TY - JOUR A1 - Vainshtein, Yevhen A1 - Sanchez, Mayka A1 - Brazma, Alvis A1 - Hentze, Matthias W. A1 - Dandekar, Thomas A1 - Muckenthaler, Martina U. T1 - The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays N2 - Background: Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. Results: The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls. Conclusions: ICEP is a stand-alone Windows application to obtain optimal data quality from custom-designed microarrays and is freely available here (see “Additional Files” section) and at: http://www.alice-dsl.net/evgeniy. vainshtein/ICEP/ KW - Microarray KW - ICEP KW - IronChip Evaluation Package Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-67869 ER - TY - THES A1 - Schlosser, Daniel T1 - Quality of Experience Management in Virtual Future Networks T1 - Netzwerkmanagement unter Berücksichtigung der vom Benutzer erfahrenen Dienstgüte in virtuellen zukünftigen Netzen N2 - Aktuell beobachten wir eine drastische Vervielfältigung der Dienste und Anwendungen, die das Internet für den Datentransport nutzen. Dabei unterscheiden sich die Anforderungen dieser Dienste an das Netzwerk deutlich. Das Netzwerkmanagement wird durch diese Diversität der nutzenden Dienste aber deutlich erschwert, da es einem Datentransportdienstleister kaum möglich ist, die unterschiedlichen Verbindungen zu unterscheiden, ohne den Inhalt der transportierten Daten zu analysieren. Netzwerkvirtualisierung ist eine vielversprechende Lösung für dieses Problem, da sie es ermöglicht für verschiedene Dienste unterschiedliche virtuelle Netze auf dem gleichen physikalischen Substrat zu betreiben. Diese Diensttrennung ermöglicht es, jedes einzelne Netz anwendungsspezifisch zu steuern. Ziel einer solchen Netzsteuerung ist es, sowohl die vom Nutzer erfahrene Dienstgüte als auch die Kosteneffizienz des Datentransports zu optimieren. Darüber hinaus wird es mit Netzwerkvirtualisierung möglich das physikalische Netz so weit zu abstrahieren, dass die aktuell fest verzahnten Rollen von Netzwerkbesitzer und Netzwerkbetreiber entkoppelt werden können. Darüber hinaus stellt Netzwerkvirtualisierung sicher, dass unterschiedliche Datennetze, die gleichzeitig auf dem gleichen physikalischen Netz betrieben werden, sich gegenseitig weder beeinflussen noch stören können. Diese Arbeit  beschäftigt sich mit ausgewählten Aspekten dieses Themenkomplexes und fokussiert sich darauf, ein virtuelles Netzwerk mit bestmöglicher Dienstqualität für den Nutzer zu betreiben und zu steuern. Dafür wird ein Top-down-Ansatz gewählt, der von den Anwendungsfällen, einer möglichen Netzwerkvirtualisierungs-Architektur und aktuellen Möglichkeiten der Hardwarevirtualisierung ausgeht. Im Weiteren fokussiert sich die Arbeit dann in Richtung Bestimmung und Optimierung der vom Nutzer erfahrenen Dienstqualität (QoE) auf Applikationsschicht und diskutiert Möglichkeiten zur Messung und Überwachung von wesentlichen Netzparametern in virtualisierten Netzen. N2 - Currently, we observe a strong growth of services and applications, which use the Internet for data transport. However, the network requirements of these applications differ significantly. This makes network management difficult, since it complicated to separate network flows into application classes without inspecting application layer data. Network virtualization is a promising solution to this problem. It enables running different virtual network on the same physical substrate. Separating networks based on the service supported within allows controlling each network according to the specific needs of the application. The aim of such a network control is to optimize the user perceived quality as well as the cost efficiency of the data transport. Furthermore, network virtualization abstracts the network functionality from the underlying implementation and facilitates the split of the currently tightly integrated roles of Internet Service Provider and network owner. Additionally, network virtualization guarantees that different virtual networks run on the same physical substrate do not interfere with each other. This thesis discusses different aspects of the network virtualization topic. It is focused on how to manage and control a virtual network to guarantee the best Quality of Experience for the user. Therefore, a top-down approach is chosen. Starting with use cases of virtual networks, a possible architecture is derived and current implementation options based on hardware virtualization are explored. In the following, this thesis focuses on assessing the Quality of Experience perceived by the user and how