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25th IEEE International Parallel and Distributed Processing Symposium, Workshops and Phd Forum, IPDPSW 2011

作者： Da Cruz, Eduardo Henrique Molina Alves, Marco Antonio Zanata Carissimi, Alexandre Navaux, Philippe Olivier Alexandre Ribeiro, Christiane Pousa Méhaut, Jean-François PPGC Graduate Program in Computer Science Institute of Informatics UFRGS Federal University of Rio Grande do Sul Porto Alegre RS Brazil INRIA Mescal Research Team LIG Laboratory Grenoble University France

ISBN: (纸本)9780769543857

In parallel programs, the tasks of a given application must cooperate in order to accomplish the required computation. However, the communication time between the tasks may be different depending on which core they are executing and how the memory hierarchy and interconnection are used. The problem is even more important in multi-core machines with NUMA characteristics, since the remote access imposes high overhead, making them more sensitive to thread and data mapping. In this context, process mapping is a technique that provides performance gains by improving the use of resources such as interconnections, main memory and cache memory. The problem of detecting the best mapping is considered NP-Hard. Furthermore, in shared memory environments, there is an additional difficulty of finding the communication pattern, which is implicit and occurs through memory accesses. This work aims to provide a method for static mapping for NUMA architectures which does not require any prior knowledge of the application. Different metrics were adopted and an heuristic method based on the Edmonds matching algorithm was used to obtain the mapping. In order to evaluate our proposal, we use the NAS Parallel Benchmarks (NPB) and two modern multi-core NUMA machines. Results show performance gains of up to 75% compared to the native scheduler and memory allocator of the operating system. © 2011 IEEE.

关键词： Cache memory

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Improving node localization in WSN by using obstruction level indicator

Improving node localization in WSN by using obstruction leve...

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IEEE International Conference on Systems, Man and Cybernetics

作者： Salvador Jauregui-Ortiz Mario Siller Felix Ramos Edson Escalabrin Electrical Engineering and Computer Science Department Center of Research and Advanced Studies Guadalajara Jalisco Mexico Graduate Program in Computer Science Pontifical Catholic University of Parana Brazil Curitiba Parana Brazil

Wireless sensor networks can be used in habitat monitoring for detecting fire, in disaster for helping rescue teams and in agriculture for sensing humidity. Node localization is essential for some important sensor network applications. Despite the high relative accuracy of some localization algorithms, node localization is still an opened research area, due to the physical phenomena such as attenuation, reflection, diffraction, scattering and so forth. The current developed algorithms have different accuracy when are tested under dissimilar environments. We propose to use Smart Beacon Nodes (SBNs) to infer the Obstruction Level Indicator over an occupied area, then, use this indicator for estimating the distance among nodes. In our experimental simulation, SBNs decrease the node localization error of Triangular Centroid Localization and Weighted Centroid Localization up to 18%.

关键词： Accuracy Wireless sensor networks Estimation Testing Attenuation Databases Radar

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Simultaneous identification for synergistic transcription factors and their transcription factor binding sites

Simultaneous identification for synergistic transcription fa...

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5th International Conference on Complex, Intelligent and Software Intensive Systems, CISIS 2011

作者： Tsai, Zing Tsung-Yeh Huang, Grace Tzu-Wei Tsai, Huai-Kuang Institute of Information Science Academia Sinica Taipei 115 Taiwan Bioinformatics Program Taiwan International Graduate Program Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Joint CMU-Pitt PhD Program in Computational Biology University of Pittsburgh Carnegie Mellon University Pittsburgh PA United States Research Center for Information Technology Innovation Taipei 115 Taiwan Computer Science and Engineering National Taiwan Ocean University Keelung 202 Taiwan

ISBN: (纸本)9780769543734

Identifying transcription factor binding sites (TFBSs) is crucial for understanding the mechanism of transcriptional regulation. It is known that transcription factors (TFs) often cooperate to regulate genes. While traditional approaches can be used to discover binding motifs of a group of co-regulated genes, they often fail to accurately assign motifs to the corresponding TFs. Here, we consider two TFs together to infer their TFBSs and their synergistic relationship simultaneously. The basic idea is that if two TFs interact, their TFBSs, if distinct, would be conserved across species and coincided in the promoter regions of the genes they co-regulated. Applying our method to Saccharomyces cerevisiae chromatin immunoprecipitation data, we predicted 110 TF pairs with statistically significant motif assignments. A majority of these TF pairs have literature support to be synergistic, and the designated motifs to TFs match well with their known consensus. We further examined the synergism of predicted TF pairs in seven experimental conditions using ANOVA, and identified significant interactions. © 2011 IEEE.

