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Computer Science - Software Engineering | User-Level Workflow Design - A Bioinformatics Perspective

User-Level Workflow Design

A Bioinformatics Perspective

Lamprecht, Anna-Lena

2013, XXII, 223 p. 84 illus.

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  • The application of user-level workflow design makes the approach accessible to users with almost no programming expertise
  • Describes four realistic application scenarios in bioinformatics
  • Paves the way for a novel way of scientific workflow modeling based on jABC framework
The continuous trend in computer science to lift programming to higher abstraction levels increases scalability and opens programming to a wider public. In particular, service-oriented programming and the support of semantics-based frameworks make application development accessible to users with almost no programming expertise. This monograph establishes requirement-centric scientific workflow design as an instance of consequent constraint-driven development. Requirements formulated in terms of user-level constraints are automatically transformed into running applications using temporal logic-based synthesis technology. The impact of this approach is illustrated by applying it to four very different bioinformatics scenarios: phylogenetic analysis, the dedicated GeneFisher-P scenario, the FiatFlux-P scenario, and microarray data analyses.

Content Level » Research

Keywords » EDAM ontology - bioinformatics - constraint-driven design - constraints - domain modeling - formal methods - jABC - jETI - loose programming - model checking - scientific workflows - workflow design

Related subjects » Bioinformatics - Database Management & Information Retrieval - Software Engineering - Theoretical Computer Science

Table of contents 

The Bio-jETI Framework.- Phylogenetic Analysis Workflows.- GeneFisher-P.- FiatFlux-P.- Microarray Data Analysis Pipelines.

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