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BMC Medical Imaging 2008年第1期8卷 1-20页

作者： Lee, Joel T. Munch, Kristin R. Carlis, John V. Pardo, José V. Cognitive Neuroimaging Unit VA Medical Center Minneapolis MN 55417 United States Computer Science Department University of Minnesota Minneapolis MN 55455 United States

Background: Visualizing 3-dimensional (3-D) datasets is an important part of modern neuroimaging research. Many tools address this problem;however, they often fail to address specific needs and flexibility, such as the ability to work with different data formats, to control how and what data are displayed, to interact with values, and to undo mistakes. Results: iiV, an interactive software program for displaying 3-D brain images, is described. This tool was programmed to solve basic problems in 3-D data visualization. It is written in java so it is extensible, is platform independent, and can display images within web pages. iiV displays 3-D images as 2-dimensional (2-D) slices with each slice being an independent object with independent features such as location, zoom, colors, labels, etc. Feature manipulation becomes easier by having a full set of editing capabilities including the following: undo or redo changes;drag, copy, delete and paste objects;and save objects with their features to a file for future editing. It can read multiple standard positron emission tomography (PET) and magnetic resonance imaging (MRI) file formats like ECAT, ECAT7, ANALYZE, NIfTI-1 and DICOM. We present sample applications to illustrate some of the features and capabilities. Conclusion: iiV is an image display tool with many useful features. It is highly extensible, platform independent, and web-compatible. This report summarizes its features and applications, while illustrating iiV's usefulness to the biomedical imaging community. © 2008 Lee et al;licensee BioMed Central Ltd.

关键词： Positron Emission Tomography Graphical User Interface File Type Structural Magnetic Resonance Imaging java virtual machine

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Discretionary capability confinement

Discretionary capability confinement

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11th European Symposium on Research in Computer Security

作者： Fong, Philip W. L. Univ Regina Dept Comp Sci Regina SK S4S 0A2 Canada

ISBN: (纸本)354044601X

Motivated by the need of application-level access control in dynamically extensible systems, this work proposes a static annotation system for modeling capabilities in a java-like programming language. Addressing a common critique of capability systems, the proposed annotation system can provably enforce capability confinement. This confinement guarantee is leveraged to model a strong form of separation of duty known as hereditary mutual suspicion. The annotation system has been fully implemented in a standard java virtual machine.

关键词： language-based security access control capability confinement scoping rule java virtual machine

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Flexible task graphs: A unified restricted thread programming model for java 08

Flexible task graphs: A unified restricted thread programmin...

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Conference on Languages, Compilers and Tools for Embedded Systems

作者： Auerbach, Joshua Bacon, David F. Guerraoui, Rachid Spring, Jesper Honig Vitek, Jan IBM Res Yorktown Hts NY 10598 USA Ecole Polytech Fed Lausanne CH-1015 Lausanne Switzerland Purdue Univ Dept Comp Sci W Lafayette IN 47907 USA

ISBN: (纸本)9781605581040

The disadvantages of unconstrained shared-memory multi-threading in java, especially with regard to latency and determinism in real-time systems, have given rise to a variety of language extensions that place restrictions on how threads allocate, share, and communicate memory, leading to order-of-magnitude reductions in latency and jitter. However, each model makes different trade-offs with respect to expressiveness, efficiency, enforcement, and latency, and no one model is best for all applications. In this paper we present Flexible Task Graphs (Flexotasks), a single system that allows different isolation policies and mechanisms to be combined in an orthogonal manner, subsuming four previously proposed models as well as making it possible to use new combinations best suited to the needs of particular applications. We evaluate our implementation on top of the IBM Web-Sphere Real Time java virtual machine using both a microbenchmark and a 30 KLOC avionics collision detector. We show that Flexotasks are capable of executing periodic threads at 10 KHz with a standard deviation of 1.2 mu s and that it achieves significantly better performance than RTSJ's scoped memory constructs while remaining impervious to interference from global garbage collection.

关键词： languages experimentation real-time systems java virtual machine memory management ownership types

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Impact of JVM superoperators on energy consumption in resource-constrained embedded systems 08

Impact of JVM superoperators on energy consumption in resour...

