Bio-jETI is a framework for model-based, graphical development and execution of bioinformatics analysis processes. With the GeneSys code generation framework we can automatically compile the workflow models into nativ...
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ISBN:
(纸本)9781424444830
Bio-jETI is a framework for model-based, graphical development and execution of bioinformatics analysis processes. With the GeneSys code generation framework we can automatically compile the workflow models into native, stand-alone program code. We show via a phylogenetic analysis workflow designed by the DNA Data Bank of Japan (DDBJ) how we generate 6 variants of java code from the corresponding process model realized in Bio-jETI. Performance measurements show that 1) the overall workflow execution time is dominated by the remote services it uses, and thus 2)all 6 variants are almost as fast as the handwritten java of DDBJ. This way, we obtain efficient native code essentially without programming. Thus, we demonstrate in this paper that model-based workflow development in Bio-jETI offers several advantages over manual implementation - including higher agility, greater transparency and better maintainability - without compromising the runtime performance.
This paper presents a transactional framework for low-latency, high-performance, concurrent;event processing in java. At the heart of our framework lies Reflexes, a restricted programming model for highly responsive s...
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ISBN:
(纸本)9783642020520
This paper presents a transactional framework for low-latency, high-performance, concurrent;event processing in java. At the heart of our framework lies Reflexes, a restricted programming model for highly responsive systems. A Reflex task is ail event processor that can run at a higher priority and preempt any other java thread, including the garbage collector. It runs in an obstruction-free manner with time-oblivious code. We extend Reflexes with a publish/subscribe communication system, itself based on an optimistic transactional event processing scheme, that provides efficient coordination between time-critical, low-latency tasks. We report on the comparison with a commercial JVM, and show that it is possible for tasks to achieve 50 mu s response times with way less than 1% of the executions failing to meet their deadlines.
Code based ("white box") approach to testing can be divided into two main types: control flow coverage and data flow coverage methods. Dataflow testing was introduced for structural programminglanguages and...
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ISBN:
(纸本)9780769536743
Code based ("white box") approach to testing can be divided into two main types: control flow coverage and data flow coverage methods. Dataflow testing was introduced for structural programminglanguages and later adopted for object languages. Among many tools supporting code based testing of object programs, only JaBUTi and DFC (Data Flow Coverage) support dataflow testing of Jaya programs. DFC is a tool implemented at the Institute of Computer Science Warsaw University of Technology as an Eclipse plug-in. The objective of this paper is to present dataflow coverage testing of Jaya programs supported by DFC. DFC finds all definition-uses pairs in tested unit and provides also the definition-uses graph for methods. After the execution of test information which def-uses pairs were covered is shown. An example of data flow testing of Jaya program is also presented.
java PathFinder (JPF) is a popular model checker for java programs. JPF was used to generate object graphs as test inputs for object-oriented programs. Specifically JPF was used as an implementation engine for the Kor...
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ISBN:
(纸本)9781424437757
java PathFinder (JPF) is a popular model checker for java programs. JPF was used to generate object graphs as test inputs for object-oriented programs. Specifically JPF was used as an implementation engine for the Korat algorithm. Korat takes two inputs-a java predicate that encodes properties of desired object graphs and a bound on the size of the graph-and generates all graphs (within the given bound) that satisfy the encoded properties. Korat uses a systematic search to explore the bounded state space of object graphs. Korat search was originally implemented in JPF using a simple instrumentation of the java predicate. However, JPF is a general-purpose model checker and such direct implementation results in an unnecessarily slow search. We present our results on speeding up Korat search in JPF The experiments on ten data structure subjects show that our modifications of JPF reduce the search time by over an order of magnitude.
This paper addresses functionality and implementation of a HP java version of the Adlib collective communication library for data parallel programming. We begin by illustrating typical use of the library, through an e...
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The Topic Maps Application programming Interface (TM- API) provides a standardized way for working with Topic Maps on the java platform. TMAPI implementations in other programminglanguages not available for the JVM u...
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ISBN:
(纸本)9783941608061
The Topic Maps Application programming Interface (TM- API) provides a standardized way for working with Topic Maps on the java platform. TMAPI implementations in other programminglanguages not available for the JVM use a different stack - not harnessing the existing java code. In this paper we describe a different approach, reusing java TMAPI implementations to build a high level Topic Maps API for the Ruby programminglanguage without a heavy wrapper layer around the java Objects. The high level API greatly simplifies implementations on top of the new API compared to TMAPI with minimal overhead. The plain TMAPI methods can be invoked without any overhead at all. The implementation was thought to be straight forward in the beginning but - As usual - some pitfalls were encountered. The according solutions will be outlined in this paper. The library, documentation, and tutorials can be found on the project's website1.
This paper presents a technique for enhancing the capabilities of SVG graphics generated via the Batik library and the java Abstract Windowing Toolkit (AWT). The enhancements include CSS stylesheet support with multip...
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This paper presents a technique for enhancing the capabilities of SVG graphics generated via the Batik library and the java Abstract Windowing Toolkit (AWT). The enhancements include CSS stylesheet support with multiple media types, support for high quality patterns, enhancements to enable interactivity and animation, and an enhancement that adds logical grouping to the SVG objects created on introspection of the java stack. These enhancements can be applied to any tool that uses AWT. For the purposes of this paper the enhancements are applied to charts created by the JFreeChart charting library. The enhancements bring the SVG output of the tool up to par with its native java AWT abilties, and in some instances allow it to surpass its native AWT capability.
Symbolic execution is a popular technique used in formal verification of software and hardware systems. In this paper we examine three different ways of performing symbolic execution for the purpose of formal model ch...
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Method names in java are natural language phrases describing behaviour, encoded to make them easy for machines to parse. Programmers rely on the meaning encoded in method names to understand code. We know little about...
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ISBN:
(纸本)9783642004339
Method names in java are natural language phrases describing behaviour, encoded to make them easy for machines to parse. Programmers rely on the meaning encoded in method names to understand code. We know little about the language used in this encoding, its rules and structure, leaving the programmer without guidance in expressing her intent. Yet the meaning of the method names - or phrases - is readily available in the body of the methods they name. By correlating names and implementations, we can figure out the meaning of the original phrases, and uncover the rules of the phrase language as well. In this paper, we present an automatically generated proof-of-concept phrase book for java, based on a large software corpus. The phrase book captures both the grammatical structure and the meaning of method phrases as commonly used by java programmers.
With the rapid development of computer and Internet technologies, the virtual and remote laboratories have become an important part of the educational process. To develop interactive virtual and remote laboratories (V...
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