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Cloud Technologies for Bioinformatics Applications

IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS 2011年第6期22卷 998-1011页

作者： Ekanayake, Jaliya Gunarathne, Thilina Qiu, Judy Indiana Univ Sch Informat & Comp Bloomington IN 47408 USA Indiana Univ Pervas Technol Inst Bloomington IN 47408 USA

Executing large number of independent jobs or jobs comprising of large number of tasks that perform minimal intertask communication is a common requirement in many domains. Various technologies ranging from classic job schedulers to the latest cloud technologies such as MapReduce can be used to execute these "many-tasks" in parallel. In this paper, we present our experience in applying two cloud technologies Apache Hadoop and Microsoft DryadLINQ to two bioinformatics applications with the above characteristics. The applications are a pairwise Alu sequence alignment application and an Expressed Sequence Tag (EST) sequence assembly program. First, we compare the performance of these cloud technologies using the above applications and also compare them with traditional MPI implementation in one application. Next, we analyze the effect of inhomogeneous data on the scheduling mechanisms of the cloud technologies. Finally, we present a comparison of performance of the cloud technologies under virtual and nonvirtual hardware platforms.

关键词： Distributed programming parallel systems performance programming paradigms

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The inevitable cycle: Graphical tools and programming paradigms

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COMPUTER 2007年第8期40卷 24-30页

作者： Soukup, Jiri Soukup, Martin Code Farms Nortel

The prevalence of graphical tools suggests that current software design has become too complex to easily manage. Returning to more compact textual programming requires new programming languages and paradigms.

关键词： Graphical Tools programming paradigms Software Design

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Non-procedural Implementation of Local Heuristic Search in Control Network programming

Non-procedural Implementation of Local Heuristic Search in C...

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14th International Conference on Knowledge-Based and Intelligent Information and Engineering Systems

作者： Kratchanov, Kostadin Golemanova, Emilia Golemanov, Tzanko Ercan, Tuncay Yasar Univ Dept Software Engn Univ Cad Yagacli Yol 35-37 TR-35100 Bornova Turkey Rousse Univ Dept Computing Rousse Bulgaria

The report describes the type of improved uninformed or heuristic search algorithms that are well-suited for non-procedural implementation in Control network programming, and how this can be achieved using the tools f... 详细信息

ISBN: (纸本)9783642153891

关键词： Control network programming heuristic algorithms programming paradigms programming languages nonprocedural programming local search automated programming

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Control Network programming with SPIDER: Dynamic Search Control

Control Network Programming with SPIDER: Dynamic Search Cont...

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14th International Conference on Knowledge-Based and Intelligent Information and Engineering Systems

作者： Kratchanov, Kostadin Golemanov, Tzanko Golemanova, Emilia Ercan, Tuncay Yasar Univ Dept Software Engn Univ Cad Yagacli Yol 35-37 TR-35100 Bornova Turkey Rousse Univ Dept Computing Rousse Bulgaria

The report describes the means for dynamic control of the computation process that are available in Spider - a language for Control Network programming.

ISBN: (纸本)9783642153891

The report describes the means for dynamic control of the computation process that are available in Spider - a language for Control Network programming.

关键词： Control network programming programming paradigms programming languages non-procedural programming search control computation control dynamic control heuristic algorithms

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Service Composition Issues in Pervasive Computing

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IEEE PERVASIVE COMPUTING 2010年第1期9卷 62-70页

作者： Bronsted, Jeppe Hansen, Klaus Marius Ingstrup, Mads Aarhus Univ Dept Comp Sci DK-8000 Aarhus C Denmark Univ Iceland IS-101 Reykjavik Iceland

Providing new services by combining existing ones—or service composition—is an idea pervading pervasive computing. Pervasive computing technologies seek to concurrently exhibit context awareness, manage contingencies, leverage device heterogeneity, and empower users. These four goals prompt service-composition-mechanism design requirements that are unique to pervasive computing. This article catalogs service composition mechanisms and describes their variation points, which indicate how well the resulting compositions meet the four goals.

关键词： Personal digital assistants Runtime Servers Web services Context Context-aware services programming paradigms service composition context awareness user composition heterogeneous system contingency management survey design concepts organization and design operating systems reusable software configuration management

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Magic Potion: Incorporating New Development paradigms through Metaprogramming

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IEEE SOFTWARE 2010年第5期27卷 38-44页

作者： Djuric, Dragan Devedzic, Vladan Univ Belgrade Belgrade 11001 Serbia

Today\'s applications require mixing and matching languages, platforms, and paradigms, which increases a solution\'s complexity. The authors propose a lighter approach that borrows a desired paradigm and incorporates it as an integral part of a preferred development environment. They\'ve applied metaprogramming to internalize the ontology-modeling paradigm into a programming environment that\'s based on the Java ecosystem. Their method is also lightweight and suitable for small teams. They implemented an embedded domain-specific metalanguage, called Magic Potion, in the Clojure development environment, where it blends ontology, functional, object-oriented, and concurrent paradigms.