it can be optimized on application layer. Furthermore, options for measuring and monitoring significant network parameters of virtual networks are considered. T3 - Würzburger Beiträge zur Leistungsbewertung Verteilter Systeme - 01/12 KW - Netzwerkmanagement KW - Dienstgüte KW - Netzwerkvirtualisierung KW - QoS KW - QoE KW - Network Virtualization KW - Quality of Experience KW - Network Management KW - Quality of Service Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-69986 ER - TY - INPR A1 - Nassourou, Mohamadou T1 - Towards a Knowledge-Based Learning System for The Quranic Text N2 - In this research, an attempt to create a knowledge-based learning system for the Quranic text has been performed. The knowledge base is made up of the Quranic text along with detailed information about each chapter and verse, and some rules. The system offers the possibility to study the Quran through web-based interfaces, implementing novel visualization techniques for browsing, querying, consulting, and testing the acquired knowledge. Additionally the system possesses knowledge acquisition facilities for maintaining the knowledge base. KW - Wissensbanksystem KW - Wissensmanagement KW - Text Mining KW - Visualisierung KW - Koran KW - Knowledge-based System KW - Knowledge Management System KW - Text Mining KW - Visualization KW - Quran Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-70003 ER - TY - INPR A1 - Nassourou, Mohamadou T1 - Computing Generic Causes of Revelation of the Quranic Verses Using Machine Learning Techniques N2 - Because many verses of the holy Quran are similar, there is high probability that, similar verses addressing same issues share same generic causes of revelation. In this study, machine learning techniques have been employed in order to automatically derive causes of revelation of Quranic verses. The derivation of the causes of revelation is viewed as a classification problem. Initially the categories are based on the verses with known causes of revelation, and the testing set consists of the remaining verses. Based on a computed threshold value, a naïve Bayesian classifier is used to categorize some verses. After that, using a decision tree classifier the remaining uncategorized verses are separated into verses that contain indicators (resultative connectors, causative expressions…), and those that do not. As for those verses having indicators, each one is segmented into its constituent clauses by identification of the linking indicators. Then a dominant clause is extracted and considered either as the cause of revelation, or post-processed by adding or subtracting some terms to form a causal clause that constitutes the cause of revelation. Concerning remaining unclassified verses without indicators, a naive Bayesian classifier is again used to assign each one of them to one of the existing classes based on features and topics similarity. As for verses that could not be classified so far, manual classification was made by considering each verse as a category on its own. The result obtained in this study is encouraging, and shows that automatic derivation of Quranic verses’ generic causes of revelation is achievable, and reasonably reliable for understanding and implementing the teachings of the Quran. KW - Text Mining KW - Koran KW - Text mining KW - Statistical classifiers KW - Text segmentation KW - Causes of revelation KW - Quran Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-66083 ER - TY - INPR A1 - Nassourou, Mohamadou T1 - Design and Implementation of a Model-driven XML-based Integrated System Architecture for Assisting Analysis, Understanding, and Retention of Religious Texts:The Case of The Quran N2 - Learning a book in general involves reading it, underlining important words, adding comments, summarizing some passages, and marking up some text or concepts. Once deeper understanding is achieved, one would like to organize and manage her/his knowledge in such a way that, it could be easily remembered and efficiently transmitted to others. This paper discusses about modeling religious texts using semantic XML markup based on frame-based knowledge representation, with the purpose of assisting understanding, retention, and sharing of knowledge they contain. In this study, books organized in terms of chapters made up of verses are considered as the source of knowledge to model. Some metadata representing the multiple perspectives of knowledge modeling are assigned to each chapter and verse. Chapters and verses with their metadata form a meta-model, which is represented using frames, and published on