Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes

Margaria, Tiziana; Kubczak, Christian; Steffen, Bernhard

doi:10.1186/1471-2105-9-s4-s12

Cited by 46 publications

(24 citation statements)

References 19 publications

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“…Model checking can be undertaken using temporal logic properties. Bio-jETI (Bioinformatics Java Electronic Tool Integration [24]) makes use of jABC to create bioinformatics workflows that are designed graphically and can be verified through model checking. The work in this article shares a common interest in formal methods, though the work also supports formally based validation in addition to formal verification.…”

Section: Computational Workflowsmentioning

confidence: 99%

Workflows for quantitative data analysis in the social sciences

Turner

Lambert

2014

Int J Softw Tools Technol Transfer

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The background is given to how statistical analysis is used by quantitative social scientists. Developing statistical analyses requires substantial effort, yet there are important limitations in current practice. This has motivated the authors to create a more systematic and effective methodology with supporting tools. The approach to modelling quantitative data analysis in the social sciences is presented. Analysis scripts are treated abstractly as mathematical functions and concretely as web services. This allows individual scripts to be combined into high-level workflows. A comprehensive set of tools allows workflows to be defined, automatically validated and verified, and automatically implemented. The workflows expose opportunities for parallel execution, can define support for proper fault handling, and can be realised by non-technical users. Services, workflows and datasets can also be readily shared. The approach is illustrated with a realistic case study that analyses occupational position in relation to health.

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Section: Computational Workflowsmentioning

confidence: 99%

Workflows for quantitative data analysis in the social sciences

Turner

Lambert

2014

Int J Softw Tools Technol Transfer

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“…All of them are model-driven and service oriented, and use the jABC framework [4,20] for design, composition, and execution of the mediator and the jETI [8,13] technology for the integration and enactment of (a) remote planners/model generation tools and (b) remote heterogeneous services.…”

Section: Profile Of the Jabc-based Solutionsmentioning

confidence: 99%

Evolution support in heterogeneous service-oriented landscapes

2010

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We present an approach that provides automatic or semi-automatic support for evolution and change management in heterogeneous legacy landscapes where (1) legacy heterogeneous, possibly distributed platforms are integrated in a service oriented fashion, (2) the coordination of functionality is provided at the service level, through orchestration, (3) compliance and correctness are provided through policies and business rules, (4) evolution and correctness-by-design are supported by the eXtreme Model Driven Development paradigm (XMDD) offered by the jABC (Margaria and Steffen in Annu. Rev. Commun. 57, 2004)-the model-driven service oriented development platform we use here for integration, design, evolution, and governance. The artifacts are here semantically enriched, so that automatic synthesis plugins can field the vision of Enterprise Physics: knowledge driven business process development for the end user.We demonstrate this vision along a concrete case study that became over the past three years a benchmark for Semantic Web Service discovery and mediation. We enhance the Mediation Scenario of the Semantic Web Service Challenge along the 2 central evolution paradigms that occur in practice: (a) Platform migration: platform substitution of a T. Margaria ( ) Chair legacy system by an ERP system and (b) Backend extension: extension of the legacy Customer Relationship Management (CRM) and Order Management System (OMS) backends via an additional ERP layer.

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“…Several application domains have been successfully covered with the jABC, including complex supply chain management with IKEA [HMM + 08], modeling and execution of bioinformatics workflows [MKS07], the Semantic Web Service challenge [KMSN08], dataflow analysis of Java programs [LMS06a], a management framework for remote intelligent configuration of systems [BM06], online decision support systems [KM06] and graphical construction of game strategies [BJM09]. These projects were very different in nature, nevertheless we observed a surprisingly high potential of synergy, which was due to the XMDD approach.…”

Section: The Jabc Frameworkmentioning

confidence: 99%

Assuring property conformance of code generators via model checking

2011

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Abstract. Automatic code generation is an essential cornerstone of today's model-driven approaches to software engineering. Thus a key requirement for the success of this technique is the reliability and correctness of code generators. This article describes how we employ standard model checking-based verification to check that code generator models developed within our code generation framework Genesys conform to (temporal) properties. Genesys is a graphical framework for the high-level construction of code generators on the basis of an extensible library of well-defined building blocks along the lines of the Extreme Model-Driven Development (XMDD) paradigm. We will illustrate our verification approach by examining complex constraints for code generators, which even span entire model hierarchies. We also show how this leads to a knowledge base of rules for code generators, which we constantly extend by e.g. combining constraints to bigger constraints, or by deriving common patterns from structurally similar constraints. In our experience, the development of code generators with Genesys boils down to re-instantiating patterns or slightly modifying the graphical process model, activities which are strongly supported by verification facilities presented in this article.

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Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes

Abstract: Background: With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms for an LC/MS analysis of FAAH gene knockout.

Cited by 46 publications

References 19 publications

Workflows for quantitative data analysis in the social sciences

Workflows for quantitative data analysis in the social sciences

Evolution support in heterogeneous service-oriented landscapes

Assuring property conformance of code generators via model checking

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