004 Datenverarbeitung; Informatik
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Lessons Learned
(2014)
This chapter summarizes the experience and the lessons we learned concerning the application of the jABC as a framework for design and execution of scientific workflows. It reports experiences from the domain modeling (especially service integration) and workflow design phases and evaluates the resulting models statistically with respect to the SIB library and hierarchy levels.
The Course's SIB Libraries
(2014)
This chapter gives a detailed description of the service framework underlying all the example projects that form the foundation of this book. It describes the different SIB libraries that we made available for the course “Process modeling in the natural sciences” to provide the functionality that was required for the envisaged applications. The students used these SIB libraries to realize their projects.
Background: The development of bioinformatics databases, algorithms, and tools throughout the last years has lead to a highly distributedworld of bioinformatics services. Without adequatemanagement 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. Results: In this paper, we demonstrate by means of two examples how Semantic Web technology together with an adequate domain modelling frees in silico researchers from dealing with interfaces, types, and inconsistencies. In Bio-jETI, bioinformatics services can be graphically combined to complex services without worrying about details of their interfaces or about type mismatches of the composition. These issues are taken care of at the semantic level by Bio-jETI’s model checking and synthesis features. Whenever possible, they automatically resolve type mismatches in the considered service setting. Otherwise, they graphically indicate impossible/incorrect service combinations. In the latter case, the workflow developermay either modify his service composition using semantically similar services, or ask for help in developing the missing mediator that correctly bridges the detected type gap. Newly developed mediators should then be adequately annotated semantically, and added to the service library for later reuse in similar situations. Conclusion: We show the power of semantic annotations in an adequately modelled and semantically enabled domain setting. Using model checking and synthesis methods, users may orchestrate complex processes from a wealth of heterogeneous services without worrying about interfaces and (type) consistency. The success of this method strongly depends on a careful semantic annotation of the provided services and on its consequent exploitation for analysis, validation, and synthesis. We are convinced that these annotations will become standard, as they will become preconditions for the success and widespread use of (preferred) services in the Semantic Web
We summarize here the main characteristics and features of the jABC framework, used in the case studies as a graphical tool for modeling scientific processes and workflows. As a comprehensive environment for service-oriented modeling and design according to the XMDD (eXtreme Model-Driven Design) paradigm, the jABC offers much more than the pure modeling capability. Associated technologies and plugins provide in fact means for a rich variety of supporting functionality, such as remote service integration, taxonomical service classification, model execution, model verification, model synthesis, and model compilation. We describe here in short both the essential jABC features and the service integration philosophy followed in the environment. In our work over the last years we have seen that this kind of service definition and provisioning platform has the potential to become a core technology in interdisciplinary service orchestration and technology transfer: Domain experts, like scientists not specially trained in computer science, directly define complex service orchestrations as process models and use efficient and complex domain-specific tools in a simple and intuitive way.
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.
Solving problems combining task and motion planning requires searching across a symbolic search space and a geometric search space. Because of the semantic gap between symbolic and geometric representations, symbolic sequences of actions are not guaranteed to be geometrically feasible. This compels us to search in the combined search space, in which frequent backtracks between symbolic and geometric levels make the search inefficient.We address this problem by guiding symbolic search with rich information extracted from the geometric level through culprit detection mechanisms.
In the early days of computer graphics, research was mainly driven by the goal to create realistic synthetic imagery. By contrast, non-photorealistic computer graphics, established as its own branch of computer graphics in the early 1990s, is mainly motivated by concepts and principles found in traditional art forms, such as painting, illustration, and graphic design, and it investigates concepts and techniques that abstract from reality using expressive, stylized, or illustrative rendering techniques. This thesis focuses on the artistic stylization of two-dimensional content and presents several novel automatic techniques for the creation of simplified stylistic illustrations from color images, video, and 3D renderings. Primary innovation of these novel techniques is that they utilize the smooth structure tensor as a simple and efficient way to obtain information about the local structure of an image. More specifically, this thesis contributes to knowledge in this field in the following ways. First, a comprehensive review of the structure tensor is provided. In particular, different methods for integrating the minor eigenvector field of the smoothed structure tensor are developed, and the superiority of the smoothed structure tensor over the popular edge tangent flow is demonstrated. Second, separable implementations of the popular bilateral and difference of Gaussians filters that adapt to the local structure are presented. These filters avoid artifacts while being computationally highly efficient. Taken together, both provide an effective way to create a cartoon-style effect. Third, a generalization of the Kuwahara filter is presented that avoids artifacts by adapting the shape, scale, and orientation of the filter to the local structure. This causes directional image features to be better preserved and emphasized, resulting in overall sharper edges and a more feature-abiding painterly effect. In addition to the single-scale variant, a multi-scale variant is presented, which is capable of performing a highly aggressive abstraction. Fourth, a technique that builds upon the idea of combining flow-guided smoothing with shock filtering is presented, allowing for an aggressive exaggeration and an emphasis of directional image features. All presented techniques are suitable for temporally coherent per-frame filtering of video or dynamic 3D renderings, without requiring expensive extra processing, such as optical flow. Moreover, they can be efficiently implemented to process content in real-time on a GPU.
A workflow for visualizing server connections using the Google Maps API was built in the jABC. It makes use of three basic services: An XML-based IP address geolocation web service, a command line tool and the Static Maps API. The result of the workflow is an URL leading to an image file of a map, showing server connections between a client and a target host.