in next generation sequencing technologies have dramatically reduced the cost and improved latency and throughput, there exist few bioinformatics tools and libraries that can efficiently process the data sets at the current generation rate of 1.8 terabases every 3 days. We present Kmerind, a high performance k-mer indexing library for distributed memory environments. The Kmerind library provides a set of simple and consistent APIs with sequential semantics and parallel implementations that are designed to be flexible and extensible. Using Kmerind, a user can easily instantiate application-specific indices, such as k-mer counter and position index, from biult-in or user-supplied components without extensive high performance computing expertise. Kmerind's k-mer counter performs similarly or better than existing, best-inclass k-mer counting tools even on shared memory systems. In a distributed memory environment, Kmerind counts k-mers in a 120 GB sequence read data set in less than 13 seconds on 1024 Xeon CPU cores, and fully indexes their positions in approximately 17 seconds. Querying for 1% of the k-mers in these indices can be completed in 0.23 seconds and 28 seconds, respectively. To our knowledge, Kmerind is the first k-mer indexing library for distributed memory environments, and the first fully customizable and extensible library for general k-mer indexing and counting. Kmerind is available from https://***/ParBLiSS/kmerind.

关键词： k-mer counting k-mer index next generation sequencing distributed computing parallel computing MPI SIMD

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Geo Mesa: a distributed architecture for spatio-temporal fusion 5

Geo Mesa: a distributed architecture for spatio-temporal fus...

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Conference on Geospatial Informatics, Fusion, and Motion Video Analytics V

作者： Hughes, James N. Annex, Andrew Eichelberger, Christopher N. Fox, Anthony Hulbert, Andrew Ronquest, Michael Commonwealth Comp Res Inc Charlottesville VA 22901 USA

ISBN: (纸本)9781628415896

Recent advances in distributed databases and computing have transformed the landscape of spatio-temporal machine learning. This paper presents GeoMesa, a distributed spatio-temporal database built on top of Hadoop and column-family databases such as Accumulo and HBase, that includes a suite of tools for indexing, managing and analyzing both vector and raster data. The indexing techniques use space filling curves to map multidimensional data to the single lexicographic list managed by the underlying distributed database. In contrast to traditional non-distributed RDBMS, GeoMesa is capable of scaling horizontally by adding more resources at runtime;the index rebalances across the additional resources. In the raster domain, GeoMesa leverages Accumulo's server-side iterators and aggregators to perform raster interpolation and associative map algebra operations in parallel at query time. The paper concludes with two geo-time data fusion examples: using GeoMesa to aggregate Twitter data by keywords;and georegistration to drape full-motion video (FMV) over terrain.

关键词： distributed computing distributed databases Accumulo NoSQL Geohash Space Filling Curve GeoMesa spatio-temporal fusion

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HERA: A reconfigurable and mixed-mode parallel computing engine on platform FPGAs

HERA: A reconfigurable and mixed-mode parallel computing eng...

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proceedings of the 16th IASTED International Conference on parallel and distributed computing and Systems

作者： Wang, Xiaofang Ziavras, Sotirios G. Department of Electrical Engineering New Jersey Institute of Technology Newark NJ 07102 United States

The high price, long design and development cycles, programming difficulty and high maintenance cost of supercomputers limit their range of potential applications. Recent advances in Field-Programmable Gate Arrays (FPGAs) have made feasible the development of high-performance and programmable parallel systems on a programmable chip (PSOPC). PSOPC's yield high-performance at low cost for many parallel applications. We present in this paper the design and implementation of our HERA (HEterogeneous Reconfigurable Architecture) machine that employs FPGAs to allow the simultaneous execution of a variety of parallel processing modes, including SIMD (Single-Instruction, Multiple-Data), MIMD (Multiple-Instruction, Multiple-Data) and M-SIMD (Multiple-SIMD). The processing element is centered on a single-precision IEEE 754 floating-point unit (FPU) and employs a 7-stage pipeline. To demonstrate the robustness and viability of our approach, we propose a data partitioning scheme and employ mixed-mode scheduling for Cannon's matrix-matrix multiplication algorithm with matrices of arbitrary size and shape. Performance results on our 64-PE machine that employs a dual-FPGA system are better than the optimized performance on a dual-Xeon PC.

关键词： parallel processing systems

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Efficient Simulations of Spiking Neurons on parallel and distributed Platforms: Towards Large-Scale Modeling in Computational Neuroscience

Efficient Simulations of Spiking Neurons on Parallel and Dis...

