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Biological LC/MS preprocessing and analysis with jABC, jETI and xcms

Biological LC/MS preprocessing and analysis with jABC, jETI ...

引用

2nd International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, ISoLA 2006

作者： Kubczak, Christian Margaria, Tiziana Fritsch, Arno Steffen, Bernhard Department of Software Engineering University of Dortmund Germany Department of Service and Software Engineering University of Potsdam Germany Department of Mathematical Statistics and Biometric Applications University of Dortmund Germany Department of Programming Systems University of Dortmund Germany

ISBN: (纸本)0769530710

LC/MS is a successful analysis technique for the statistical analysis used in several branches of biology. It requires an intense screening and combination of the raw data, which is usually done with programs and libraries invoked by scripts in the domain-specific statistics language S or R. We show here how to model and implement this complex workflow in a service-oriented fashion, using the jABC service definition environment and jETI for remote service integration and execution. © 2007 IEEE.

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FormulaBuilder: A tool for graph-based modelling and generation of formulae

FormulaBuilder: A tool for graph-based modelling and generat...

引用

28th International Conference on software engineering 2006, ICSE '06

作者： Jörges, Sven Margaria, Tiziana Steffen, Bernhard Department of Programming Systems Otto-Hahn-Str. 14 44227 Dortmund Germany Department of Service and Software Engineering August-Bebel-Str. 89 14482 Potsdam

ISBN: (纸本)1595933751

In this paper we present the FormulaBuilder, a flexible tool for graph-based modelling and generation of formulae. The FormulaBuilder allows easy and intuitive creation of formulae by using basic components called Formula Building Blocks (FBBs) and arranging them as graphs according to the syntactic structure of a formula. Such a graph can then be validated and used to generate the corresponding formula on the basis of a specific syntax which is chosen from a list of syntaxes supported by the FormulaBuilder. An important application of the FormulaBuilder is the formal specification of properties that describe the requirements of a system. Such property specifications are usually needed by verification tools like model checkers, that help software engineers to detect errors in a specified system. The FormulaBuilder allows users to model property specifications as formula graphs by using commonly-occurring specification patterns.

关键词： Computer aided software engineering

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The FMICS-jETI platform: Status and perspectives

The FMICS-jETI platform: Status and perspectives

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2nd International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, ISoLA 2006

作者： Margaria, Tiziana Kubczak, Christian Steffen, Bernhard Naujokat, Stefan Department of Service and Software Engineering Universität Potsdam August Bebel Str. 89 14482 Potsdam Germany Department of Software Engineering Universität Dortmund Otto-Hahn-Str. 14 44227 Dortmund Germany Department of Programming Systems Universität Dortmund Otto-Hahn-Str. 14 44227 Dortmund Germany

ISBN: (纸本)0769530710

One of the goals of FMICS, the ERCIM Working Group on Formal Methods for Industrial Critical Systems (FMICS) [8], is to transfer and promote the use formal methods technology in industry. The ongoing Verified software Repository Grand Challenge [11] offers a great opportunity to reach this goal, resulting in a more robust and solid software industry in Europe. We demonstrate here the current status of the FMICS-jETI platform1, a collaborative demonstrator based on the jETI technology2, that provides as repository a collection of verification tools stemming from the activities of the FMICS working group and facilities to orchestrate them in a remote and simple way. At the same time FMICS-jETI itself is a contribution to the VSR repository and thus to the Grand Challenge. © 2007 IEEE.

关键词： Formal methods

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Modeling aspect-oriented compositions

引用

MoDELS 2005 International Workshops OCLWS, MoDeVA, MARTES, AOM, MTiP, WiSME, MODAUI, NfC, MDD, WUsCAM

作者： Cottenier, Thomas Van Berg, Aswin Den Elrad, Tzilla Software and Systems Engineering Research Motorola Labs 1300 E Algonquin Road Schaumburg IL 60173 United States Concurrent Programming Research Group Illinois Institute of Technology 3300 S Federal Street Chicago IL 60616 United States

ISBN: (纸本)3540317805

Crosscutting concerns are pervasive in embedded software, because of the various constraints imposed by the environment and the stringent QoS requirements on the system. This paper presents a framework for modularizing crosscutting concerns in embedded and distributed software, and automating their composition at the modeling level, for simulation and validation purposes. The proposed approach does not extend the semantics of the UML in order to represent aspects. Rather, it dedicates a metamodel to the representation of the composition semantics between aspects and core models. The paper illustrates this approach by presenting a model weaver for SDL statecharts developed at Motorola Labs. Crosscutting behavior is designed with plain SDL statecharts and encapsulated into modules called aspect beans. The weaver looks at the aspect beans and the core SDL statecharts from a perspective that is defined by lightweight extensions to the SDL and UML metamodels. A connector metamodel defines the structure of the aspect-to-core binding definition. Finally, a weaver behavioral metamodel defines composition primitives for specifying weaving strategies. © Springer-Verlag Berlin Heidelberg 2006.

