In this paper we describe a method for simulation-based verification of microprocessor units based on cycle-accurate contract specifications. Such specifications describe behavior of a unit in the form of precondition...
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Background: PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using workflow techniques. We apply ...
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Background: PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using workflow techniques. We apply a service-oriented approach to model and implement GeneFisher-P, a process-based version of the GeneFisher web application, as a part of the Bio-jETI platform for service modeling and execution. We show how to introduce a flexible process layer to meet the growing demand for improved user-friendliness and flexibility. Results: Within Bio-jETI, we model the process using the jABC framework, a mature model-driven, service-oriented process definition platform. We encapsulate remote legacy tools and integrate web services using jETI, an extension of the jABC for seamless integration of remote resources as basic services, ready to be used in the process. Some of the basic services used by GeneFisher are in fact already provided as individual web services at BiBiServ and can be directly accessed. Others are legacy programs, and are made available to Bio-jETI via the jETI technology. The full power of service-based process orientation is required when more bioinformatics tools, available as web services or via jETI, lead to easy extensions or variations of the basic process. This concerns for instance variations of data retrieval or alignment tools as provided by the European Bioinformatics Institute (EBI). Conclusions: The resulting service-and process-oriented GeneFisher-P demonstrates how basic services from heterogeneous sources can be easily orchestrated in the Bio-jETI platform and lead to a flexible family of specialized processes tailored to specific tasks.
This paper provides an experience report on the use of aspect-oriented technology as a means to modularize the implementation of business rules in an object-oriented, large scale case study. The goal of this refactori...
ISBN:
(纸本)9781424426133
This paper provides an experience report on the use of aspect-oriented technology as a means to modularize the implementation of business rules in an object-oriented, large scale case study. The goal of this refactoring of the system was to provide a proof-of-concept implementation of how such an aspect-oriented solution can improve the modularity and the extensibility of the business rule implementation. This paper focusses on the approach taken in refactoring the system and the difficulties of integrating the aspect solution into the build process.
We present the design of S-NET, a coordination language and component technology based on stream processing. S-NET achieves a near-complete separation between application code, written in a conventional programming la...
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We present the design of S-NET, a coordination language and component technology based on stream processing. S-NET achieves a near-complete separation between application code, written in a conventional programming language, and coordination code, written in S-NET itself. S-NET boxes integrate existing sequential code as stream-processing components into streaming networks, whose construction is based on algebraic formulae built out of four network combinators. Subtyping on the level of boxes and networks and a tailor-made inheritance mechanism achieve flexible software reuse.
In this paper, we consider the Grand Challenge under a very specific perspective: the enabling of application experts without programming knowledge to reliably model their business processes/applications in a fashion ...
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ISBN:
(纸本)9783540691471
In this paper, we consider the Grand Challenge under a very specific perspective: the enabling of application experts without programming knowledge to reliably model their business processes/applications in a fashion that allows for a subsequent automatic realization on a given platform. This goal, which aims at simplifying the tasks of the many at the cost of ambitious and laborious tasks for the few, adds a new dimension to the techniques and concepts aimed at by the Grand Challenge: the application-specific design of platforms tailored for the intended goal. We are convinced that the outlined perspective provides a realistic and economically important milestone for the Grand Challenge.
We have designed and implemented game-themed programming assignment modules targeted specifically for adoption in existing introductory programming classes. These assignments are self-contained, so that faculty member...
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ISBN:
(纸本)9781605580579
We have designed and implemented game-themed programming assignment modules targeted specifically for adoption in existing introductory programming classes. These assignments are self-contained, so that faculty members with no background in graphics/gaming can selectively pick and choose a subset to combine with their own assignments in existing classes. This paper begins with a survey of previous results, followed by a description of the game-themed assignment modules. The paper then focuses on our efforts in assessing the assignments: including details of the procedures and instruments for evaluating student achievement of learning outcomes and attitudes towards the assignments, as well as the extra effort required of faculty to adopt the assignments in existing clases. Copyright 2008 ACM.
Our approach to the model-driven collaborative design of IKEA's P3 Delivery Management Process uses the jABC [9] for model driven mediation and choreography to complement a RUP-based (Rational (Unified Process) de...
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ISBN:
(纸本)9783540884781
Our approach to the model-driven collaborative design of IKEA's P3 Delivery Management Process uses the jABC [9] for model driven mediation and choreography to complement a RUP-based (Rational (Unified Process) development process. jABC is a framework for service development based oil Lightweight Process Coordination. Users (product developers and system/software designers) easily develop services and applications by composing reusable building-blocks into (flow-) graph structures that can be animated, analyzed, simulated, verified, executed, and compiled. This way of handling the collaborative design of complex embedded systems has proven to be effective and adequate for the cooperation of mid non-technical people, which is the focus of this contribution, and it is now being rolled out in the operative practice.
An almost synchronous stream consists of a sequence of proper messages and pauses transmitted over a directed channel. The paper presents the transformational design of a communicating component which coordinates two ...
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An almost synchronous stream consists of a sequence of proper messages and pauses transmitted over a directed channel. The paper presents the transformational design of a communicating component which coordinates two almost synchronous streams. A proper message on one input channel is forwarded to the corresponding output channel as soon as there arrives a proper message on the other input channel as well. We refine the stream-based input/output behaviour to a state-based implementation exploiting two major transformations. The first transformation refines the component's infinite behaviour to a finite behaviour. The second transformation implements the component's finite behaviour by a state transition machine. The component's internal state is extracted from the input histories using a history abstraction function. Altogether, we explicate a formal method how to refine a specified infinite input/output behaviour of a communicating component by a state transition machine in the setting of almost synchronous streams.
The optimal transformation of one tree into another by means of elementary edit operations is an important algorithmic problem that has several interesting applications to computational biology. Here, we introduce a c...
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The optimal transformation of one tree into another by means of elementary edit operations is an important algorithmic problem that has several interesting applications to computational biology. Here, we introduce a constrained form of this problem in which a partial mapping of a set of nodes (the "seeds") in one tree to a corresponding set of nodes in the other tree is given, and present efficient algorithms for both ordered and unordered trees. Whereas ordered tree matching based on seeded nodes has applications in pattern matching of RNA structures, unordered tree matching based on seeded nodes has applications in cospeciation and phylogeny reconciliation. The latter involves the solution of the planar tanglegram layout problem, for which a polynomial-time algorithm is given here.
This paper shows how the agility provided by the Bio-jETI platform helps to interactively design bioinformatics analysis processes. Bio-jETI is a platform for the integration, orchestration and provision of services. ...
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ISBN:
(纸本)9783540794493
This paper shows how the agility provided by the Bio-jETI platform helps to interactively design bioinformatics analysis processes. Bio-jETI is a platform for the integration, orchestration and provision of services. The agility in design and execution is demonstrated by developing seven variations on a multiple sequence alignment workflow.
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