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Agile parallel bioinformatics workflow management using Pwrake

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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SOI TFET $I_{\rm ON}/I_{\rm OFF}$ Enhancement via Back Biasing

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IEEE Transactions on Electron Devices 2011年第10期58卷 3283-3285页

作者： Alex Guo Peter Matheu Tsu-Jae King Liu University of California Berkeley CA USA Applied Science & Technology Graduate Program University of California Berkeley CA USA Department of Electrical Engineering and Computer Sciences University of California Berkeley CA USA

The effect of back biasing on the performance of a planar tunnel field-effect transistor (TFET) implemented on a silicon-on-insulator substrate is investigated. It is found that reverse back biasing reduces the subthreshold swing SS and increases the range of drain current over which SS is less than ( k B T / q ) ln (10); hence, it is effective for improving the TFET on/off current ratio for low operating voltages (≤ 0.5 V).

关键词： Logic gates Tunneling Doping Transistors Silicon Photonic band gap Junctions

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Automatic intelligence application for office environment

Automatic intelligence application for office environment

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International Conference on Information Networking

作者： Woongsoo Na Gunwoo Lee Sungrae Cho Youngil Choi School of Computer Engineering and Science Chung-Ang University Seoul South Korea Cognitive Service Control Research Team Service Platform Research Department Electronics and Telecommunications Research Institute Daejeon South Korea

ISBN: (纸本)9781612846613

Ambient networks aim to provide a unified networking concept that can adapt to the very heterogeneous environment of different radio technologies and service and network environments. One of the important issues in the ambient network is to aware complex contexts in various environments. This complex context is determined by a surrounding environments or variety of situations. Office is one of the most appropriate environments to apply this ambient network service. In this application, the main product would be central storage controller (CSC), which is able to receive command from employee in the office. The CSC receives information from devices of the network and this information is saved at the CSC. The ambient network can support the CSC to process this command very efficiently. In this paper, we applied ambient network concept to office environment and show our automatic intelligence application.

关键词： Context Ambient networks Printers Mobile computing Wireless communication Security

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Complex context information for video streaming service

Complex context information for video streaming service

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International Conference on Information Networking

作者： Gunwoo Lee Woongsoo Na Sungrae Cho Eungha Kim School of Computer Engineering and Science Chung-Ang University Seoul South Korea Cognitive Service Control Research Team Service Platform Research Department Electronics and Telecommunications Research Institute Daejeon South Korea

ISBN: (纸本)9781612846613

Advances in computer networking combined with powerful home computers and modern operating systems made streaming media practical and affordable for ordinary consumers. We are enjoying different streaming services such as DMB, PMP, smart phone, etc. that have never experienced before. In the future computing environment such as ubiquitous environment, user can be served video streaming service by complex contexts. In the paper, we suggest and simulate the complex context information for multimedia streaming. In this paper, we applied complex context awareness concept to video streaming service and demonstrate our applications.

关键词： Context Streaming media Context modeling Computational modeling Multimedia communication computers Topology

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Characteristics of step-graded InxGa1-xAs and InGaPySb1-y metamorphic buffer layers on GaAs substrates

Characteristics of step-graded InxGa1-xAs and InGaPySb1-y me...

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作者： Kirch, J. Dudley, P. Kim, T. Radavich, K. Ruder, S. Mawst, L.J. Kuech, T.F. Lalumondiere, S.D. Sin, Y. Lotshaw, W.T. Moss, S.C. Department of Electrical and Computer Engineering University of Wisconsin - Madison 1415 Engineering Dr. Madison WI 53706 United States Materials Science Program University of Wisconsin - Madison 1415 Engineering Dr. Madison WI 53706 United States Department of Chemical and Biological Engineering University of Wisconsin - Madison 1415 Engineering Dr. Madison WI 53706 United States Aerospace Corporation Electronics and Photonics Lab El Segundo CA 90245 United States

ISBN: (纸本)9781457717536

Step-graded InGaPySb1-y and InxGa 1-xAs metamorphic buffer layer (MBL) structures are grown on GaAs substrates by metal-organic chemical vapor deposition (MOCVD). AFM analysis indicates that graded group V InGaPySb1-y MBLs exhibit significantly lower surface roughness (∼4.7nm) compared with more conventional graded group III InxGa1-xAs MBLs, which typically have rms surface roughness in the range of 7- 14nm. To reduce the surface roughness of the InxGa1-xAs MBL, a post growth Chemical-Mechanical Polishing (CMP) procedure is implemented. AFM image analysis indicates the CMP process is effective in reducing the step-graded In xGa1-xAs MBL surface roughness from ∼7.3 nm (as-grown) to 2.3 nm post CMP. Preliminary studies indicate that bulk InGaAs layers regrown on top of the MBL subjected to CMP exhibit improved static and transient PL characteristics compared with those deposited on as-grown MBLs. © VDE VERLAG GMBH.

