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Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

JOURNAL OF CHEMINFORMATICS 2011年第1期3卷 1-15页

作者： O'Boyle, Noel M. Guha, Rajarshi Willighagen, Egon L. Adams, Samuel E. Alvarsson, Jonathan Bradley, Jean-Claude Filippov, Igor V. Hanson, Robert M. Hanwell, Marcus D. Hutchison, Geoffrey R. James, Craig A. Jeliazkova, Nina Lang, Andrew S. I. D. Langner, Karol M. Lonie, David C. Lowe, Daniel M. Pansanel, Jerome Pavlov, Dmitry Spjuth, Ola Steinbeck, Christoph Tenderholt, Adam L. Theisen, Kevin J. Murray-Rust, Peter Natl Univ Ireland Univ Coll Cork Analyt & Biol Chem Res Facil Cork Ireland NIH Ctr Translat Therapeut Rockville MD 20878 USA Karolinska Inst Inst Environm Med Div Mol Toxicol S-17177 Stockholm Sweden Univ Cambridge Dept Chem Unilever Ctr Mol Sci Informat Cambridge CB2 1EW England Uppsala Univ Dept Pharmaceut Biosci S-75124 Uppsala Sweden Drexel Univ Dept Chem Philadelphia PA 19104 USA NCI Biol Chem Lab Basic Res Program SAIC Frederick Inc Frederick MD 21702 USA St Olaf Coll Northfield MN 55057 USA Kitware Inc Clifton Pk NY 12065 USA Univ Pittsburgh Dept Chem Pittsburgh PA 15260 USA eMolecules Inc Solana Beach CA 92075 USA Ideaconsult Ltd Sofia 1000 Bulgaria Oral Roberts Univ Dept Engn Comp Sci Phys & Math Tulsa OK 74171 USA Leiden Univ Leiden Inst Chem NL-2333 CC Leiden Netherlands SUNY Buffalo Dept Chem Buffalo NY 14260 USA Univ Strasbourg IPHC CNRS UMR7178 F-67037 Strasbourg France GGA Software Serv LLC St Petersburg 194342 Russia EBI Cheminformat & Metab Team Cambridge England Univ Washington Dept Chem Seattle WA 98195 USA iChemLabs Piscataway NJ 08854 USA

Background: The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. Results: This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions: We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.

关键词： Open Source Open Data Resource Description Framework java virtual machine Chemical Markup Language

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OSCAR4: a flexible architecture for chemical text-mining

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JOURNAL OF CHEMINFORMATICS 2011年第1期3卷 1-12页

作者： Jessop, David M. Adams, Sam E. Willighagen, Egon L. Hawizy, Lezan Murray-Rust, Peter Univ Cambridge Dept Chem Unilever Ctr Mol Sci Informat Cambridge CB2 1EW England

The Open-Source Chemistry Analysis Routines (OSCAR) software, a toolkit for the recognition of named entities and data in chemistry publications, has been developed since 2002. Recent work has resulted in the separation of the core OSCAR functionality and its release as the OSCAR4 library. This library features a modular API (based on reduction of surface coupling) that permits client programmers to easily incorporate it into external applications. OSCAR4 offers a domain-independent architecture upon which chemistry specific text-mining tools can be built, and its development and usage are discussed.

关键词： Plain Text European Patent Office European Bioinformatics Institute java virtual machine Client Programmer

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Discretionary capability confinement

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INTERNATIONAL JOURNAL OF INFORMATION SECURITY 2008年第2期7卷 137-154页

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

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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Accurate Reification of Complete Supertype Information for Dynamic Analysis on the JVM 2017

Accurate Reification of Complete Supertype Information for D...

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16th ACM SIGPLAN International Conference on Generative Programming - Concepts and Experiences (GPCE) co-located with SPLASH Conference

作者： Rosa, Andrea Rosales, Eduardo Binder, Walter Univ Svizzera Italiana Fac Informat Lugano Switzerland

ISBN: (纸本)9781450355247

Reflective supertype information (RSI) is useful for many instrumentation-based dynamic analyses on the java virtual machine (JVM). On the one hand, while such information can be obtained when performing the instrumentation within the same JVM process executing the instrumented program, in-process instrumentation severely limits the code coverage of the analysis. On the other hand, performing the instrumentation in a separate process can achieve full code coverage, but complete RSI is generally not available, often requiring expensive runtime checks in the instrumented program. Providing accurate and complete RSI in the instrumentation process is challenging because of dynamic class loading and classloader namespaces. In this paper, we present a novel technique to accurately reify complete RSI in a separate instrumentation process. We implement our technique in the dynamic analysis framework DiSL and evaluate it on a task profiler, achieving speedups of up to 45% for an analysis with full code coverage.

