Anna-Lena Lamprecht

Semantics-based composition of EMBOSS services

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.

Loose programming with PROPHETS

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, 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.

GeneFisher-P: variations of GeneFisher as processes in Bio-jETI

BackgroundPCR 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.ResultsWithin Bio-jETI, we model the process using the jABC framework, a mature model-driven, service-oriented process definition platform. We encapsulate remote legacy tools and integrate web services using jETI, an extension of the jABC for seamless integration of remote resources as basic services, ready to be used in the process. Some of the basic services used by GeneFisher are in fact already provided as individual web services at BiBiServ and can be directly accessed. Others are legacy programs, and are made available to Bio-jETI via the jETI technology.The full power of service-based process orientation is required when more bioinformatics tools, available as web services or via jETI, lead to easy extensions or variations of the basic process. This concerns for instance variations of data retrieval or alignment tools as provided by the European Bioinformatics Institute (EBI).ConclusionsThe resulting service- and process-oriented GeneFisher-P demonstrates how basic services from heterogeneous sources can be easily orchestrated in the Bio-jETI platform and lead to a flexible family of specialized processes tailored to specific tasks.

Synthesis-Based Loose Programming

In this paper we present loose programming, an approach designed to enable process developers to design their application-specific processes in an intuitive style. Key to this approach is the concept of loose specification, a graphical formalism that allows developers to express their processes just by sketching them as kinds of flow graphs without caring about types, precise knowledge about the available process components or the availability of resources. They only have to specify the rough process flow graphically in terms of ontologically defined `semantic entities. These loose specifications are then concretized to fully executable process code automatically by means of a combination of 1) data-flow analysis, ensuring the availability of the required resources, 2) temporal logic-based process synthesis, resolving type conflicts and taking care of correct component instantiation, and 3) model checking, to ensure global intents and invariants expressed in temporal logic.

Seven variations of an alignment workflow: an illustration of agile process design and management in bio-jETI

This paper shows how the agility provided by the Bio-jETI platform helps to interactively design bioinformatics analysis processes.Bio-jETI is a platform for the integration, orchestration and provision ofservices. The agility in design and execution is demonstrated by developingseven variations on a multiple sequence alignment workflow.

A constraint-based variability modeling framework

Constraint-based variability modeling is a flexible, declarative approach to managing solution-space variability. Product variants are defined in a top-down manner by successively restricting the admissible combinations of product artifacts until a specific product variant is determined. In this paper, we illustrate the range of constraint-based variability modeling by discussing two of its extreme flavors: constraint-guarded variability modeling and constraint-driven variability modeling. The former applies model checking to establish the global consistency of product variants which are built by manual specification of variations points, whereas the latter uses synthesis technology to fully automatically generate product variants that satisfy all given constraints. Each flavor is illustrated by means of a concrete case study.

User-Level Workflow Design

Just as driving a car needs no engineer, steering a computer should need no programmer and the development of user-specific software should be in the hands of the user. Service-oriented and model-based approaches have become the methods of choice for user-centric development of variant-rich workflows in many application domains. Formal methods can be integrated to further support the workflow development process at different levels. Particularly effective with regard to user-level workflow design are constraint-based methods, where the key role of constraints is to capture intents about the developed applications in the user’s specific domain language. This book follows the loose programming paradigm, a novel approach to user-level workflow design, which makes essential use of constraint-driven workflow synthesis : Constraints provide high-level, declarative descriptions of individual components and entire workflows. Process synthesis techniques are then used to automatically translate the high-level specifications into concrete workflows that conform to the constraints by design. Loose programming is moreover characterized by its unique holistic perspective on workflow development: being fully integrated into a mature process development framework, it profits seamlessly from the availability of various already established features and methods. In this book, the applicability of this framework is evaluated with a particular focus on the bioinformatics application domain. For this purpose, the first reference implementation of the loose programming paradigm is applied to a series of real-life bioinformatics workflow scenarios, whose different characteristics allow for a detailed evaluation of the features, capabilities, and limitations of the approach. The applications show that the proposed approach to constraint-driven design of variant-rich workflows enables the user to effectively create and manage software processes in his specific domain language and frees him from dealing with the technicalities of the individual services and their composition. Naturally, the quality of the synthesis solutions crucially depends on the provided domain model and on the applied synthesis strategy and constraints.

Process Design for Natural Scientists

A major part of the scientific experiments that are carried out today requires thorough computational support. While database and algorithm providers face the problem of bundling resources to create and sustain powerful computation nodes, the users have to deal with combining sets of (remote) services into specific data analysis and transformation processes. Today’s attention to “big data” amplifies the issues of size, heterogeneity, and process-level diversity/integration. In the last decade, especially workflow-based approaches to deal with these processes have enjoyed great popularity. This book concerns a particularly agile and model-driven approach to manage scientific workflows that is based on the XMDD paradigm. In this chapter we explain the scope and purpose of the book, briefly describe the concepts and technologies of the XMDD paradigm, explain the principal differences to related approaches, and outline the structure of the book.

Simplicity-first model-based plug-in development

In this article, we present our experience with over a decade of strict simplicity orientation in the development and evolution of plug‐ins. The point of our approach is to enable our graphical modeling framework jABC to capture plug‐in development in a domain‐specific setting. The typically quite tedious and technical plug‐in development is shifted this way from a programming task to the modeling level, where it can be mastered also by application experts without programming expertise. We show how the classical plug‐in development profits from a systematic domain‐specific API design and how the level of abstraction achieved this way can be further enhanced by defining adequate building blocks for high‐level plug‐in modeling. As the resulting plug‐in models can be compiled and deployed automatically, our approach decomposes plug‐in development into three phases where only the realization phase requires plug‐in‐specific effort. By using our modeling framework jABC, this effort boils down to graphical, tool‐supported process modeling. Furthermore, we support the automatic completion of process sketches for executability. All this will be illustrated along the most recent plug‐in‐based evolution of the jABC framework, which witnessed quite some bootstrapping effects. Copyright

Variability Management beyond Feature Models

When new customer and regulatory requirements arise, the ability to quickly adapt business information system processes is crucial to stay ahead of competitors. A proposed synthesis-based framework enables the development of business processes that automatically yield fully executable variants.