ImageJ2: ImageJ for the next generation of scientific image data

ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. Due to these new and emerging challenges in scientific imaging, ImageJ is at a critical development crossroads. We present ImageJ2, a total redesign of ImageJ offering a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. ImageJ2 provides a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs

Cloudbus Toolkit for Market-Oriented Cloud Computing

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

Obvious: a meta-toolkit to encapsulate information visualization toolkits. One toolkit to bind them all

This article describes “Obvious”: a meta-toolkit that abstracts and encapsulates information visualization toolkits implemented in the Java language. It intends to unify their use and postpone the choice of which concrete toolkit(s) to use later-on in the development of visual analytics applications. We also report on the lessons we have learned when wrapping popular toolkits with Obvious, namely Prefuse, the InfoVis Toolkit, partly Improvise, JUNG and other data management libraries. We show several examples on the uses of Obvious, how the different toolkits can be combined, for instance sharing their data models. We also show how Weka and RapidMiner, two popular machine-learning toolkits, have been wrapped with Obvious and can be used directly with all the other wrapped toolkits. We expect Obvious to start a co-evolution process: Obvious is meant to evolve when more components of Information Visualization systems will become consensual. It is also designed to help information visualization systems adhere to the best practices to provide a higher level of interoperability and leverage the domain of visual analytics

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

A Semantic Grid Oriented to E-Tourism

With increasing complexity of tourism business models and tasks, there is a clear need of the next generation e-Tourism infrastructure to support flexible automation, integration, computation, storage, and collaboration. Currently several enabling technologies such as semantic Web, Web service, agent and grid computing have been applied in the different e-Tourism applications, however there is no a unified framework to be able to integrate all of them. So this paper presents a promising e-Tourism framework based on emerging semantic grid, in which a number of key design issues are discussed including architecture, ontologies structure, semantic reconciliation, service and resource discovery, role based authorization and intelligent agent. The paper finally provides the implementation of the framework.Comment: 12 PAGES, 7 Figure

AstroGrid-D: Enhancing Astronomic Science with Grid Technology

We present AstroGrid-D, a project bringing together astronomers and experts in Grid technology to enhance astronomic science in many aspects. First, by sharing currently dispersed resources, scientists can calculate their models in more detail. Second, by developing new mechanisms to efficiently access and process existing datasets, scientific problems can be investigated that were until now impossible to solve. Third, by adopting Grid technology large instruments such as robotic telescopes and complex scientific workflows from data aquisition to analysis can be managed in an integrated manner. In this paper, we present prominent astronomic use cases, discuss requirements on a Grid middleware and present our approach to extend/augment existing middleware to facilitate the improvements mentioned above

A Taxonomy of Workflow Management Systems for Grid Computing

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

The PAX Toolkit and its Applications at Tevatron and LHC

At the CHEP03 conference we launched the Physics Analysis eXpert (PAX), a C++ toolkit released for the use in advanced high energy physics (HEP) analyses. This toolkit allows to define a level of abstraction beyond detector reconstruction by providing a general, persistent container model for HEP events. Physics objects such as particles, vertices and collisions can easily be stored, accessed and manipulated. Bookkeeping of relations between these objects (like decay trees, vertex and collision separation, etc.) including deep copies is fully provided by the relation management. Event container and associated objects represent a uniform interface for algorithms and facilitate the parallel development and evaluation of different physics interpretations of individual events. So-called analysis factories, which actively identify and distinguish different physics processes and study systematic uncertainties, can easily be realized with the PAX toolkit. PAX is officially released to experiments at Tevatron and LHC. Being explored by a growing user community, it is applied in a number of complex physics analyses, two of which are presented here. We report the successful application in studies of t-tbar production at the Tevatron and Higgs searches in the channel t-tbar-Higgs at the LHC and give a short outlook on further developments