关键词： Dynamic analysis reflective information byte-code instrumentation java virtual machine

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Comprehensive aspect weaving for java

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SCIENCE OF COMPUTER PROGRAMMING 2011年第11期76卷 1015-1036页

作者： Villazon, Alex Binder, Walter Moret, Philippe Ansaloni, Danilo Univ Lugano Fac Informat CH-6900 Lugano Switzerland

Aspect-oriented programming (AOP) has been successfully applied to application code thanks to techniques such as java bytecode instrumentation. Unfortunately, with existing AOP frameworks for java such as AspectJ, aspects cannot be woven into the standard java class library. This restriction is particularly unfortunate for aspects that would benefit from comprehensive aspect weaving with complete method coverage, such as profiling or debugging aspects. In this article we present MAJOR, a new tool for comprehensive aspect weaving, which ensures that aspects are woven into all classes loaded in a java virtual machine, including those in the standard java class library. MAJOR includes the pluggable module CARAJillo, which supports efficient access to a complete and customizable calling context representation. We validate our approach with three case studies. Firstly, we weave existing profiling aspects with MAJOR which otherwise would generate incomplete profiles. Secondly, we introduce an aspect for memory leak detection that also benefits from comprehensive weaving. Thirdly, we present an aspect subsuming the functionality of ReCrash, an existing tool based on low-level bytecode instrumentation techniques that generates unit tests to reproduce program failures. Our aspect-based tools are concisely implemented in a few lines of code, and leverage MAJOR and CARAJillo for comprehensive aspect weaving and for efficient access to calling context information. (C) 2010 Elsevier B.V. All rights reserved.

关键词： Aspect-oriented programming Aspect weaving Bytecode instrumentation Profiling Debugging Detecting memory leaks Recreating crashing conditions java virtual machine

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Static Analysis of java Bytecode

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Wuhan University Journal of Natural Sciences 2001年第Z1期6卷 383-390页

作者： Jian\|jun Zhao Department of Computer Science and Engineering, Fukuoka Institute of Technology, Fukuoka 811 0295,Japan Department of Computer Science and Engineering Fukuoka Institute of Technology Fukuoka 811-0295 Japan

Understanding control flows in a computer program is essential for many software engineering tasks such as testing, debugging, reverse engineering, and maintenance. In this paper ,we present a control flow analysis technique to analyze the control flow in java bytecode. To perform the analysis, we construct a control flow graph(CFG) for java bytecode not only at the intraprocedural level but also at the interprocedural level. We also discuss some applications of a CFG in a maintenance environment for java bytecode.

关键词： Control flow analysis java virtual machine software testing software maintenance.

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A method-level comparison of the java Grande and SPEC JVM98 benchmark suites

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CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE 2005年第7-8期17卷 757-773页

作者： Gregg, D Power, J Waldron, J Natl Univ Ireland Dept Comp Sci Maynooth Kildare Ireland Univ Dublin Trinity Coll Dept Comp Sci Dublin 2 Ireland

In this paper we seek to provide a foundation for the study of the level of use of object-oriented techniques in java programs in general, and scientific applications in particular. Specifically, we investigate the profiles of java programs from a number of perspectives, including the use of class library methods, the size of methods called, the mode of invoke instruction used and the polymorphicity of call sites. We also present a categorization of the nature of small methods used in java programs. We compare the java Grande and SPEC JVM98 benchmark suites, and note a significant difference in the nature and composition of these suites, with the programs from the java Grande suite demonstrating a less object-oriented approach. Copyright (c) 2005 John Wiley & Sons, Ltd.

