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2013 | Buch

Introduction Kapitel lesen Erstes Kapitel lesen

User-Level Workflow Design

A Bioinformatics Perspective

herausgegeben von: Anna-Lena Lamprecht

Verlag: Springer Berlin Heidelberg

Buchreihe : Lecture Notes in Computer Science

Enthalten in: Springer Professional "Wirtschaft+Technik" , Springer Professional "Technik" , Springer Professional "Wirtschaft"

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Über dieses Buch

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.

Inhaltsverzeichnis

Frontmatter

Framework

Frontmatter
Introduction
Abstract
This book addresses the challenge of user-level workflow design with a particular focus on the bioinformatics application domain. Towards this aim, it follows a novel, constraint-driven approach to domain-specific design and management of variant-rich workflows and systematically evaluates its features based on a selection of bioinformatics application scenarios. This introductory chapter motivates the work (Section 1.1) and outlines the results and structure of this book (Sections 1.2 and 1.3, respectively).
Anna-Lena Lamprecht
The Bio-jETI Framework
Abstract
Bio-jETI [201, 174] is a comprehensive framework for management of variantrich bioinformatics workflows that has largely been conceived in the scope of this work. It is based on the jABC framework [306, 229] for model-driven, service-oriented workflow development. Providing comprehensive means for the design, execution and deployment of workflows, already the standard jABC framework covers the common aspects of workflow management.
Anna-Lena Lamprecht

Applications

Frontmatter
Phylogenetic Analysis Workflows
Abstract
This first example scenario is concerned with phylogenetic analyses. As they are comparatively easy to understand (also for non-biologists) and there is also a plethora of easy-to-use software tools available for the individual analysis steps, phylogenetic analyses have become a frequently used, quasistandard application for illustrating bioinformatics workflow technology (cf., e.g., [256, 134, 155, 265, 165]). Furthermore, the annotation with semantic meta-data is particularly advanced for this discipline [179], which is advantageous for the application of the constraint-driven workflow design methodology.
Anna-Lena Lamprecht
GeneFisher-P
Abstract
This second application scenario is based on the GeneFisher web application for PCR primer design [109, 124]. To provide a more flexible alternative to the monolithic web application, it has been realized as Bio-jETI workflow. With the resulting GeneFisher-P [177], workflow variants that are not covered by the web application, such as using alternative services for individual analysis steps or batch processing of input data sets, can easily be built at the user level.
Anna-Lena Lamprecht
FiatFlux-P
Abstract
This third application scenario is concerned with the automation of timeconsuming metabolic flux analysis procedures based on the software Fiat- Flux [353]. In addition to the integration of its principal functionality as elementary services, new services were implemented that emulate the user interaction with FiatFlux in order to enable automation. Like GeneFisher-P, the resulting FiatFlux-P facilitates building variants and defining batch processing workflows at the user level.
Anna-Lena Lamprecht
Microarray Data Analysis Pipelines
Abstract
This fourth and final example considered in this book deals with workflows for the analysis of microarray data based on the statistical methods provided by Bioconductor [105]. This kind of bioinformatics workflows is frequently referred to as data analysis “pipelines”, as they typically have a simple, in fact mostly linear, workflow structure, while the (often considerable) complexity of the individual analysis steps is encapsulated by the services. Consequently, the constraint-driven workflow composition functionality of the PROPHETS plugin, which is based on a linear-time logic synthesis algorithm, can conveniently be used for complete, start-to-end generation of the workflows.
Anna-Lena Lamprecht

Discussion

Frontmatter
Lessons Learned
Abstract
The application examples presented in Part II (Chapters 3 - 6) demonstrate that in silico experiments of different flavors can be realized with the BiojETI framework. They cover a broad range of typical bioinformatics workflow scenarios, concerned with different thematic areas, different software components, different service technologies, and also workflows of different complexity. They illustrate how the constraint-driven workflow development methodology helps mastering the manifold workflow variants and how PROPHETS’ ability to flexibly formulate domain-specific and problemspecific constraints supports the workflow development process. As such, the application scenarios provide on the one hand qualitative evidence of the method’s applicability on real-world application scenarios, and on the other hand they are suitable as a proper basis for further considerations about the applied workflow development technology. In this context, this chapter focuses specifically on the “lessons learned” regarding the constraint-driven workflow design methodology that has been introduced to the Bio-jETI framework in the scope of the work underlying this book.
Anna-Lena Lamprecht
Related Work
Abstract
Due to massive effort in tailoring workflow management systems towards the bioinformatics domain and the development of thoroughly specific systems in the last years, several frameworks that support service orchestration in bioinformatics are available today. They provide a wide range of different features, adding convenience for the user in different ways. This chapter discusses the relation of Bio-jETI to other approaches to bioinformatics workflow management. Therefore, Section 8 reviews a number of different bioinformatics workflow systems and compares them to Bio-jETI. Then, Section 8.2 takes a closer look at the substantial differences between the capabilities of controlflow and data-flow modeling: The nature of the data flow and control flow specifications is essential for the semantic interpretation of a workflow model, while other features are usually less inherent in the systems. The study is carried out by means of a detailed comparison of Bio-jETI and Taverna, two systems for bioinformatics workflow management that look very similar at the first glance, but are in fact very different precisely because they follow different paradigms for control-flow and data-flow modeling.
Anna-Lena Lamprecht
Conclusion
Abstract
This book has addressed the development of a framework for user-level workflow design, its application to different bioinformatics application scenarios, and the evaluation of the approach in itself and in comparison to related work. This chapter concludes by summarizing the work and clarifying achievements and major remaining challenges in Section 9.1, before outlining directives for future work in Section 9.2.
Anna-Lena Lamprecht
Backmatter
Metadaten
Titel
User-Level Workflow Design
herausgegeben von
Anna-Lena Lamprecht
Copyright-Jahr
2013
Verlag
Springer Berlin Heidelberg
Electronic ISBN
978-3-642-45389-2
Print ISBN
978-3-642-45388-5
DOI
https://doi.org/10.1007/978-3-642-45389-2

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