004 Datenverarbeitung; Informatik
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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.
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.
Software maintenance encompasses any changes made to a software system after its initial deployment and is thereby one of the key phases in the typical software-engineering lifecycle. In software maintenance, we primarily need to understand structural and behavioral aspects, which are difficult to obtain, e.g., by code reading. Software analysis is therefore a vital tool for maintaining these systems: It provides - the preferably automated - means to extract and evaluate information from their artifacts such as software structure, runtime behavior, and related processes. However, such analysis typically results in massive raw data, so that even experienced engineers face difficulties directly examining, assessing, and understanding these data. Among other things, they require tools with which to explore the data if no clear question can be formulated beforehand. For this, software analysis and visualization provide its users with powerful interactive means. These enable the automation of tasks and, particularly, the acquisition of valuable and actionable insights into the raw data. For instance, one means for exploring runtime behavior is trace visualization. This thesis aims at extending and improving the tool set for visual software analysis by concentrating on several open challenges in the fields of dynamic and static analysis of software systems. This work develops a series of concepts and tools for the exploratory visualization of the respective data to support users in finding and retrieving information on the system artifacts concerned. This is a difficult task, due to the lack of appropriate visualization metaphors; in particular, the visualization of complex runtime behavior poses various questions and challenges of both a technical and conceptual nature. This work focuses on a set of visualization techniques for visually representing control-flow related aspects of software traces from shared-memory software systems: A trace-visualization concept based on icicle plots aids in understanding both single-threaded as well as multi-threaded runtime behavior on the function level. The concept’s extensibility further allows the visualization and analysis of specific aspects of multi-threading such as synchronization, the correlation of such traces with data from static software analysis, and a comparison between traces. Moreover, complementary techniques for simultaneously analyzing system structures and the evolution of related attributes are proposed. These aim at facilitating long-term planning of software architecture and supporting management decisions in software projects by extensions to the circular-bundle-view technique: An extension to 3-dimensional space allows for the use of additional variables simultaneously; interaction techniques allow for the modification of structures in a visual manner. The concepts and techniques presented here are generic and, as such, can be applied beyond software analysis for the visualization of similarly structured data. The techniques' practicability is demonstrated by several qualitative studies using subject data from industry-scale software systems. The studies provide initial evidence that the techniques' application yields useful insights into the subject data and its interrelationships in several scenarios.
Process models specify behavioral execution constraints between activities as well as between activities and data objects. A data object is characterized by its states and state transitions represented as object life cycle. For process execution, all behavioral execution constraints must be correct. Correctness can be verified via soundness checking which currently only considers control flow information. For data correctness, conformance between a process model and its object life cycles is checked. Current approaches abstract from dependencies between multiple data objects and require fully specified process models although, in real-world process repositories, often underspecified models are found. Coping with these issues, we introduce the concept of synchronized object life cycles and we define a mapping of data constraints of a process model to Petri nets extending an existing mapping. Further, we apply the notion of weak conformance to process models to tell whether each time an activity needs to access a data object in a particular state, it is guaranteed that the data object is in or can reach the expected state. Then, we introduce an algorithm for an integrated verification of control flow correctness and weak data conformance using soundness checking.
Geometric generalization is a fundamental concept in the digital mapping process. An increasing amount of spatial data is provided on the web as well as a range of tools to process it. This jABC workflow is used for the automatic testing of web-based generalization services like mapshaper.org by executing its functionality, overlaying both datasets before and after the transformation and displaying them visually in a .tif file. Mostly Web Services and command line tools are used to build an environment where ESRI shapefiles can be uploaded, processed through a chosen generalization service and finally visualized in Irfanview.
Moderne Kraftfahrzeuge verfügen über eine Vielzahl an Sensoren, welche für einen reibungslosen technischen Betrieb benötigt werden. Hierzu zählen neben fahrzeugspezifischen Sensoren (wie z.B. Motordrehzahl und Fahrzeuggeschwindigkeit) auch umweltspezifische Sensoren (wie z.B. Luftdruck und Umgebungstemperatur). Durch die zunehmende technische Vernetzung wird es möglich, diese Daten der Kraftfahrzeugelektronik aus dem Fahrzeug heraus für die verschiedensten Zwecke zu verwenden.