关键词： III-V semiconductors

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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

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

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Low-Frequency Noise in “Graphene-Like” Exfoliated Thin Films of Topological Insulators

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MRS Online Proceedings Library 2011年第1期1344卷 1-5页

作者： M. Z. Hossain S. L. Rumyantsev K. M. F. Shahil D. Teweldebrhan M. Shur A. A. Balandin Nano-Device Laboratory Department of Electrical Engineering and Materials Science and Engineering Program University of California Riverside USA Department of Electrical Computer and Systems Engineering and Center for Integrated Electronics Rensselaer Polytechnic Institute Troy USA Ioffe Institute Russian Academy of Sciences St. Petersburg Russia

We report results of the study of the low-frequency noise in thin films of bismuth selenide topological insulators, which were mechanically exfoliated from bulk crystals via “graphene-like” procedures. From the resistance dependence on the film thickness, it was established that the surface conduction contributions to electron transport were dominant. It was found that the current fluctuations have the noise spectral density SI ∞ 1/ f (where f is the frequency) for the frequency range up to 10 kHz. The obtained noise data are important for transport experiments with topological insulators and for any proposed device applications of these materials.

关键词： devices electrical properties thin film

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When social networking meets the next generation network

When social networking meets the next generation network

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Asia-Pacific Network Operations and Management Symposium (APNOMS)

作者： R. Chen Meng-Hsun Tsai Tony Wrobel Jui-Ming Chen Sih-Han Wang Shu-Shan Ku Jen-Huei Jung Jeu-Yih Jeng IBM Taipei Taiwan Department of Computer Science and Information Engineering National Cheng Kung University Tainan Taiwan IBM USA Networked Communications Program Taipei Taiwan Department of Computer Science National Chiao Tung University Hsinchu Taiwan Telecommunication Laboratories Chunghwa Telecom Company Limited Taipei Taiwan

As mobile technologies evolved, the mobile networks provided users not only high mobility, but also high data rates and flexible services. Meanwhile, Internet services had been very successful from 1970s to date. However, the Internet and the mobile telecommunications evolved separately and were not compatible until 3GPP proposed the IP Multimedia Subsystem (IMS). In this paper, we first introduce mobile Web 2.0 application creation in the next generation IMS network. Then we propose a proof-of-concept service called “JoinMe” on the IBM-NCTU IMS network to study how a social networking service can be created for mobile networks.

关键词： Mobile communication Servers Mobile computing Next generation networking Telecommunications Social network services Internet

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AdaBoost for Text Detection in Natural Scene

AdaBoost for Text Detection in Natural Scene

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International Conference on Document Analysis and Recognition

作者： Jung-Jin Lee Pyoung-Hean Lee Seong-Whan Lee Alan Yuille Christof Koch Department of Brain and Cognitive Engineering Korea University Seoul South Korea Departments of Statistics Psychology Computer Science UCLA Los Angeles CA USA Computation and Neural Systems California Institute of Technology Pasadena CA USA

Detecting text regions in natural scenes is an important part of computer vision. We propose a novel text detection algorithm that extracts six different classes features of text, and uses Modest AdaBoost with multi-scale sequential search. Experiments show that our algorithm can detect text regions with a f= 0.70, from the ICDAR 2003 datasets which include images with text of various fonts, sizes, colors, alphabets and scripts.

关键词： Feature extraction Image edge detection Image color analysis Algorithm design and analysis Histograms Optimization Energy measurement

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K, T and D-like fuzzy Kripke models

K, T and D-like fuzzy Kripke models

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Annual Meeting of The North American Fuzzy Information Processing Society

作者： Bedregal, Benjamin Santiago, Regivan H. N. Benevides, Mario Viana, Petrucio Group of Logic Language Information Theory and Applications - LoLITA Department of Informatics and Applied Mathematics Federal University of Rio Grande Do Norte 59072-970 Natal-RN Brazil Program of Engineering of Systems and Computing - PESC Department of Computer Science Federal University of Rio de Janeiro 21941-972 Rio de Janeiro-RJ Brazil Department of Analysis Fluminense Federal University 24020-140 Niterói-RJ Brazil

ISBN: (纸本)9781612849676

The idea of a Kripke semantics endowed with possibility/plausibility information is not new;in fact there are different approaches for that;see: [6], [13], [16], [19]. This paper follows the approach found in [6], but whereas [6] provides a fixed interpretation for connectives into [0,1] here we provide a characterization of a fuzzy semantics for connectives in such a way that the resulting fuzzy frames: K, T and D, are described precisely by the set of statements which also describes, respectively, the usual modal systems K, T and D. © 2011 IEEE.

关键词： Semantics

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