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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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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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Opposition-based shuffled PSO with passive congregation applied to FM matching synthesis

Opposition-based shuffled PSO with passive congregation appl...

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Congress on Evolutionary Computation

作者： Daniel M. Muñoz Carlos H. Llanos Leandro dos S. Coelho Mauricio Ayala-Rincón Department of Mechanical Engineering Automation and Control Group/GRACO University of Brasilia Brasilia Brazil Industrial and Systems Engineering Graduate Program LAS/PPGEPS Pontifical Catholic University of Paraná Curitiba Parana Brazil Department of Computer Science and Mathematics University of Brasilia Brasilia Brazil

Synthesis of musical instruments or human voice is a time consuming process which requires theoretical and experimental knowledge about the synthesis engine. Commonly, performers need to deal with synthesizer interfaces and a process of trial and error for creating musical sounds similar to a target sound. This drawback can be overcome by adjusting automatically the synthesizer parameters using optimization algorithms. In this paper a hybrid particle swarm optimization (PSO) algorithm is proposed to solve the frequency modulation (FM) matching synthesis problem. The proposed algorithm takes advantage of a shuffle process for exchanging information between particles and applies the selective passive congregation and the opposition-based learning approaches to preserve swarm diversity. Both approaches for injecting diversity are based on simple operators, preserving the easy implementation philosophy of the particle swarm optimization. The proposed hybrid particle swarm optimization algorithm was validated for a three-nested FM synthesizer, which represents a 6-dimensional multimodal optimization problem with strong epistasis. Simulation results revealed that the proposed algorithm presented promising results in terms of quality of solutions.

关键词： Frequency modulation Optimization Equations Convergence Particle swarm optimization Genetic algorithms

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Low-frequency 1/f noise in bismuth selenide Topological Insulators

Low-frequency 1/f noise in bismuth selenide Topological Insu...

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International Conference on Noise and Fluctuations (ICNF)

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

ISBN: (纸本)9781457701894

Topological insulators is a newly discovered class of materials with the Dirac cone type dispersion at the surface and conventional band in the volume of the material. We present results of the study of the low-frequency excess noise in thin films made of Bi 2 Se 3 topological insulator material. The films were prepared through mechanically cleavage from the bulk crystal via the “graphene-like” exfoliation procedure. We verified the quality and crystallinity of Bi 2 Se 3 samples with the micro-Raman spectroscopy. Our fabricated devices have linear current voltage characteristics in the low bias region with the current fluctuation noise spectral density SI proportional to 1/f for frequency f less than 10 kHz. The noise spectral density SI showed the square law dependence on the source-drain current and changed from about ~10 -22 to 10 -18 A 2 /Hz as current changes form ~10 -7 to 10 -5 A. Our results can be used for understanding electron transport and trap dynamics, and for reducing low-frequency noise in topological insulator devices.

关键词： Noise Insulators Films Crystals Temperature measurement Resistance

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Comparison of disturbance rejection performance between sliding-mode control and equivalent-input-disturbance approach

Comparison of disturbance rejection performance between slid...

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International Conference on Mechatronics (ICM)

作者： Jinhua She Yaodong Pan Hiroshi Hashimoto Min Wu School of Computer Science Tokyo University of Technology Hachioji Tokyo Japan Control Systems Eng Honeywell Canada Mississauga ONT Canada Master Program of Innovation for Design and Eng Advanced Institute of Industrial Technology Tokyo Japan School of Information Science and Engineering Central South University Changsha China

Sliding mode control (SMC) has been considered as a powerful method for disturbances rejection. On the other hand, we have presented an equivalent-input disturbance (EID) approach to reject disturbances. This paper takes a dual-stage feed drive as an example to compare these two methods. The example shows that, while the EID approach obtains almost the same disturbance rejection performance for matched disturbances as that of the SMC does, it can reject unmatched disturbances. This shows the superiority of the EID approach over SMC method.

关键词： Equations Observers Manganese Frequency control

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A Propositional Dynamic Logic for concurrent programs based on the π-Calculus

A Propositional Dynamic Logic for concurrent programs based ...

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作者： Benevides, Mario R. F. Schechter, L. Menasché Computer Science Department and Systems and Computer Engineering Program Federal University of Rio de Janeiro Brazil Systems and Computer Engineering Program Federal University of Rio de Janeiro Brazil

This work presents a Propositional Dynamic Logic (πDL) in which the programs are described in a language based on the π-Calculus without replication. Our goal is to build a dynamic logic that is suitable for the description and verification of properties of communicating concurrent systems, in a similar way as PDL is used for the sequential case. We build a simple Kripke semantics for this logic, provide a complete axiomatization for it and show that it has the finite model property. © 2010 Elsevier B.V. All rights reserved.

