The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.

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UCSF Chimera--a visualization system for exploratory research and analysis.

Is there such a thing anymore as a software system that doesn’t need to be secure? Almost every softwarecontrolled system faces threats from potential adversaries, from Internet-aware client applications running on PCs, to complex telecommunications and power systems accessible over the Internet, to commodity software with copy protection mechanisms. Software engineers must be cognizant of these threats and engineer systems with credible defenses, while still delivering value to customers. In this paper, we present our perspectives on the research issues that arise in the interactions between software engineering and security.

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Software engineering for security: a roadmap

Autonomous robots are complex systems that require the interaction between numerous heterogeneous
components (software and hardware). Because of the increase in complexity of robotic
applications and the diverse range of hardware, robotic middleware is designed to manage the
complexity and heterogeneity of the hardware and applications, promote the integration of new
technologies, simplify software design, hide the complexity of low-level communication and the
sensor heterogeneity of the sensors, improve software quality, reuse robotic software infrastructure
across multiple research efforts, and to reduce production costs. This paper presents a literature
survey and attribute-based bibliography of the current state of the art in robotic middleware design.
The main aim of the survey is to assist robotic middleware researchers in evaluating the
strengths and weaknesses of current approaches and their appropriateness for their applications.
Furthermore, we provide a comprehensive set of appropriate bibliographic references that are classified
based on middleware attributes.

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Robotics Middleware: A Comprehensive Literature Survey and Attribute-Based Bibliography

ThetextitService Component Architecture (SCA) is a technology-independent standard for developing distributed Service-oriented Architectures (SOA). The SCA standard promotes the use of components and architecture descriptors, and mostly covers the lifecycle steps of implementation and deployment. Unfortunately, SCA does not address the governance of SCA applications and provides no support for the maintenance of deployed components. This article covers this issue and introduces the FRASCATI platform, a run-time support for SCA with dynamic reconfiguration capabilities and run-time management features. This article presents the internal component-based architecture of the FRASCATI platform, and highlights its key features. The component-based design of the FRASCATI platform introduces many degrees of flexibility and configurability in the platform itself and it can host the SOA applications. This article reports on micro-benchmarks highlighting that run-time manageability in the FRASCATI platform does not decrease its performance when compared with the de facto reference SCA implementation: Apache TUSCANY. Finally, a smart home scenario illustrates the extension capabilities and the various reconfigurations of the FRASCATI platform. Copyright © 2011 John Wiley & Sons, Ltd.

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A component-based middleware platform for reconfigurable service-oriented architectures

Modern scientific experiments acquire large amounts of data that must be analyzed in subtle and complicated ways to extract the best results. The Laser Interferometer Gravitational Wave Observatory (LIGO) is an ambitious effort to detect gravitational waves produced by violent events in the universe, such as the collision of two black holes or the explosion of supernovae [37,258]. The experiment records approximately 1 TB of data per day, which is analyzed by scientists in a collaboration that spans four continents. LIGO and distributed computing have grown up side by side over the past decade, and the analysis strategies adopted by LIGO scientists have been strongly influenced by the increasing power of tools to manage distributed computing resources and the workflows to run on them. In this chapter, we use LIGO as an application case study in workflow design and implementation. The software architecture outlined here has been used with great efficacy to analyze LIGO data [2–5] using dedicated computing facilities operated by the LIGO Scientific Collaboration, the LIGO Data Grid. It is just the first step, however. Workflow design and implementation lies at the interface between computing and traditional scientific activities. In the conclusion, we outline a few directions for future development and provide some long-term vision for applications related to gravitational wave data analysis.

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Padmapriya Vasudevan

Papers

Common object request broker architecture (CORBA)