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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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Towards the conception of scientific workflows for in silico experiments in software engineering 10

Towards the conception of scientific workflows for in silico...

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Proceedings of the 2010 ACM-IEEE International Symposium on Empirical Software engineering and Measurement

作者： Pereira, Wallace M. Travassos, Guilherme H. Federal University of Rio de Janeiro/COPPE Systems Engineering and Computer Science Program Brazil

ISBN: (纸本)9781450300391

The evolution of science has been supported by complex computerized infrastructures with growing interest in simulation based experiments. This trend can also be observed in Software engineering. Our capacity of acquiring evidences to describe phenomena of interest in the field allowed the building of in silico models that can virtually replicate feasible software behaviors and improve our capacity of observation. In silico experiments demand additional concerns for its planning. One of them is regarding the scientific workflow conception. This task is not easy and to apply ad-hoc approaches can risky the experiment execution, validity and future replications. Regarding this topic, this paper presents some initial results from our research towards an approach to support the conception of scientific workflows for in silico experiments in Software engineering are presented. © 2010 ACM.

关键词： computer software

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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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K, T and D-like fuzzy Kripke models

K, T and D-like fuzzy Kripke models

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Conference of the North American Fuzzy Information Processing Society - NAFIPS

作者： Benjamin Bedregal Regivan H. N. Santiago Mario Benevides Petrúcio Viana Group of Logic Language Information Theory and Applications-LoLITA Department of Informatics and Applied Mathematics Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil Program of Engineering of Systems and Computing-PESC Department of Computer Science Federal University of Rio de Janeiro Rio de Janeiro Rio de Janeiro Brazil Department of Analysis Fluminense Federal University (UFF) Niteroi Rio de Janeiro Brazil

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.

关键词： Semantics Fuzzy sets Fuzzy logic Bismuth Electronic mail Uncertainty Reliability

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Using co-evolved RTS opponents to teach spatial tactics

Using co-evolved RTS opponents to teach spatial tactics

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2010 IEEE Conference on Computational Intelligence and Games, CIG2010

作者： Smith, Greg Avery, Phillipa Houmanfar, Ramona Louis, Sushil Behavior Analysis Program Dept. of Psychology United States Evolutionary Computing Systems Laboratory Dept. of Computer Science and Engineering University of Nevada Reno NE United States

ISBN: (纸本)9781424462971

This paper describes a co-evolutionary algorithm for generating simple spatially oriented tactics and considers whether students can learn better by playing against co-evolved opponents or by playing against an expert system or other similar hard-coded opponent. Although a number of artificially intelligent tutoring and e-learning systems exist, our work looks at using co-evolution to generate competent opponents for human students to learn from. This paper describes and discusses early results on using computationally intelligent opponents for tactical training of human students. Initial results indicate that the learning environment for human players, measured by game difficulty and transfer of training, is comparable across co-evolved and hard-coded computer opponents. © 2010 IEEE.

关键词： Students

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