a web mashup. An XML-based annotation and visualization system equipped with user interfaces for creating static and dynamic metadata, annotating chapters’ contents according to user selected semantics, and templates for publishing generated knowledge on the Internet, has been developed. The system has been applied to the Quran, and the result obtained shows that multiple perspectives of information modeling can be successfully applied to religious texts, in order to support analysis, understanding, and retention of the texts. KW - Wissensrepräsentation KW - Wissensmanagement KW - Content Management KW - XML KW - Koran KW - Knowledge representation KW - Meta-model KW - Frames KW - XML model KW - Knowledge Management KW - Content Management KW - Quran Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-65737 ER - TY - INPR A1 - Nassourou, Mohamadou T1 - Computer-based Textual Documents Collation System for Reconstructing the Original Text from Automatically Identified Base Text and Ranked Witnesses N2 - Given a collection of diverging documents about some lost original text, any person interested in the text would try reconstructing it from the diverging documents. Whether it is eclecticism, stemmatics, or copy-text, one is expected to explicitly or indirectly select one of the documents as a starting point or as a base text, which could be emended through comparison with remaining documents, so that a text that could be designated as the original document is generated. Unfortunately the process of giving priority to one of the documents also known as witnesses is a subjective approach. In fact even Cladistics, which could be considered as a computer-based approach of implementing stemmatics, does not present or recommend users to select a certain witness as a starting point for the process of reconstructing the original document. In this study, a computational method using a rule-based Bayesian classifier is used, to assist text scholars in their attempts of reconstructing a non-existing document from some available witnesses. The method developed in this study consists of selecting a base text successively and collating it with remaining documents. Each completed collation cycle stores the selected base text and its closest witness, along with a weighted score of their similarities and differences. At the end of the collation process, a witness selected more often by majority of base texts is considered as the probable base text of the collection. Witnesses’ scores are weighted using a weighting system, based on effects of types of textual modifications on the process of reconstructing original documents. Users have the possibility to select between baseless and base text collation. If a base text is selected, the task is reduced to ranking the witnesses with respect to the base text, otherwise a base text as well as ranking of the witnesses with respect to the base text are computed and displayed on a bar diagram. Additionally this study includes a recursive algorithm for automatically reconstructing the original text from the identified base text and ranked witnesses. KW - Textvergleich KW - Text Mining KW - Textual document collation KW - Base text KW - Reconstruction of original text KW - Gothenburg model KW - Bayesian classifier KW - Textual alterations weighting system Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-65749 ER - TY - INPR A1 - Nassourou, Mohamadou T1 - Philosophical and Computational Approaches for Estimating and Visualizing Months of Revelations of Quranic Chapters N2 - The question of why the Quran structure does not follow its chronology of revelation is a recurring one. Some Islamic scholars such as [1] have answered the question using hadiths, as well as other philosophical reasons based on internal evidences of the Quran itself. Unfortunately till today many are still wondering about this issue. Muslims believe that the Quran is a summary and a copy of the content of a preserved tablet called Lawhul-Mahfuz located in the heaven. Logically speaking, this suggests that the arrangement of the verses and chapters is expected to be similar to that of the Lawhul-Mahfuz. As for the arrangement of the verses in each chapter, there is unanimity that it was carried out by the Prophet himself under the guidance of Angel Gabriel with the recommendation of God. But concerning the ordering of the chapters, there are reports about some divergences [3] among the Prophet’s companions as to which chapter should precede which one. This paper argues that Quranic chapters might have been arranged according to months