21,469 research outputs found

    COEL: A Web-based Chemistry Simulation Framework

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    The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl

    High-Performance Cloud Computing: A View of Scientific Applications

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    Scientific computing often requires the availability of a massive number of computers for performing large scale experiments. Traditionally, these needs have been addressed by using high-performance computing solutions and installed facilities such as clusters and super computers, which are difficult to setup, maintain, and operate. Cloud computing provides scientists with a completely new model of utilizing the computing infrastructure. Compute resources, storage resources, as well as applications, can be dynamically provisioned (and integrated within the existing infrastructure) on a pay per use basis. These resources can be released when they are no more needed. Such services are often offered within the context of a Service Level Agreement (SLA), which ensure the desired Quality of Service (QoS). Aneka, an enterprise Cloud computing solution, harnesses the power of compute resources by relying on private and public Clouds and delivers to users the desired QoS. Its flexible and service based infrastructure supports multiple programming paradigms that make Aneka address a variety of different scenarios: from finance applications to computational science. As examples of scientific computing in the Cloud, we present a preliminary case study on using Aneka for the classification of gene expression data and the execution of fMRI brain imaging workflow.Comment: 13 pages, 9 figures, conference pape

    Integration via Meaning: Using the Semantic Web to deliver Web Services

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    Presented at the CRIS2002 Conference in Kassel.-- 9 pages.-- Contains: Conference paper (PDF) + PPT presentation.The major developments of the World Wide Web (WWW) in the last two years have been Web Services and the Semantic Web. The former allows the construction of distributed systems across the WWW by providing a lightweight middleware architecture. The latter provides an infrastructure for accessing resources on the WWW via their relationships with respect to conceptual descriptions. In this paper, I shall review the progress undertaken in each of these two areas. Further, I shall argue that in order for the aims of both the Semantic Web and the Web Services activities to be successful, then the Web Service architecture needs to be augmented by concepts and tools of the Semantic Web. This infrastructure will allow resource discovery, brokering and access to be enabled in a standardised, integrated and interoperable manner. Finally, I survey the CLRC Information Technology R&D programme to show how it is contributing to the development of this future infrastructure

    Cloudbus Toolkit for Market-Oriented Cloud Computing

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    This keynote paper: (1) presents the 21st century vision of computing and identifies various IT paradigms promising to deliver computing as a utility; (2) defines the architecture for creating market-oriented Clouds and computing atmosphere by leveraging technologies such as virtual machines; (3) provides thoughts on market-based resource management strategies that encompass both customer-driven service management and computational risk management to sustain SLA-oriented resource allocation; (4) presents the work carried out as part of our new Cloud Computing initiative, called Cloudbus: (i) Aneka, a Platform as a Service software system containing SDK (Software Development Kit) for construction of Cloud applications and deployment on private or public Clouds, in addition to supporting market-oriented resource management; (ii) internetworking of Clouds for dynamic creation of federated computing environments for scaling of elastic applications; (iii) creation of 3rd party Cloud brokering services for building content delivery networks and e-Science applications and their deployment on capabilities of IaaS providers such as Amazon along with Grid mashups; (iv) CloudSim supporting modelling and simulation of Clouds for performance studies; (v) Energy Efficient Resource Allocation Mechanisms and Techniques for creation and management of Green Clouds; and (vi) pathways for future research.Comment: 21 pages, 6 figures, 2 tables, Conference pape

    Formal Aspects of Grid Brokering

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    Coordination in distributed environments, like Grids, involves selecting the most appropriate services, resources or compositions to carry out the planned activities. Such functionalities appear at various levels of the infrastructure and in various means forming a blurry domain, where it is hard to see how the participating components are related and what their relevant properties are. In this paper we focus on a subset of these problems: resource brokering in Grid middleware. This paper aims at establishing a semantical model for brokering and related activities by defining brokering agents at three levels of the Grid middleware for resource, host and broker selection. The main contribution of this paper is the definition and decomposition of different brokering components in Grids by providing a formal model using Abstract State Machines

    Leveraging Semantic Web Technologies for Managing Resources in a Multi-Domain Infrastructure-as-a-Service Environment

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    This paper reports on experience with using semantically-enabled network resource models to construct an operational multi-domain networked infrastructure-as-a-service (NIaaS) testbed called ExoGENI, recently funded through NSF's GENI project. A defining property of NIaaS is the deep integration of network provisioning functions alongside the more common storage and computation provisioning functions. Resource provider topologies and user requests can be described using network resource models with common base classes for fundamental cyber-resources (links, nodes, interfaces) specialized via virtualization and adaptations between networking layers to specific technologies. This problem space gives rise to a number of application areas where semantic web technologies become highly useful - common information models and resource class hierarchies simplify resource descriptions from multiple providers, pathfinding and topology embedding algorithms rely on query abstractions as building blocks. The paper describes how the semantic resource description models enable ExoGENI to autonomously instantiate on-demand virtual topologies of virtual machines provisioned from cloud providers and are linked by on-demand virtual connections acquired from multiple autonomous network providers to serve a variety of applications ranging from distributed system experiments to high-performance computing

    A Taxonomy of Workflow Management Systems for Grid Computing

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    With the advent of Grid and application technologies, scientists and engineers are building more and more complex applications to manage and process large data sets, and execute scientific experiments on distributed resources. Such application scenarios require means for composing and executing complex workflows. Therefore, many efforts have been made towards the development of workflow management systems for Grid computing. In this paper, we propose a taxonomy that characterizes and classifies various approaches for building and executing workflows on Grids. We also survey several representative Grid workflow systems developed by various projects world-wide to demonstrate the comprehensiveness of the taxonomy. The taxonomy not only highlights the design and engineering similarities and differences of state-of-the-art in Grid workflow systems, but also identifies the areas that need further research.Comment: 29 pages, 15 figure

    Grid service discovery with rough sets

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    Copyright [2008] IEEE. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Brunel University's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to [email protected]. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.The computational grid is evolving as a service-oriented computing infrastructure that facilitates resource sharing and large-scale problem solving over the Internet. Service discovery becomes an issue of vital importance in utilising grid facilities. This paper presents ROSSE, a Rough sets based search engine for grid service discovery. Building on Rough sets theory, ROSSE is novel in its capability to deal with uncertainty of properties when matching services. In this way, ROSSE can discover the services that are most relevant to a service query from a functional point of view. Since functionally matched services may have distinct non-functional properties related to Quality of Service (QoS), ROSSE introduces a QoS model to further filter matched services with their QoS values to maximise user satisfaction in service discovery. ROSSE is evaluated in terms of its accuracy and efficiency in discovery of computing services
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