Towards a lightweight generic computational grid framework for biological research

Background: An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations – a characteristic of the emerging field of systems biology. Results: In this paper we present a lightweight generic framework for combining disparate computational resources at multiple sites (ranging from local computers and clusters to established national Grid services). A detailed guide describing how to set up the framework is available from the following URL: http://igrid-ext.cryst.bbk.ac.uk/portal_guide/. Conclusion: This approach is particularly (but not exclusively) appropriate for large-scale biology projects with multiple collaborators working at different national or international sites. The framework is relatively easy to set up, hides the complexity of Grid middleware from the user, and provides access to resources through a single, uniform interface. It has been developed as part of the European ImmunoGrid project

Enabling Social Applications via Decentralized Social Data Management

An unprecedented information wealth produced by online social networks, further augmented by location/collocation data, is currently fragmented across different proprietary services. Combined, it can accurately represent the social world and enable novel socially-aware applications. We present Prometheus, a socially-aware peer-to-peer service that collects social information from multiple sources into a multigraph managed in a decentralized fashion on user-contributed nodes, and exposes it through an interface implementing non-trivial social inferences while complying with user-defined access policies. Simulations and experiments on PlanetLab with emulated application workloads show the system exhibits good end-to-end response time, low communication overhead and resilience to malicious attacks.Comment: 27 pages, single ACM column, 9 figures, accepted in Special Issue of Foundations of Social Computing, ACM Transactions on Internet Technolog

The Litigating States' Proposed Remedy for Microsoft

State officials face well-funded, well-organized coalitions of in-state businesses arguing for the prosecution of an out-of-state company, an unequal political contest. Accordingly, the state attorneys general (AGs) have resisted settlement attempts and have pushed both the Justice Department and the courts for stronger action against Microsoft. In the process, the interests of consumers, the AGs' nominal clients, have been paid little more than lip service. The nine litigating states and the District of Columbia together account for just 27 percent of the U. S. population. But they do represent many of Microsoft's most vocal rivals. California is home to Apple, Palm, Oracle, Sun Microsystems, and Netscape. Massachusetts is home to the Lotus division of IBM as well as major operations of Sun and Oracle. Utah is home to Novell. By far, the most overreaching provision in the litigating states' proposal is the prohibition on 'binding' middleware code to Microsoft's operating system software. In short, the litigating states would require Microsoft to allow licensees to remove the software code for any function that a Windows licensee could conceivably single out, while still requiring Microsoft to maintain the performance of the operating system. If Microsoft were able to comply technically, which is far from clear, it would have to rewrite Windows from scratch as a combination of thousands of separable, modular components. This would balkanize Windows as a platform for applications software. Developers would no longer be able to count on the presence of key segments of software code. Indeed, to ensure that their software worked properly, developers would have to provide those features themselves. As a result, consumers would encounter different flavors of Windows with differing capabilities. Adding to Microsoft's (and consumers') woes, the litigating states would require Microsoft to license large amounts of its intellectual property to competitors for little or no compensation. Competitors would get Microsoft's software code for free. But consumers would suffer in the long term from decreased innovation since Microsoft would be left with little incentive to develop Windows or many of its applications programs.Technology and Industry

Survey and Analysis of Production Distributed Computing Infrastructures

This report has two objectives. First, we describe a set of the production distributed infrastructures currently available, so that the reader has a basic understanding of them. This includes explaining why each infrastructure was created and made available and how it has succeeded and failed. The set is not complete, but we believe it is representative. Second, we describe the infrastructures in terms of their use, which is a combination of how they were designed to be used and how users have found ways to use them. Applications are often designed and created with specific infrastructures in mind, with both an appreciation of the existing capabilities provided by those infrastructures and an anticipation of their future capabilities. Here, the infrastructures we discuss were often designed and created with specific applications in mind, or at least specific types of applications. The reader should understand how the interplay between the infrastructure providers and the users leads to such usages, which we call usage modalities. These usage modalities are really abstractions that exist between the infrastructures and the applications; they influence the infrastructures by representing the applications, and they influence the ap- plications by representing the infrastructures

Servicing the federation : the case for metadata harvesting

The paper presents a comparative analysis of data harvesting and distributed computing as complementary models of service delivery within large-scale federated digital libraries. Informed by requirements of flexibility and scalability of federated services, the analysis focuses on the identification and assessment of model invariants. In particular, it abstracts over application domains, services, and protocol implementations. The analytical evidence produced shows that the harvesting model offers stronger guarantees of satisfying the identified requirements. In addition, it suggests a first characterisation of services based on their suitability to either model and thus indicates how they could be integrated in the context of a single federated digital library

Machine Learning in Wireless Sensor Networks: Algorithms, Strategies, and Applications

Wireless sensor networks monitor dynamic environments that change rapidly over time. This dynamic behavior is either caused by external factors or initiated by the system designers themselves. To adapt to such conditions, sensor networks often adopt machine learning techniques to eliminate the need for unnecessary redesign. Machine learning also inspires many practical solutions that maximize resource utilization and prolong the lifespan of the network. In this paper, we present an extensive literature review over the period 2002-2013 of machine learning methods that were used to address common issues in wireless sensor networks (WSNs). The advantages and disadvantages of each proposed algorithm are evaluated against the corresponding problem. We also provide a comparative guide to aid WSN designers in developing suitable machine learning solutions for their specific application challenges.Comment: Accepted for publication in IEEE Communications Surveys and Tutorial

Integrating Peer-to-Peer Networking and Computing in the AgentScape Framework

The combination of peer-to-peer networking and agentbased computing seems to be a perfect match. Agents are cooperative and communication oriented, while peerto -peer networks typically support distributed systems in which all nodes have equal roles and responsibilities. AgentScape is a framework designed to support large-scale multi-agent systems. Pole extends this framework with peerto -peer computing. This combination facilitates the development and deployment of new agent-based peer-to-peer applications and services

Supporting Cyber-Physical Systems with Wireless Sensor Networks: An Outlook of Software and Services

Sensing, communication, computation and control technologies are the essential building blocks of a cyber-physical system (CPS). Wireless sensor networks (WSNs) are a way to support CPS as they provide fine-grained spatial-temporal sensing, communication and computation at a low premium of cost and power. In this article, we explore the fundamental concepts guiding the design and implementation of WSNs. We report the latest developments in WSN software and services for meeting existing requirements and newer demands; particularly in the areas of: operating system, simulator and emulator, programming abstraction, virtualization, IP-based communication and security, time and location, and network monitoring and management. We also reflect on the ongoing efforts in providing dependable assurances for WSN-driven CPS. Finally, we report on its applicability with a case-study on smart buildings