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BackgroundMore than in other domains the heterogeneous services world in bioinformatics demands for a methodology to classify and relate resources in a both human and machine accessible manner. The Semantic Web, which is meant to address exactly this challenge, is currently one of the most ambitious projects in computer science. Collective efforts within the community have already led to a basis of standards for semantic service descriptions and meta-information. In combination with process synthesis and planning methods, such knowledge about types and services can facilitate the automatic composition of workflows for particular research questions.ResultsIn this study we apply the synthesis methodology that is available in the Bio-jETI workflow management framework for the semantics-based composition of EMBOSS services. EMBOSS (European Molecular Biology Open Software Suite) is a collection of 350 tools (March 2010) for various sequence analysis tasks, and thus a rich source of services and types that imply comprehensive domain models for planning and synthesis approaches. We use and compare two different setups of our EMBOSS synthesis domain: 1) a manually defined domain setup where an intuitive, high-level, semantically meaningful nomenclature is applied to describe the input/output behavior of the single EMBOSS tools and their classifications, and 2) a domain setup where this information has been automatically derived from the EMBOSS Ajax Command Definition (ACD) files and the EMBRACE Data and Methods ontology (EDAM). Our experiments demonstrate that these domain models in combination with our synthesis methodology greatly simplify working with the large, heterogeneous, and hence manually intractable EMBOSS collection. However, they also show that with the information that can be derived from the (current) ACD files and EDAM ontology alone, some essential connections between services can not be recognized.ConclusionsOur results show that adequate domain modeling requires to incorporate as much domain knowledge as possible, far beyond the mere technical aspects of the different types and services. Finding or defining semantically appropriate service and type descriptions is a difficult task, but the bioinformatics community appears to be on the right track towards a Life Science Semantic Web, which will eventually allow automatic service composition methods to unfold their full potential.

Abstract. Loose programming is an extension to graphical process modeling that is tailored to automatically complete underspecified (loose) models using a combination of data-flow analysis and LTL synthesis. In this tool demonstration we present PROPHETS 1 , our current implementation of the loose programming concept. The first part of the demonstration focuses on the preparative domain modeling, where a domain expert annotates the available services with semantic (ontological) information. The second part is then concerned with the actual loose programming, where a process modeler orchestrates the services without having to care about technical details like correct typing, interface compatibility, or platform-specific details. The orchestrated process skeletons are treated as loose service orchestrations that are automatically completed to running applications.

Background: The development of bioinformatics databases, algorithms, and tools throughout the last years has lead to a highly distributed world of bioinformatics services. Without adequate management and development support, in silico researchers are hardly able to exploit the potential of building complex, specialized analysis processes from these services. The Semantic Web aims at thoroughly equipping individual data and services with machine-processable meta-information, while workflow systems support the construction of service compositions. However, even in this combination, in silico researchers currently would have to deal manually with the service interfaces, the adequacy of the semantic annotations, type incompatibilities, and the consistency of service compositions.

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.

Abstract. Building applications based on the reuse of existing components or services has noticeably increased in the geospatial application domain, but researchers still face a variety of technical challenges designing workflows for their specific objectives and preferences. Hence, means for automatic service composition that provide semantics-based assistance in the workflow design process have become a frequent demand especially of end users who are not IT experts. This paper presents a method for automatic composition of workflows for analyzing the impacts of sea-level rise based on semantic domain modeling. The domain modeling comprises the design of adequate services, the definition of ontologies to provide domain-specific vocabulary for referring to types and services, and the input/output annotation of the services using the terms defined in the ontologies. We use the PROPHETS plugin of the jABC workflow framework to show how users can benefit from such a domain model when they apply its constraintsdriven synthesis methods to obtain the workflows that match their intentions.

Abstract. This paper describes how the jABC, a generic framework for library-based program development, and two of its plugins -the Model Checker and a flow graph converter -form a framework for intraprocedural data-flow analysis via model checking. Based on functionalities provided by the Soot program analysis platform, the converter generates graph structures from Java classes. Data flow analyses are then expressed as formulas in the modal µ-calculus. Executing the analysis is carried out by checking the validity of the formulas on the flow graph.The tool demonstration will illustrate the interplay of the involved components, which elegantly provides a fully integrated implementation of Data-Flow Analysis as Model Checking in a software development environment.

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