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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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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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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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LINC power amplifiers for reducing out-of-band spectral re-growth: A comparative study

LINC power amplifiers for reducing out-of-band spectral re-g...

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2010 IEEE 11th Annual Wireless and Microwave Technology Conference, WAMICON 2010

作者： Baylis, Charles Moldovan, Matthew Wang, Loria Martin, Josh Wireless and Microwave Circuits and Systems Program Department of Electrical and Computer Engineering Baylor University Waco TX 76798 United States

ISBN: (纸本)9781424466887

The Linear Amplification with Nonlinear Components (LINC) power amplifier structure combiner implementation has an effect on the linearity and efficiency of the design. Understanding and using this tradeoff is helpful to radar and communication designers and can be used to assist in operating with optimum efficiency while meeting spectral mask requirements instituted by regulatory agencies. In this paper, a simulation-based investigation is performed into implementations with a 180-degree coupler and with a Chireix outphasing network. In general, the overall efficiency in both designs is a function of the amplitude modulation of the message signal in the LINC configuration;however, the 180-degree coupler has a potential to obtain higher linearity in many cases due to the isolation of its two input ports. In certain cases of amplitude modulation, however, much of the output power in the 180-degree coupler design is delivered to an unused termination rather than to the network output. ©2010 IEEE.

关键词： Power amplifiers

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Understanding transistor channel temperature in nonlinear microwave measurements and device operation

Understanding transistor channel temperature in nonlinear mi...

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76th ARFTG Microwave Measurement Conference: Millimeter-Wave Measurements and Modeling, ARFTG 2010

作者： Baylis, Charles Jean, Buford Randall Martin, Josh Wang, Loria Moldovan, Matthew Miller, Hunter Wireless and Microwave Circuits and Systems Program Department of Electrical and Computer Engineering Baylor University Waco TX 76798 United States

ISBN: (纸本)9781424474486

With the widespread use of high-voltage GaN devices and other high-power transistors, understanding the heating of a device during large-signal excitation and measurement is critical, both to ensure efficient operation and to prevent destruction of devices during measurement. Device self-heating during RF excitation is directly dependent upon the power-added efficiency of operation. All DC and RF power that is not converted to output RF power is dissipated in the device as heat. When properly applied, the traditional electrothermal model used in circuit simulators adequately calculates this self heating and yields some interesting results. In this paper, it is demonstrated that the load impedance providing maximum power-added efficiency also results in the lowest average dissipated power, and hence the lowest channel temperature, of the device. The variation in average dissipated power (and hence channel temperature) is also examined for different loading conditions;it is shown that some loading conditions produce a dissipated power that is actually higher than the DC power, a situation which often can lead to device failure during load-pull measurements. ©2010 IEEE.

关键词： Efficiency

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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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Towards a threat model for provenance in e-Science

Towards a threat model for provenance in e-Science

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3rd International Provenance and Annotation Workshop, IPAW 2010

作者： Gadelha Jr., Luiz M.R. Mattoso, Marta Wilde, Michael Foster, Ian Computer and Systems Engineering Program Federal University of Rio de Janeiro Brazil Computation Institute University of Chicago Argonne National Laboratory United States

ISBN: (纸本)3642178189

Scientists increasingly rely on workflow management systems to perform large-scale computational scientific experiments. These systems often collect provenance information that is useful in the analysis and reproduction of such experiments. On the other hand, this provenance data may be exposed to security threats which can result, for instance, in compromising the analysis of these experiments, or in illegitimate claims of attribution. In this work, we describe our ongoing work to trace security requirements for provenance systems in the context of e-Science, and propose some security controls to fulfill them. © 2010 Springer-Verlag Berlin Heidelberg.

关键词： e-Science

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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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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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Comparison of optimal solutions to real-time path planning for a mobile vehicle

Comparison of optimal solutions to real-time path planning f...

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作者： Yang, Jian Qu, Zhihua Wang, Jing Conrad, Kevin Delta Tau Data Systems Inc. Los Angeles CA 91311 United States Department of Electrical and Computer Engineering University of Central Florida Orlando FL 32816 United States Computer Engineering Program Bethune-Cookman University Daytona Beach FL 32114 United States Elbit Systems of America FortWorth TX 76179 United States

In this paper, we present two near-optimal methods to determine the real-time collision-free path for a mobile vehicle moving in a dynamically changing environment. The proposed designs are based on the polynomial parameterization of feasible trajectories by explicitly taking into account boundary conditions, kinematic constraints, and collision-avoidance criteria. The problems of finding optimal solutions to the parameterized feasible trajectories are then formulated with respect to a near-minimal control-energy performance index and a near-shortest distance performance index, respectively. The obtained optimal solutions are analytical and suitable for practical applications which may require real-time trajectory planning and replanning. computer simulations are provided to validate the effectiveness of the proposed near-optimal trajectory-planning methods. © 2010 IEEE.

关键词： Trajectories

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