关键词： Semantics

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Visualization of signalized intersections in driving simulator and validity of driving behaviors in virtual environments

Advances in Transportation Studies

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Advances in Transportation Studies 2011年第26期 17-28页

作者： Yan, X. Abdel-Aty, M. Guo, D. Radwan, E. MOE Key Laboratory for Transportation Complex Systems Theory and Technology Beijing Jiaotong University Beijing 100044 China Department of Civil and Environmental Engineering University of Central Florida Orlando FL 32816-2450 United States Computer Science Program College of Business Florida Gulf Coast University 10501 FGCU Boulevard South Fort Myers FL 33965-6565 United States Center for Advanced Transportation Systems Simulation University of Central Florida Orlando FL 32816-2450 United States

Visualization of highway traffic environments in virtual reality plays a key role on fidelity of simulation and validity of driving behaviors in driving simulator studies. This paper describes a procedure to replicate a signalized intersection with many complex features into a driving simulator's 3-D databases through building a graphical visual database, constructing a road motion database, and creating simulated traffic. The validity of the visualization was assessed via the comparison of the drivers' speeds in the simulator and the speed data at the real intersection. It was found that both speed data follow normal distributions and have equal means for each intersection approach;however, that the speeds measured in the driving simulator have a larger variability than those measured in the field. The users' subjective evaluation results indicated that 92% subjects could recognize the simulated intersection in the driving simulator experiment. Therefore, the strategy of geo-specific environment modeling would be useful for studying driving behaviors in virtual environments.

关键词： Visualization

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An estimation procedure to determine the effort required to model business processes

An estimation procedure to determine the effort required to ...

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作者： Cappelli, Claudia Santoro, Flávia Maria Nunes, Vanessa De Barros, Márcio O. Dutra, José Roberto Postgraduate Information Systems Program UNIRIO Av. Pasteur 458 Urca - Rio de Janeiro RJ Brazil COPPE/UFRJ Systems Engineering and Computer Science Program P.O. Box 68511 Rio de Janeiro RJ Brazil

ISBN: (纸本)9789898425065

Business processes modeling projects are increasingly widespread in organizations. Companies have several processes to be identified and modeled. They usually invest much in hiring expert consultants to do such job. However, they still find no guidelines to help them estimate how much a process modeling project will cost or how long this will take. We propose an approach to estimate the effort required to conduct a BPM project and discuss results obtained from over 50 projects in a large Brazilian company.

关键词： Process engineering

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EvolTrack: Improving design evolution awareness in software development

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Journal of the Brazilian computer Society 2010年第2期16卷 117-131页

作者： de Cepêda, Rafael da Silva Viterbo Magdaleno, Andréa Magalhães Murta, Leonardo Gresta Paulino Werner, Cláudia Maria Lima COPPE/UFRJ-Systems Engineering and Computer Science Department Zip 21945-970 P.O. Box 68511 Rio de Janeiro RJ Brazil IC/UFF-Instituto de Computação Universidade Federal Fluminense Niterói RJ Brazil

Software differs from most manufactured products because it is intangible. This characteristic makes it difficult to detect, control, and understand how it evolves. This paper presents an approach based on software visualization that can detect and externalize design evolution made in a software project during its initial development or at any further phase. By using this approach, a developer can be aware of the current state of the software as a whole and can additionally verify if the current design, also called emerging design, is evolving according to the team expectations and leader guidance, preventing problems caused by misunderstandings of the expected software solution. The approach was evaluated with free/open source software (FOSS) projects. The results indicate that the approach behaves as expected when applied to real software development projects, with minor performance bottlenecks. © 2010 The Brazilian computer Society.

关键词： Software design

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Context-based process line

Context-based process line

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作者： Nunes, Vanessa Werner, Claudia Santoro, Flavia Maria COPPE/UFRJ Systems Engineering and Computer Science Program P.O. Box 68511 Rio de Janeiro RJ Brazil NP2Tec and Postgraduate Information Systems Program UNIRIO Av. Pasteur 458 Urca - Rio de Janeiro RJ Brazil

ISBN: (纸本)9789898425065

Complexity and dynamism of day-to-day activities in organizations are inextricably linked, one impacting the other, increasing the challenges for constant adaptation of the way to organize work to address emerging demands. In this scenario, there are a variety of information, insight and reasoning being processed between people and systems, during process execution. We argue that process variations could be decided in real time, using context information collected. This paper presents a proposal for a business process line cycle, with a set of activities encapsulated in the form of components as central artefact. We explain how composition and adaptation of work may occur in real time and discuss a scenario for this proposal.

关键词： Enterprise resource management

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