关键词： Yeast

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MLEA： A Solution for Users of Android in UTPVirtual

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computer Technology and Application 2011年第5期2卷 406-412页

作者： Gisela Torres de Clunie Sergio Crespo Coelho da Silva Pinto Aris Linet Castillo Lucas Monteiro Braz Tasia Serrao Norman Rangel Jeanette Riley Olinda de Barraza Kexy Rodriguez Computer Systems Engineering Department Technological University of Panama Panama 0819 Panama Computer Science Research and Graduate Program in Applied Computing University of the Sinos Valley （UNISINOS） RS 93022-000 Brazil CIDITIC Technological University of Panama Panama 0819 Panama

This paper describes a design of an educational platform for a mobile learning architecture, which is a state of the an topic in distance education. The product will allow users to interact in an efficient, flexible, and transparent fashion with a web-based education environment, in this case Module Object-Oriented Dynamic Learning Environment （Moodle）, using Android mobile devices. In order to provide a strong and lasting architecture, the Service Oriented Architecture （SOA） methodology is used given that it allows easy software re-utilization as well as integration of heterogeneous services. The architecture is based on web services implemented with Representational State Transfer （REST）, as it has been demonstrated to be lighter and less consuming than other protocols, for devices with limited resources such as mobile devices. Web services provide the communication means between the server side and the client side of the architecture, whereas agents are used to deliver the services itself. The authors propose the development of an environment that facilitates the integration of various educational resources to support m-learning. An important aspect of the proposal is the offering of a tool to provide customized alerts for students and teachers, enabling them to remain updated about activities taking place in the courses.

关键词： Distance learning virtual education m-learning service oriented architecture （SOA） mobile learning mobile computing interoperability representational state transfer （REST）.

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Agile parallel bioinformatics workflow management using Pwrake

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BMC research Notes 2011年第1期4卷 1-8页

作者： Mishima, Hiroyuki Sasaki, Kensaku Tanaka, Masahiro Tatebe, Osamu Yoshiura, Koh-Ichiro Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences Nagasaki Nagasaki 1-12-4 Sakamoto Japan Nagasaki University Global Center of Excellence Program Nagasaki Nagasaki 1-12-4 Sakamoto Japan Center for Computational Sciences University of Tsukuba Tsukuba Ibaraki 1-1-1 Tennodai Japan Core Research for Evolutional Science and Technology Japan Science and Technology Agency Kawaguchi Saitama 4-1-8 Honcho Japan Departmentent of Computer Science Graduate School of Systems and Information Engineering University of Tsukuba Tsukuba Ibaraki 1-1-1 Tennodai Japan

Background: In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions: Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability

关键词： Ruby Iterative Development Agile Software Development Host Language Bioinformatics Domain

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Optimization of defect hole placement in resonant cavities

Optimization of defect hole placement in resonant cavities

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作者： Kang, Christopher Weiss, Sharon M. Vlasov, Yurii A. Assefa, Solomon Interdisciplinary Graduate Program in Materials Science Vanderbilt University Nashville TN 37235 United States Department of Physics and Astronomy Vanderbilt University Nashville TN 37235 United States Department of Electrical Engineering and Computer Science Vanderbilt University 37235 United States IBM T.J. Watson Research Center Yorktown Heights NY 10536 United States

We demonstrate the resonance wavelength and quality factor dependence of 50nm defect-hole placement within photonic crystal L3 microcavities. Proper placement of defect-holes leads to a 12% increase in photonic crysta... 详细信息

ISBN: (纸本)9781557529107

关键词： Photonic crystals

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Optimization of defect hole placement in resonant cavities

Optimization of defect hole placement in resonant cavities

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Conference on Lasers and Electro-Optics (CLEO)

作者： Christopher Kang Sharon M. Weiss Yurii A. Vlasov Solomon Assefa Interdisciplinary Graduate Program in Materials Science Vanderbilt University Nashville TN USA Department of Electrical Engineering and Computer Science Vanderbilt University USA IBM T.J Watson Research Center Yorktown Heights NY USA

ISBN: (纸本)9781557529107

关键词： Cavity resonators Lattices Photonic crystals Optical waveguides Sensitivity Slabs Q factor

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A roadmap to the Collaboration Maturity Model (CollabMM) evolution

A roadmap to the Collaboration Maturity Model (CollabMM) evo...