Die vorliegende Arbeit soll einen Beitrag dazu leisten, diese neue Art an massenhaften Daten im Sinne des Konzepts der „Extended Floating Car Data“ (XFCD) als Geoinformationen nutzbar zu machen und diese für raumzeitliche Visualisierungen (zur visuellen Analyse) anwenden zu können. In diesem Zusammenhang wird speziell die Perspektive des Umwelt- und Verkehrsmonitoring betrachtet, wobei die Anforderungen und Potentiale mit Hilfe von Experteninterviews untersucht werden. Es stellt sich die Frage, welche Daten durch die Kraftfahrzeugelektronik geliefert und wie diese möglichst automatisiert erfasst, verarbeitet, visualisiert und öffentlich bereitgestellt werden können. Neben theoretischen und technischen Grundlagen zur Datenerfassung und -nutzung liegt der Fokus auf den Methoden der kartographischen Visualisierung. Dabei soll der Frage nachgegangenen werden, ob eine technische Implementierung ausschließlich unter Verwendung von Open Source Software möglich ist. Das Ziel der Arbeit bildet ein zweigliedriger Ansatz, welcher zum einen die Visualisierung für ein exemplarisch gewähltes Anwendungsszenario und zum anderen die prototypische Implementierung von der Datenerfassung im Fahrzeug unter Verwendung der gesetzlich vorgeschriebenen „On Board Diagnose“-Schnittstelle und einem Smartphone-gestützten Ablauf bis zur webbasierten Visualisierung umfasst.
The term Linked Data refers to connected information sources comprising structured data about a wide range of topics and for a multitude of applications. In recent years, the conceptional and technical foundations of Linked Data have been formalized and refined. To this end, well-known technologies have been established, such as the Resource Description Framework (RDF) as a Linked Data model or the SPARQL Protocol and RDF Query Language (SPARQL) for retrieving this information. Whereas most research has been conducted in the area of generating and publishing Linked Data, this thesis presents novel approaches for improved management. In particular, we illustrate new methods for analyzing and processing SPARQL queries. Here, we present two algorithms suitable for identifying structural relationships between these queries. Both algorithms are applied to a large number of real-world requests to evaluate the performance of the approaches and the quality of their results. Based on this, we introduce different strategies enabling optimized access of Linked Data sources. We demonstrate how the presented approach facilitates effective utilization of SPARQL endpoints by prefetching results relevant for multiple subsequent requests. Furthermore, we contribute a set of metrics for determining technical characteristics of such knowledge bases. To this end, we devise practical heuristics and validate them through thorough analysis of real-world data sources. We discuss the findings and evaluate their impact on utilizing the endpoints. Moreover, we detail the adoption of a scalable infrastructure for improving Linked Data discovery and consumption. As we outline in an exemplary use case, this platform is eligible both for processing and provisioning the corresponding information.
Analyses of metagenomes in life sciences present new opportunities as well as challenges to the scientific community and call for advanced computational methods and workflows. The large amount of data collected from samples via next-generation sequencing (NGS) technologies render manual approaches to sequence comparison and annotation unsuitable. Rather, fast and efficient computational pipelines are needed to provide comprehensive statistics and summaries and enable the researcher to choose appropriate tools for more specific analyses. The workflow presented here builds upon previous pipelines designed for automated clustering and annotation of raw sequence reads obtained from next-generation sequencing technologies such as 454 and Illumina. Employing specialized algorithms, the sequence reads are processed at three different levels. First, raw reads are clustered at high similarity cutoff to yield clusters which can be exported as multifasta files for further analyses. Independently, open reading frames (ORFs) are predicted from raw reads and clustered at two strictness levels to yield sets of non-redundant sequences and ORF families. Furthermore, single ORFs are annotated by performing searches against the Pfam database