关键词： domain engineering domain-specific languages metaprogramming multiparadigm languages ontology languages programming languages programming paradigms programming techniques Computer programming Languages metaprogram Sorcery programming TECHNIQUES Magic

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Streamlining Development for Networked Embedded Systems Using Multiple paradigms

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IEEE SOFTWARE 2010年第5期27卷 45-52页

作者： Huygens, Christophe Hughes, Danny Lagaisse, Bert Joosen, Wouter Katholieke Univ Leuven Dept Comp Sci Louvain Belgium Xian Jiaotong Liverpool Univ Dept Comp Sci & Software Engn Xian Peoples R China Katholieke Univ Leuven Distrinet Res Grp Louvain Belgium

Limitations on networked embedded systems imposed by mobility and adaptation scenarios amid scarce energy and system resources mandate optimization throughout the hardware-software life cycle. Deployment, operational activities, and maintenance require software development activities that must all be aligned to become integral parts of the development process. Yet the actors participating in the life cycle are highly diverse, and an integrated approach must respect this diversity. In addition to traditional software development according to component-based engineering principles that deliver business and application logic, the activities in networked-embedded systems' life cycle phases include developing the following: predeployment artifacts using aspect-oriented composition, deployment artifacts using declarative abstractions to describe the actors' goals and the applications' compositions, and specific runtime artifacts using declarative or imperative policies. Developing these complementary artifacts corresponds to multiparadigm programming, since all artifacts are essential but can't be programmed using a single paradigm. This article identifies the proposed actors contributing to the development phases in this integrated multiparadigm programming approach and their activities in terms of methods and artifacts.

关键词： computing equipment management embedded systems programming paradigms software system integration and implementation wireless sensor networks computer software Systems Integration streamlined shape Equipment Management Artifacts Software design Embedded systems PROCESS DEVELOPMENT actor

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USING DOMAIN SPECIFIC LANGUAGE FOR MODELING AND SIMULATION: SCALATION AS A CASE STUDY

USING DOMAIN SPECIFIC LANGUAGE FOR MODELING AND SIMULATION: ...

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2010 Winter Simulation Conference

作者： Miller, John A. Han, Jun Hybinette, Maria Univ Georgia Dept Comp Sci Athens GA 30602 USA

ISBN: (纸本)9781424498642

Progress in programming paradigms and languages has over time influenced the way that simulation programs are written. Modern object-oriented, functional programming languages are expressive enough to define embedded Domain Specific Languages (DSLs). The Scala programming language is used to implement ScalaTion that supports several popular simulation modeling paradigms. As a case study, ScalaTion is used to consider how language features of object-oriented, functional programming languages and Scala in particular can be used to write simulation programs that are clear, concise and intuitive to simulation modelers. The dichotomy between "model specification" and "simulation program" is also considered both historically and in light of the potential narrowing of the gap afforded by embedded DSLs.

关键词： DSL ScalaTion simulation domain specific language object-oriented programming programming languages programming languages programming paradigms scala programming language simulation program

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Software Renovation: An In-house Perspective with Case Studies

Software Renovation: An In-house Perspective with Case Studi...

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作者： Brian Horton University of New Orleans

学位级别：硕士

Programs are not only a tool for the simplification or automation of everyday tasks; they also represent a significant time and money investment. A program's life may span years, or even decades, which creates certain risks for the stakeholders involved. To mitigate the risks associated with these legacy systems, software renovation can be undertaken. Software renovation can be described as a series of processes and/or tools used to modernize a legacy system, thereby preserving and maintaining the investment it represents while decreasing the risks associated with it. In this thesis, the focus is on renovation of software created by in-house development. A series of case studies will be examined to demonstrate basic renovation strategies, including the formation of goals for a renovation and exploring trade-offs between robustness, performance, and usability.

关键词： Methodologies Code Design programming paradigms Maintenance

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Empirical investigation towards the effectiveness of Test First programming

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INFORMATION AND SOFTWARE TECHNOLOGY 2009年第1期51卷 182-194页

作者： Huang, Liang Holcombe, Mike Univ Sheffield Dept Comp Sci Sheffield S10 2TN S Yorkshire England

The Test First (TF) programming, which is based on an iterative process of "setting up test cases, implementing the functionality, and having all test cases passed", has been put forward for decades, however knowledge of the evidence of the Test First programming's success is limited. This paper describes a controlled experiment that investigated the distinctions between the effectiveness of Test First and that of Test Last (TL) (the traditional approach). The experimental results showed that Test First teams spent a larger percentage of time on testing. The achievable minimum external quality of delivered software applications increased with the percentage of time spent on testing regardless of the testing strategy (TF or TL) applied, although there does not exist a linear correlation between them. With four years' data, it is also found that a strong linear correlation between the amount of effort spent on testing and coding in Test First teams, while this phenomenon was not observed in Test Last teams. (C) 2008 Elsevier B.V. All rights reserved.

关键词： Agile methods Empirical software engineering Software testing Testing strategies Software engineering process programming paradigms

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