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IEEE Recent advances in Intelligent Computational Systems (RAICS)

作者： Nair, Manjusha Surya, Shan Kumar, Revathy S. Nair, Bipin Diwakar, Shyam Amrita Univ Amrita Vishwa Vidyapeetham Amrita Sch Engn Dept Comp Sci & Applicat Kollam 690525 Kerala India Amrita Univ Amrita Vishwa Vidyapeetham Amrita Sch Biotechnol Amritapuri CampusClappana PO Kollam 690525 Kerala India

ISBN: (纸本)9781467366700

Human brain communicates information by means of electro-chemical reactions and processes it in a parallel, distributed manner. Computational models of neurons at different levels of details are used in order to make predictions for physiological dysfunctions. advances in the field of brain simulations and brain computer interfaces have increased the complexity of this modeling process. With a focus to build large-scale detailed networks, we used high performance computing techniques to model and simulate the granular layer of the cerebellum. Neuronal firing patterns of cerebellar granule neurons were modeled using two mathematical models Hodgkin- Huxley (HH) and Adaptive Exponential Leaky Integrate and Fire(AdEx). The performance efficiency of these modeled neurons was tested against a detailed multicompartmental model of the granule cell. We compared different schemes suitable for large scale simulations of cerebellar networks. Large networks of neurons were constructed and simulated. Graphic Processing Units (GPU) was employed in the pleasantly parallel implementation while Message Passing Interface (MPI) was used in the distributed computing approach. This allowed to explore constraints of different parallel architectures and to efficiently load balance the tasks by maximally utilizing the available resources. For small scale networks, the observed absolute speedup was 6X in an MPI based approach with 32 processors while GPUs gave 10X performance gain compared to a single CPU implementation. In large networks, GPUs gave approximately 5X performance gain in processing time compared to the MPI implementation. The results enabled us to choose parallelization schemes suitable for large-scale simulations of cerebellar circuits. We are currently extending the network model based on large scale simulations evaluated in this paper and using a hybrid - heterogeneous MPI based multi-GPU architecture for incorporating millions of cerebellar neurons for assessing physiologi

关键词： cerebellum computational neuroscience HH neuron spiking neurons GPU MPI parallel

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Discovering Rare Association Rules Using Probability Apriori in Grid Environments

Discovering Rare Association Rules Using Probability Apriori...

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International Conference on Soft computing for Problem Solving (SocProS 2011)

作者： Rawat, Sandeep Singh Rajamani, Lakshmi Guru Nanak Inst Technol Hyderabad Andhra Pradesh India Osmania Univ Engn Coll Hyderabad Andhra Pradesh India

ISBN: (纸本)9788132204909

It is necessary to combine different technologies for implementing high performance distributed knowledge discovery systems. We think grids can offer an effective support to the implementation and use of parallel data mining systems. In the literature, an effort has been made to extract rare association rules with multiple minimum supports. This paper proposes the development of probability apriori multiple minimum support (PAMMS) algorithm to discover both frequent and rare and association rules in grid environment. Experimental results show that the proposed approach is efficient.

关键词： Rare association rules grid computing high performance

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An Enhanced MapReduce Framework for Solving Protein Folding Problem Using a parallel Genetic Algorithm

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48th Annual Convention of Computer Society of India (CSI)

作者： Narayanan, A. G. Hari Krishnakumar, U. Judy, M. V. Amrita Vishwa Vidyapeetham Amrita Sch Arts & Sci Dept Comp Sci & IT Kochi Kerala India

ISBN: (纸本)9783319031071

parallel Genetic algorithms have proved to be a successful method for solving the protein folding problem. In this paper we propose a simple genetic algorithm with optimum population size, mutation rate and selection strategy which is parallelized with MapReduce architecture for finding the optimal conformation of a protein using the two dimensional square HP model. We have used an enhanced framework for map Reduce which increased the performance of the private clouds in distributed environment. The proposed Genetic Algorithm was tested several bench mark of synthetic sequences. The result shows that GA converges to the optimum state faster than the traditional

关键词： Protein Folding Problem Hadoop MapReduce parallel Genetic Algorithm

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Using the volunteer computing XtremWeb-CH: Lessons and perspectives

Using the volunteer computing XtremWeb-CH: Lessons and persp...