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Conference on Languages, Compilers and Tools for Embedded Systems

作者： Badea, Carmen Nicolau, Alexandru Veidenbaum, Alexander V. Univ Calif Irvine Dept Comp Sci Ctr Embedded Comp Syst Irvine CA 92717 USA

ISBN: (纸本)9781605581040

Energy consumption is one of the most important issues in resource-constrained embedded systems. Many such systems run java-based applications due to java's architecture-independent format (bytecode). Standard techniques for executing bytecode programs, e. g. interpretation or just-in-time compilation, have performance or memory issues that make them unsuitable for resource-constrained embedded systems. A superoperator-extended, lightweight java virtual machine (JVM) can be used in resource-constrained embedded systems to improve performance and reduce memory consumption. This paper shows that such a JVM also significantly reduces energy consumption. This is due primarily to a considerable reduction in the number of memory accesses and thus in energy consumption in the instruction and data TLBs and caches and, in most cases, in DRAM energy consumption. Since the fraction of processor energy dissipated in these units is approximately 60%, the energy savings achieved are significant. The paper evaluates the number of load, store, and computational instructions eliminated by the use of proposed superoperators as compared to a simple interpreter on a set of embedded benchmarks. Using cache and DRAM per access energy we estimate the total processor/DRAM energy saved by using our JVM. Our results show that with 32KB caches the reduction in energy consumption ranges from 40% to 60% of the overall processor, plus DRAM energy. Even higher savings may be achieved with smaller caches and increased access to DRAM as DRAM access energy is fairly high.

关键词： experimentation measurement performance energy estimation java virtual machine superoperators profile-guided optimization embedded systems

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Enhanced hot spot detection heuristics for embedded java just-in-time compilers

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ACM SIGPLAN NOTICES 2008年第7期43卷 13-22页

作者： Lee, Seong-Won Moon, Soo-Mook Kim, Seong-Moo Seoul Natl Univ Sch Elect Engn Seoul 151 South Korea

Most java just-in-time compilers (JITC) try to compile only hot methods since the compilation overhead is part of the running time. This requires precise and efficient hot spot detection, which includes distinguishing hot methods from cold methods, detecting them as early as possible, and paying a small runtime overhead for detection. A hot method could be identified by measuring its running time during interpretation since a long-running method is likely to be a hot method. However, precise measurement of the running time during execution is too expensive, especially in embedded systems, so many counter-based heuristics have been proposed to estimate it. The Simple heuristic counts only method invocations without any consideration of loops [1], while Sun's HotSpot heuristic counts loop iterations as well, but does not consider loop sizes or method sizes [2,14]. The static analysis heuristic estimates the running time of a method by statically analyzing loops or heavy-cost bytecodes but does not measure their dynamic counts [3]. Although the overhead of these heuristics is low, they do not estimate the running time precisely, which may lead to imprecise hot spot detection. This paper proposes a new hot spot detection heuristic which can estimate the running time more precisely than others with a relatively low overhead. It dynamically counts only important bytecodes interpreted, but with a simple arithmetic calculation it can obtain the precise count of all interpreted bytecodes. We also propose employing a static analysis technique to predict those hot methods which spend a huge execution time once invoked. This static prediction can allow compiling these methods at their first-invocation, complementing the proposed dynamic estimation technique. We implemented both, which led to a performance benefit of 10% compared to the HotSpot heuristic.

关键词： performance experimentation languages java just-in-time compilation hot spot detection Sun's HotSpot heuristic java virtual machine J2ME CDC

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Flexible task graphs: A unified restricted thread programming model for java

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ACM SIGPLAN NOTICES 2008年第7期43卷 1-11页

关键词： languages experimentation real-time systems java virtual machine memory management ownership types

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Impact of JVM superoperators on energy consumption in resource-constrained embedded systems

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ACM SIGPLAN NOTICES 2008年第7期43卷 12-30页

作者： Badea, Carmen Nicolau, Alexandru Veidenbaum, Alexander V. Univ Calif Irvine Dept Comp Sci Ctr Embedded Comp Syst Irvine CA 92717 USA

关键词： experimentation measurement performance energy estimation java virtual machine superoperators profile-guided optimization embedded systems

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Cinfony - combining Open Source cheminformatics toolkits behind a common interface

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CHEMISTRY CENTRAL JOURNAL 2008年第1期2卷 24-24页

作者： O'Boyle, Noel M. Hutchison, Geoffrey R. Cambridge Crystallog Data Ctr Cambridge CB2 1EZ England Univ Pittsburgh Dept Chem Chevron Sci Ctr Pittsburgh PA 15260 USA