and seasons of revelation. In fact, based on some verses of the Quran, it is defendable that the Lawhul-Mahfuz itself is understood to have been structured in terms of the months of the year. In this study, philosophical and mathematical arguments for computing chapters’ months of revelation are discussed, and the result is displayed on an interactive scatter plot. KW - Text Mining KW - Visualisierung KW - Koran KW - Text mining KW - Visualization KW - Chronology of revelation KW - Chapters arrangement KW - Quran KW - Lawhul-Mahfuz Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-65784 ER - TY - JOUR A1 - Schmid, Benjamin A1 - Schindelin, Johannes A1 - Cardona, Albert A1 - Longair, Martin A1 - Heisenberg, Martin T1 - A high-level 3D visualization API for Java and ImageJ N2 - Background: Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Results: Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Conclusions: Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de. KW - Visualisierung KW - Java 3D KW - ImageJ KW - framework Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-67851 ER - TY - THES A1 - Duelli, Michael T1 - Heuristic Design and Provisioning of Resilient Multi-Layer Networks T1 - Heuristische Planung und Betrieb von ausfallsicheren Mehrschichtnetzen N2 - To jointly provide different services/technologies, like IP and Ethernet or IP and SDH/SONET, in a single network, equipment of multiple technologies needs to be deployed to the sites/Points of Presence (PoP) and interconnected with each other. Therein, a technology may provide transport functionality to other technologies and increase the number of available resources by using multiplexing techniques. By providing its own switching functionality, each technology creates connections in a logical layer which leads to the notion of multi-layer networks. The design of such networks comprises the deployment and interconnection of components to suit to given traffic demands. To prevent traffic loss due to failures of networking equipment, protection mechanisms need to be established. In multi-layer networks, protection usually can be applied in any of the considered layers. In turn, the hierarchical structure of multi-layer networks also bears shared risk groups (SRG). To achieve a cost-optimal resilient network, an appropriate combination of multiplexing techniques, technologies, and their interconnections needs to be found. Thus, network design is a combinatorial problem with a large parameter and solution space. After the design stage, the resources of a multi-layer network can be provided to traffic demands. Especially, dynamic capacity provisioning requires interaction of sites and layers, as well as accurate retrieval of constraint information. In recent years, generalized multiprotocol label switching (GMPLS) and path computation elements (PCE) have emerged as possible approaches for these challenges. Like the design, the provisioning of multi-layer networks comprises a variety of optimization parameters, like blocking probability, resilience, and energy efficiency. In this work, we introduce several efficient heuristics to approach the considered optimization problems. We perform capital expenditure (CAPEX)-aware design of multi-layer networks from scratch, based on IST NOBEL phase 2 project's cost and equipment data. We comprise traffic and resilience requirements in different and multiple layers as well as different network architectures. On top of the designed networks, we consider the dynamic provisioning of multi-layer traffic based on the GMPLS and PCE architecture. We evaluate different PCE deployments, information retrieval strategies, and re-optimization. Finally, we show how information about provisioning utilization can be used to provide a feedback for network design. N2 - Um in einem Netz verschiedene Dienste/Schichten, z.B. IP und Ethernet oder IP und SDH/SONET, parallel anbieten zu können, müssen Komponenten mehrerer Technologien an den Standorten verbaut und miteinander verbunden werden. Hierbei kann eine Technologie eine Transportschicht für andere Technologien fungieren und die Zahl der verfügbaren Ressourcen durch Multiplex Techniken erhöhen. Durch die Bereitstellung eigener Switching Funktionalität erzeugt jede Technologie Verbindungen in einer logischen Schicht. Dies führt zu der Bezeichnung Mehrschichtnetz (engl. multi-layer network). Die Planung solcher Netze hat das Verbauen und Verbinden von Komponenten zum Ziel, so dass gegebene Verkehrsströme realisiert werden können. Um Unterbrechungen der Verkehrsströme aufgrund von Fehlern in