关键词： benchmark suites java virtual machine dynamic profiling

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Reflexes: Abstractions for Integrating Highly Responsive Tasks into java Applications

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ACM TRANSACTIONS ON EMBEDDED COMPUTING SYSTEMS 2010年第1期10卷 1–29页

作者： Spring, Jesper Honig Pizlo, Filip Privat, Jean Guerraoui, Rachid Vitek, Jan Ecole Polytech Fed Lausanne IC IIF LPD EPFL CH-1015 Lausanne Switzerland Purdue Univ Dept Comp Sci W Lafayette IN 47907 USA

Achieving submillisecond response times in a managed language environment such as java or C# requires overcoming significant challenges. In this article, we propose Reflexes, a programming model and runtime system infrastructure that lets developers seamlessly mix highly responsive tasks and timing-oblivious java applications. Thus enabling gradual addition of real-time features, to a non-real-time application without having to resort to recoding the real-time parts in a different language such as C or Ada. Experiments with the Reflex prototype implementation show that it is possible to run a real-time task with a period of 45 mu s with an accuracy of 99.996% (only 0.001% worse than the corresponding C implementation) in the presence of garbage collection and heavy load ordinary java threads.

关键词： Languages Experimentation Real-time systems java virtual machine memory management

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JUSTGen: Effective Test Generation for Unspecified JNI Behaviors on JVMs 21

JUSTGen: Effective Test Generation for Unspecified JNI Behav...

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43rd IEEE/ACM International Conference on Software Engineering - Software Engineering in Practice (ICSE-SEIP) / 43rd ACM/IEEE International Conference on Software Engineering - New Ideas and Emerging Results (ICSE-NIER)

作者： Hwang, Sungjae Lee, Sungho Kim, Jihoon Ryu, Sukyoung Korea Adv Inst Sci & Technol Sch Comp Daejeon South Korea Chungnam Natl Univ Dept Comp Sci & Engn Daejeon South Korea

ISBN: (纸本)9780738113197

java Native Interface (JNI) provides a way for java applications to access native libraries, but it is difficult to develop correct JNI programs. By leveraging native code, the JNI enables java developers to implement efficient applications and to reuse code written in other programming languages such as C and C++. Besides, the core java libraries already use the JNI to provide system features like a graphical user interface. As a result, many mainstream java virtual machines (JVMs) support the JNI. However, due to the complex interoperation semantics between different programming languages, implementing correct JNI programs is not trivial. Moreover, because of the performance overhead, JVMs do not validate erroneous JNI interoperations by default, but they validate them only when the debug feature, the -Xcheck:jni option, is enabled. Therefore, the correctness of JNI programs highly relies on the checks by the -Xcheck:jni option of JVMs. Questions remain, however, on the quality of the checks provided by the feature. Are there any properties that the -Xcheck:jni option fails to validate? If so, what potential issues can arise due to the lack of such validation? To the best of our knowledge, no research has explored these questions in-depth. In this paper, we empirically study the validation quality and impacts of the -Xcheck:jni option on mainstream JVMs using unspecified corner cases in the JNI specification. Such unspecified cases may lead to unexpected run-time behaviors because their semantics is not defined in the specification. For a systematic study, we propose JUSTGEN, a semi-automated approach to identify unspecified cases from a specification and generate test programs. JUSTGEN receives the JNI specification written in our domain specific language (DSL), and automatically discovers unspecified cases using an SMT solver. It then generates test programs that trigger the behaviors of unspecified cases. Using the generated tests, we empirically study the vali

关键词： java Native Interface java virtual machine Testing Empirical Study Debugging

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A performance comparison between stop-the-world and multithreaded concurrent generational garbage collection for java

A performance comparison between stop-the-world and multithr...

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IEEE International Performance, Computing, and Communications Conference

作者： Lo, CTD Srisa-An, W Chang, JM IIT Dept Comp Sci Chicago IL 60616 USA

ISBN: (纸本)0780373715

Recent popularity of java programming language has brought the automatic dynamic memory management (a.k.a., the garbage collection) into the mainstream, Traditional garbage collectors suffer from long garbage collection pauses (stop-the-world mark-sweep algorithm) or inability of collecting cyclic garbage (reference counting approach). Generational garbage collection, however, is based only on the weak generational hypothesis that most objects die young. In this paper, the performance evaluation of a new multithreaded concurrent generational garbage collector (MCGC) based on mark-sweep with the assistance of reference counting is reported. The MCGC can take advantage of multiple CPUs in an SMP system and the merits of light weight processes. Furthermore, the long garbage collection pause can be reduced and the garbage collection efficiency can be enhanced. Measurement results indicate that the MCGC improves the garbage collection pause time up to 96.75% over the traditional stop-the-world mark-sweep garbage collector. Moreover, the MCGC receives minimal time and space penalties as shown in the report of the total execution time, the memory footprint and the sticky reference count rate.

关键词： dynamic memory management object-oriented programming multithreaded programming java virtual machine concurrent garbage collection system modified buddy system parallel garbage collector

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