Background: Open Source cheminformatics toolkits such as OpenBabel, the CDK and the RDKit share the same core functionality but support different sets of file formats and forcefields, and calculate different fingerprints and descriptors. Despite their complementary features, using these toolkits in the same program is difficult as they are implemented in different languages (C++ versus java), have different underlying chemical models and have different application programming interfaces (APIs). Results: We describe Cinfony, a Python module that presents a common interface to all three of these toolkits, allowing the user to easily combine methods and results from any of the toolkits. In general, the run time of the Cinfony modules is almost as fast as accessing the underlying toolkits directly from C++ or java, but Cinfony makes it much easier to carry out common tasks in cheminformatics such as reading file formats and calculating descriptors. Conclusion: By providing a simplified interface and improving interoperability, Cinfony makes it easy to combine complementary features of OpenBabel, the CDK and the RDKit.

关键词： Python Script java virtual machine Smile String Molecule Class java Native Interface

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Portable virtual cycle accounting for large-scale distributed cycle sharing systems

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PARALLEL COMPUTING 2007年第4-5期33卷 314-327页

作者： Yamauchi, Hiroshi Xu, Dongyan Purdue Univ Dept Comp Sci W Lafayette IN 47907 USA

CPU cycle sharing among distributed heterogeneous computers is the key function in large-scale volunteer computing and desktop grid applications. One important problem in large-scale distributed cycle sharing system is how to account for the amount of computation work performed by a CPU cycle provider, in a uniform and portable fashion across heterogeneous hardware and operating system platforms. Such an accounting mechanism is especially desirable when CPU resources are traded and a lack of uniform workload accounting will hinder the enforcement of market-driven CPU pricing/trading policies in distributed cycle sharing systems. java virtual machine (JVM) has proved to be a good match for distributed cycle sharing because of its abilities to run applications on a wide variety of platforms without modification (portability) and to host untrusted applications (safety). In this paper, we present the design, implementation, and evaluation of an efficient, application-transparent virtual cycle accounting scheme integrated into JVM. Our scheme achieves portable workload accounting across heterogeneous computing platforms by accounting for JVM virtual instructions instead of real processor cycles. Different from the existing JVM CPU accounting mechanisms that involve bytecode rewriting, our scheme is transparent to applications and does not require visible changes to application and library code interfaces which would break applications that use Reflection API. Moreover, our scheme is efficient via the use of processor registers for accounting. Our experimental results demonstrate both high accounting accuracy and low runtime overhead of virtual cycle accounting. (C) 2007 Elsevier B.V. All rights reserved.

关键词： large-scale distributed cycle sharing transparent and efficient virtual cycle accounting java virtual machine

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BioPP: a tool for web-publication of biological networks

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BMC BIOINFORMATICS 2007年第1期8卷 1-6页

作者： Viswanathan, Ganesh A. Nudelman, German Patil, Sonali Sealfon, Stuart C. Mt Sinai Sch Med Ctr Translat Syst Biol New York NY 10029 USA Mt Sinai Sch Med Dept Neurol New York NY 10029 USA

Background: Cellular processes depend on the function of intracellular molecular networks. The curation of the literature relevant to specific biological pathways is important for many theoretical and experimental research teams and communities. No current tool supports web publication or hosting of user-developed large scale annotated pathway diagrams. Sharing via web publication is needed to allow real-time access to the current literature pathway knowledgebase, both privately within a research team or publicly among the outside research community. Web publication also facilitates team and/or community input into the curation process while allowing centralized control of the curation and validation process. We have developed new tool to address these needs. Biological Pathway Publisher (BioPP) is a software suite for converting CellDesigner Systems Biology Markup Language (CD-SBML) formatted pathways into a web viewable format. The BioPP suite is available for private use and for depositing knowledgebases into a newly created public repository. Results: BioPP suite is a web-based application that allows pathway knowledgebases stored in CD-SBML to be web published with an easily navigated user interface. The BioPP suite consists of four interrelated elements: a pathway publisher, an upload web-interface, a pathway repository for user-deposited knowledgebases and a pathway navigator. Users have the option to convert their CD-SBML files to HTML for restricted use or to allow their knowledgebase to be web-accessible to the scientific community. All entities in all knowledgebases in the repository are linked to public database entries as well as to a newly created public wiki which provides a discussion forum. Conclusion: BioPP tools and the public repository facilitate sharing of pathway knowledgebases and interactive curation for research teams and scientific communities. BioPP suite is accessible at http://***/pathwayPublisher/broadcast/.

关键词： java virtual machine System Biology Markup Language System Biology Markup Annotate Pathway Converted File

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