den Netzkomponenten zu verhinden, müssen Schutzmechanismen eingebaut werden. In Mehrschichtnetzen können solche Schutzmechanismen in jeder beliebigen Schicht betrachtet werden. Allerdings birgt die hierarchische Struktur von Mehrschichtnetzen das Risiko von shared risk groups (SRG). Um ein Kosten-optimales ausfallsicheres Netz zu erhalten, muss eine passende Kombination aus Multiplex Techniken, Technologien und deren Verbindungen gefunden werden. Die Netzplanung ist daher ein kombinatorisches Problem mit einem großen Parameter- und Lösungsraum. Nach der Planungsphase können die Ressourcen eines Mehrschichtnetzes für Verkehrsströme vorgehalten werden. Die Betrachtung von dynamischer Kapazitätsanforderungen erfordert die Interaktion von Knoten und Schichten sowie akkurate Gewinnung von Informationen zur Auslastung. In jüngster Zeit sind das Generalized Multiprotocol Label Switching (GMPLS) und das Path Computation Element (PCE) als mögliche Lösungsansätze für diese Herausforderungen entstanden. Wie in der Planung beinhaltet auch der Betrieb von Mehrschichtnetzen eine Vielzahl von Optimierungsparametern, wie die Blockierungswahrscheinlichkeit, Ausfallsicherheit und Energie-Effizienz. In dieser Arbeit, führen wir verschiedene effiziente Heuristiken ein, um die betrachteten Optimierungsprobleme anzugehen. Wir planen Mehrschichtnetze von Grund auf und minimieren hinsichtlich der Anschaffungskosten basierend auf den Kosten- und Komponenten-Daten des IST NOBEL Phase 2 Projekts. Wir berücksichtigen Anforderungen der Verkehrsströme und Ausfallsicherheit in verschiedenen Schichten und in mehreren Schichten gleichzeitig sowie verschiedene Netzarchitekturen. Aufsetzend auf dem geplanten Netz betrachten wir den Betrieb von Mehrschichtnetzen mit dynamischen Verkehr basiert auf der GMPLS und PCE Architektur. Wir bewerten verschiedene PCE Installationen, Strategien zur Informationsgewinnung und Re-Optimierung. Abschließend, zeigen wir wie Information über die Auslastung im Betrieb genutzt werden kann um Rückmeldung an die Netzplanung zu geben. T3 - Würzburger Beiträge zur Leistungsbewertung Verteilter Systeme - 02/12 KW - Mehrschichtsystem KW - Planung KW - Ressourcenmanagement KW - Ausfallsicheres System KW - Mehrschichtnetze KW - Pfadberechnungselement KW - Ausfallsicherheit KW - Multi-Layer KW - Design KW - Resilience KW - Resource Management KW - Path Computation Element Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-69433 ER - TY - THES A1 - Saska, Martin T1 - Trajectory planning and optimal control for formations of autonomous robots T1 - Die Bahnplanung und die optimale Steuerung für Formationen der autonomen Roboter N2 - In this thesis, we present novel approaches for formation driving of nonholonomic robots and optimal trajectory planning to reach a target region. The methods consider a static known map of the environment as well as unknown and dynamic obstacles detected by sensors of the formation. The algorithms are based on leader following techniques, where the formation of car-like robots is maintained in a shape determined by curvilinear coordinates. Beyond this, the general methods of formation driving are specialized and extended for an application of airport snow shoveling. Detailed descriptions of the algorithms complemented by relevant stability and convergence studies will be provided in the following chapters. Furthermore, discussions of the applicability will be verified by various simulations in existing robotic environments and also by a hardware experiment. N2 - In dieser Arbeit präsentieren wir neuartige Algorithmen für die Steuerung der Formationen der nichtholonomen Roboter und ihre optimale Bahnplanung. Die Algorithmen beruhen auf "leader-follower" Techniken. Die Formationen der "car-like" Roboter sind in einer bestimmten Form von "curvilinear" Koordinaten gehalten. Die Steuerungmethoden der Formationen sind spezialisiert und erweitert um ihre Anwendung auf das Flughafenschneeschaufeln. In dieser Arbeit werden die detaillierten Beschreibungen der Algorithmen durch entsprechende Stabilität- und Konvergenz-Studien gestellt. Ihre Anwendbarkeit wird durch verschiedene Simulationen und eine Hardware-Experiment überprüft. T3 - Forschungsberichte in der Robotik = Research Notes in Robotics - 3 KW - Autonomer Roboter KW - Mobiler Roboter KW - Optimale Kontrolle KW - Formation KW - Steuerung KW - formation driving KW - mobile robots KW - snow shoveling KW - receding horizon control KW - model predictive control KW - trajectory planning Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-53175 SN - 978-3-923959-56-3 ER -