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International Conference on computer Supported Cooperative Work in Design

作者： Andréa Magalhães Magdaleno Renata Mendes de Araujo Cláudia Maria Lima Werner System Engineering and Computer Science Program-COPPE NP2Tec-Research and Practice Group in Information Technology UFRJ Rio de Janeiro Rio de Janeiro Brazil System Engineering and Computer Group in Information Technology Rio de Janeiro RJ Brazil PPGI - Graduate Program in Informatics - UNIRIO NP2Tec - Research and Practice Group in Information Technology Rio de Janeiro RJ Brazil System Engineering and Computer Science Program-COPPE UFRJ Rio de Janeiro Rio de Janeiro Brazil System Engineering and Computer Science Program - COPPEIUFRJ Rio de Janeiro RJ Brazil

Organizations have been relying on collaboration for productivity improvement and knowledge sharing. The first step to foster collaboration in organizations is to make it explicit. With this aim, the Collaboration Maturity Model (CollabMM) was proposed and evaluated. The lessons learned during model applications in previous work pointed out the need to review both the model and its evaluation instruments. A literature review also showed some improvement opportunities. Therefore, the objective of this work is to develop a roadmap to highlight the main opportunities of evolution in CollabMM. These opportunities will compose our research agenda in this topic and guide future work.

关键词： Collaboration Organizations Instruments Coordinate measuring machines Capability maturity model Knowledge management

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Using Memory Access Traces to Map Threads and Data on Hierarchical Multi-core Platforms

Using Memory Access Traces to Map Threads and Data on Hierar...

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IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW)

作者： Eduardo Henrique Molina da Cruz Marco Antonio Zanata Alves Alexandre Carissimi Philippe Olivier Alexandre Navaux Christiane Pousa Ribeiro Jean-Francois Mehaut PPGC Graduate Program in Computer Science Institute of Informatics Federal University of Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil INRIA Mescal Research Team LIG Laboratory Grenoble University France

关键词： Instruction sets Memory management Linux Benchmark testing Measurement Multicore processing

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Complex-valued functional link network design by orthogonal least squares method for function approximation problems

Complex-valued functional link network design by orthogonal ...

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International Joint Conference on Neural Networks (IJCNN)

作者： Md. Faijul Amin Ramasamy Savitha Muhammad Ilias Amin Kazuyuki Murase Department of Systems Design Engineering Graduate School of Engineering University of Fukui Fukui Japan School of Electrical and Electronics Engineering Nanyang Technological University Singapore Department of Computer Science and Engineering United International University Dhaka Bangladesh Research and Education Program for Life Science University of Fukui Fukui Japan

This paper presents a fully complex-valued functional link network (CFLN). The CFLN is a single-layered neural network, which introduces nonlinearity in the input layer using nonlinear functions of the original input variables. In this study, we consider multivariate polynomials as the nonlinear functions. Unlike multilayer neural networks, the CFLN is free from local minima problem, and it offers very fast learning in parameters because of its linear structure. In the complex domain, polynomial based CFLN has an additional advantage of not requiring activation functions, which is a major concern in the complex-valued neural networks. However, it is important to select a smaller subset of polynomial terms (monomials) for faster and better performance, since the number of all possible monomials may be quite large. In this paper, we use the orthogonal least squares method in a constructive fashion (starting from lower degree to higher) for the selection of a parsimonious subset of monomials. Simulation results demonstrate that computing CFLN in purely complex domain is advantageous than in double-dimensional real domain, in terms of number of connection parameters, faster design, and possibly generalization performance. Moreover, our proposed CFLN compares favorably with several other multilayer networks in the complex domain.

关键词： Polynomials Nonhomogeneous media Educational institutions Algorithm design and analysis Function approximation Neural networks Input variables

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