关键词： Object oriented programming

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A Web-Based Runtime-Reconfigurable Role Management Service

A Web-Based Runtime-Reconfigurable Role Management Service

引用

International Workshop on Automated Specification and Verification of Web Systems, WWV

作者： Martin Karusseit Tiziana Margaria Chair of Programming Systems Universität Dortmund Germany Chair of Service and Software Engineering Universität Postdam Germany

Today Web-based applications are very complex and provide several hundred users with access to sensible data. Adequate access control mechanisms that prevent unauthorized access and gives policy-compliant access to users depending on their status are thus central. The online conference service (OCS) is a system of services which collectively provide all necessary workflows and functionalities an online decision support service needs. Here we describe its flexible role-based access control mechanism and introduce the embedded role management service, which is extensible, modifiable and reconfigurable online, during the service operations. We also discuss a first version of the personalized role management service as used in the OJS, the journal member of the product line initiated by the OCS

关键词： Conference management Access control Logic design Collaboration Switches engineering management software engineering Application software Computer science Control system synthesis

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The FMICS-jETI Platform: Status and Perspectives

The FMICS-jETI Platform: Status and Perspectives

引用

International Symposium on Leveraging Applications of Formal Methods, Verification and Validation ( ISoLA)

作者： Tiziana Margaria Christian Kubczak Bernhard Steffen Stefan Naujokat Chair of Service and Software Engineering Universität Postdam Potsdam Germany Chair of Software Engineering Universität Dortmund Dortmund Germany Chair of Programming Systems Universität Dortmund Dortmund Germany

One of the goals of FMICS, the ERCIM Working Group on Formal Methods for Industrial Critical Systems (FMICS) [8], is to transfer and promote the use formal methods technology in industry. The ongoing Verified software Repository Grand Challenge [11] offers a great opportunity to reach this goal, resulting in a more robust and solid software industry in Europe. We demonstrate here the current status of the FMICS-jETIplatform1, a collaborative demonstrator based on the jETI technology2, that provides as repository a collection of verification tools stemming from the activities of the FMICS working group and facilities to orchestrate them in a remote and simple way. At the same time FMICS-jETI itself is a contribution to the VSR repository and thus to the Grand Challenge.

关键词： software tools Application software Computer industry Testing software engineering Collaborative tools Collaborative software Robustness Solids Europe

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Biological LC/MS Preprocessing and Analysis with jABC, jETI and xcms

Biological LC/MS Preprocessing and Analysis with jABC, jETI ...

引用

International Symposium on Leveraging Applications of Formal Methods, Verification and Validation ( ISoLA)

作者： Christian Kubczak Tiziana Margaria Arno Fritsch Bernhard Steffen Chair of Software Engineering University of Dortmund Germany Chair of Service and Software Engineering University of Potsdam Germany Chair of Mathematical Statistics and Biometric Applications University of Dortmund Germany Chair of Programming Systems University of Dortmund Germany

关键词： Statistical analysis Biological system modeling Proteins Mice Mass spectroscopy Proteomics Application software software engineering Performance analysis Biometrics

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Model-based design of distributed collaborative bioinformatics processes in the jABC

Model-based design of distributed collaborative bioinformati...

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IEEE International Conference on engineering of Complex Computer Systems

作者： T. Margaria C. Kubczak M. Njoku B. Steffen Chair Servce and Software Engineering University of Potsdam Potsdam Germany Chair of Programming Systems University of Dortmund Dortmund Germany Chair of Service Engineering for Distributed Systems University of Göttingen Gottingen Germany

Our approach to the model-driven collaborative design of workflows for bioinformatic applications uses the jABC for model driven mediation and choreography to complement a Web service-based elementary service provision. jABC is a framework for service development based on lightweight process coordination. Users (product developers and system/software designers) 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 processes has proven to be effective and adequate for the cooperation of non-programmers (in this case biologists) and technical people, and it is now being rolled out in the operative practice

关键词： Collaboration Bioinformatics Collaborative work Application software Mediation software reusability software systems software design Animation Biological system modeling

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Generating optimal distinguishing sequences with a model checker

Generating optimal distinguishing sequences with a model che...

引用

1st International Workshop on Advances in Model-Based Testing, A-MOST '05

作者： Robinson-Mallett, Christopher Liggesmeyer, Peter Mücke, Tilo Goltz, Ursula University of Potsdam Hasso-Plattner-Institute Software Engineering Germany University of Kaiserslautern Fraunhofer IESE Germany University of Brunswick Institute for Programming and Reactive Systems Germany

ISBN: (纸本)1595931155

This paper presents an approach for the automatic generation of shortest Distinguishing Sequences (DS) with the Uppaal model checker. The presented method is applicable to a large number of extended finite state machines and it will find an optimal result, if a DS sequence exists for the considered automaton. Our approach is situated in an integrated testing environment that is used to generate checking sequences. The generation method is based on a DS model, which is derived from the same test model that is used for generating test cover sets. The problem of generating DS is reduced to the definition of a DS model and for this reason the complexity of our approach depends mainly on the used model checking algorithm. This means, that the presented method is automatically improved, when the model checking algorithm is improved. This includes the generation of optimal DS depending on the ability of the model checker to produce optimal results. Copyright 2005 ACM.

关键词： Model checking

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Role modelling in SelfSync with warped hierarchies

Role modelling in SelfSync with warped hierarchies

引用

2005 AAAI Fall Symposium

作者： Van Paesschen, Ellen De Meuter, Wolfgang D'Hondt, Maja Programming Technology Lab. Vrije Universiteit Brussel Pleinlaan 2 1050 Brussel System Software Engineering Lab. Vrije Universiteit Brussel Pleinlaan 2 1050 Brussel

ISBN: (纸本)1577352548

In object-oriented software engineering roles are considered both classifications and instances. To reduce the gap between the conceptual modelling of roles and a corresponding implementation, we propose a new role modelling concept based on warped inheritance hierarchies. We integrated this new modelling concept in our prototype-based object-oriented round-trip engineering environment SelfSync. In this way it is possible to model roles in an Extended Entity-Relationship diagram while the corresponding implementation objects are automatically created and synchronized with the conceptual model. We apply constraint enforcement during the lifetime of role objects, based on dependency and role combinations. Copyright © 2005, American Association for Artificial Intelligence (***). All rights reserved.

关键词： software engineering

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