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IASTED International Conference on advances in Computer Science and Engineering, ACSE 2009

作者： Abdennadher, Nabil 4 Rue Prairie 1202 Genève Switzerland

ISBN: (纸本)9780889867901

XtremWeb-CH (XWCH) is a volunteer computing middleware that makes it easy for scientists and industrials to deploy and execute their parallel and distributed applications on a public-resource computing infrastructure. XWCH supports various high performance applications, including those having large storage and communication requirements. Two high performance applications were ported and deployed on an XWCH platform. The first one is the package of programs Phylip that is employed for inferring phylogenies (evolutionary trees). The second application ported on XWCH is a medical program used to generate temporal dynamic neuronal maps. The application, named NeuroWeb, is used to better understand the connectivity and activity of neurons. NeuroWeb is a data and CPU intensive application. This paper describes the different components of an XWCH platform and the lessons learned from gridifying Phylip and NeuroWeb. It also details the new features and extensions, which are being added to XWCH in order to support new types of applications.

关键词： Middleware

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On Automated Testing of Description Logic Reasoners

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5th International Conference on distributed computing and Internet Technologies (ICDCIT)

作者： Babik, Marian Hluchy, Ladislav Department of Parallel and Distributed Computing Institute of Informatics Slovak Academy of Sciences Slovakia

ISBN: (纸本)9783540897361

OWL and RDF/RDFS are ontological languages developed by the World Wide Web Consortium (W3), which have become a de facto standard for the, ontological descriptions in various domains. The evolution of these standards was influenced by the numerous advances in the research of knowledge representation and reasoning. Although support for reasoning and standardized representation is the key benefit, of these technologies, there is a lack of existing test, frameworks, which would be capable of addressing many crucial aspects of the Semantic Web applications. In this paper we propose a methodology for automated testing of OWL reasoners based on the real-world ontologies. This specification covers both terminological and assertional reasoning as well as checking of the correctness of the answers. An open-source implementation of such framework is described and a study of initial result is provided. The tests cover an extensive set of reasoners and ontologies and provide a state-of-the-art insight, into the field of OWL reasoning.

关键词： Ontology

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Performance modeling for entity-level simulations

Performance modeling for entity-level simulations

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International parallel and distributed Processing Symposium, IPDPS 2003

作者： Su, Alan Berman, Fran Casanova, Henri Computer Science and Engineering Department University of California San Diego United States San Diego Supercomputer Center University of California San Diego United States

ISBN: (纸本)0769519261

advances across many fields of study are driving changes in the basic nature of scientific computing applications. Scientists have recognized a growing need to study phenomena by explicitly modeling interactions among individual entities, rather than by simply modeling approximate collective behavior. This entity-level approach has emerged as a promising new direction in a number of scientific fields. One of the challenges inhibiting the entity-level approach is the substantial resource requirements it entails. Unfortunately, such applications exhibit characteristics and behaviors which render traditional parallel computing techniques ineffective. Well-defined methodologies for achieving scalable performance on distributed computing platforms are needed. As an important first step, we present an abstract application model for entity-level applications, and we instantiate it for a case-study immunology application. Our experiments confirm that this model tracks application performance trends sufficiently well to study scheduling issues pertaining to entity-level applications. We identify a scalability problem inherent to the entity-level approach and use our model to quantify the potential performance improvements that remapping strategies may yield. © 2003 IEEE.

关键词： distributed computer systems

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A REVIEW OF LITERATURE IN distributed SUPPLY CHAIN SIMULATION

A REVIEW OF LITERATURE IN DISTRIBUTED SUPPLY CHAIN SIMULATIO...

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Winter Simulation Conference

作者： Mustafee, Navonil Katsaliaki, Korina Taylor, Simon J. E. Univ Exeter Sch Business Ctr Innovat & Serv Res Exeter EX4 4ST Devon England Int Hellen Univ Sch Econ & Business Adm & Legal Studies Thessaloniki 57001 Greece Brunel Univ Dept Comp Sci Modelling & Simulat Grp Uxbridge UB8 3PH Middx England

ISBN: (纸本)9781479974863

M&S is a decision support technique that enables stakeholders to make better and more informed decisions;application of this to supply chains is referred to as supply chain simulation. The increasingly interconnected enterprise of the digital age benefit from cooperative decision making through the utilization of existing technological foundations, standards and tools (e.g., computer networks, data sharing standards, tools for collaborative working). distributed Supply Chain Simulation (DSCS) facilitates such collective decision making by enabling simulation models of individual business processes/organizations to execute cooperatively over a computer network. The aim of this research is to identifying the advances in DSCS and its present state of play. Towards realization of this aim we present a methodological review of literature and complement this with our domain-specific knowledge in supply chains and parallel and distributed simulation.

关键词： decision support systems digital simulation parallel processing production engineering computing supply chain management supply chains DSCS collective decision making computer network distributed simulation distributed supply chain simulation domain-specific knowledge literature review parallel simulation simulation models Adaptation models Bibliographies Computational modeling Data models Educational institutions Supply chains

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