@phdthesis{Dramlitsch2002,
  author    = {Dramlitsch, Thomas},
  title     = {Distributed computations in a dynamic, heterogeneous Grid environment},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0000759},
  school      = {Universit{\"a}t Potsdam},
  year      = {2002},
  abstract  = {Die immer dichtere und schnellere Vernetzung von Rechnern und Rechenzentren {\"u}ber Hochgeschwindigkeitsnetzwerke erm{\"o}glicht eine neue Art des wissenschaftlich verteilten Rechnens, bei der geographisch weit auseinanderliegende Rechenkapazit{\"a}ten zu einer Gesamtheit zusammengefasst werden k{\"o}nnen. Dieser so entstehende virtuelle Superrechner, der selbst aus mehreren Grossrechnern besteht, kann dazu genutzt werden Probleme zu berechnen, f{\"u}r die die einzelnen Grossrechner zu klein sind. Die Probleme, die numerisch mit heutigen Rechenkapazit{\"a}ten nicht l{\"o}sbar sind, erstrecken sich durch s{\"a}mtliche Gebiete der heutigen Wissenschaft, angefangen von Astrophysik, Molek{\"u}lphysik, Bioinformatik, Meteorologie, bis hin zur Zahlentheorie und Fluiddynamik um nur einige Gebiete zu nennen. Je nach Art der Problemstellung und des L{\"o}sungsverfahrens gestalten sich solche "Meta-Berechnungen" mehr oder weniger schwierig. Allgemein kann man sagen, dass solche Berechnungen um so schwerer und auch um so uneffizienter werden, je mehr Kommunikation zwischen den einzelnen Prozessen (oder Prozessoren) herrscht. Dies ist dadurch begr{\"u}ndet, dass die Bandbreiten bzw. Latenzzeiten zwischen zwei Prozessoren auf demselben Grossrechner oder Cluster um zwei bis vier Gr{\"o}ssenordnungen h{\"o}her bzw. niedriger liegen als zwischen Prozessoren, welche hunderte von Kilometern entfernt liegen. Dennoch bricht nunmehr eine Zeit an, in der es m{\"o}glich ist Berechnungen auf solch virtuellen Supercomputern auch mit kommunikationsintensiven Programmen durchzuf{\"u}hren. Eine grosse Klasse von kommunikations- und berechnungsintensiven Programmen ist diejenige, die die L{\"o}sung von Differentialgleichungen mithilfe von finiten Differenzen zum Inhalt hat. Gerade diese Klasse von Programmen und deren Betrieb in einem virtuellen Superrechner wird in dieser vorliegenden Dissertation behandelt. Methoden zur effizienteren Durchf{\"u}hrung von solch verteilten Berechnungen werden entwickelt, analysiert und implementiert. Der Schwerpunkt liegt darin vorhandene, klassische Parallelisierungsalgorithmen zu analysieren und so zu erweitern, dass sie vorhandene Informationen (z.B. verf{\"u}gbar durch das Globus Toolkit) {\"u}ber Maschinen und Netzwerke zur effizienteren Parallelisierung nutzen. Soweit wir wissen werden solche Zusatzinformationen kaum in relevanten Programmen genutzt, da der Grossteil aller Parallelisierungsalgorithmen implizit f{\"u}r die Ausf{\"u}hrung auf Grossrechnern oder Clustern entwickelt wurde.},
  language  = {en}
}
@phdthesis{Lanfermann2002,
  author    = {Lanfermann, Gerd},
  title     = {Nomadic migration : a service environment for autonomic computing on the Grid},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0000773},
  school      = {Universit{\"a}t Potsdam},
  year      = {2002},
  abstract  = {In den vergangenen Jahren ist es zu einer dramatischen Vervielfachung der verf{\"u}gbaren Rechenzeit gekommen. Diese 'Grid Ressourcen' stehen jedoch nicht als kontinuierlicher Strom zur Verf{\"u}gung, sondern sind {\"u}ber verschiedene Maschinentypen, Plattformen und Betriebssysteme verteilt, die jeweils durch Netzwerke mit fluktuierender Bandbreite verbunden sind. Es wird f{\"u}r Wissenschaftler zunehmend schwieriger, die verf{\"u}gbaren Ressourcen f{\"u}r ihre Anwendungen zu nutzen. Wir glauben, dass intelligente, selbstbestimmende Applikationen in der Lage sein sollten, ihre Ressourcen in einer dynamischen und heterogenen Umgebung selbst zu w{\"a}hlen: Migrierende Applikationen suchen eine neue Ressource, wenn die alte aufgebraucht ist. 'Spawning'-Anwendungen lassen Algorithmen auf externen Maschinen laufen, um die Hauptanwendung zu beschleunigen. Applikationen werden neu gestartet, sobald ein Absturz endeckt wird. Alle diese Verfahren k{\"o}nnen ohne menschliche Interaktion erfolgen. Eine verteilte Rechenumgebung besitzt eine nat{\"u}rliche Unverl{\"a}sslichkeit. Jede Applikation, die mit einer solchen Umgebung interagiert, muss auf die gest{\"o}rten Komponenten reagieren k{\"o}nnen: schlechte Netzwerkverbindung, abst{\"u}rzende Maschinen, fehlerhafte Software. Wir konstruieren eine verl{\"a}ssliche Serviceinfrastruktur, indem wir der Serviceumgebung eine 'Peer-to-Peer'-Topology aufpr{\"a}gen. Diese "Grid Peer Service" Infrastruktur beinhaltet Services wie Migration und Spawning, als auch Services zum Starten von Applikationen, zur Datei{\"u}bertragung und Auswahl von Rechenressourcen. Sie benutzt existierende Gridtechnologie wo immer m{\"o}glich, um ihre Aufgabe durchzuf{\"u}hren. Ein Applikations-Information- Server arbeitet als generische Registratur f{\"u}r alle Teilnehmer in der Serviceumgebung. Die Serviceumgebung, die wir entwickelt haben, erlaubt es Applikationen z.B. eine Relokationsanfrage an einen Migrationsserver zu stellen. Der Server sucht einen neuen Computer, basierend auf den {\"u}bermittelten Ressourcen-Anforderungen. Er transferiert den Statusfile des Applikation zu der neuen Maschine und startet die Applikation neu. Obwohl das umgebende Ressourcensubstrat nicht kontinuierlich ist, k{\"o}nnen wir kontinuierliche Berechnungen auf Grids ausf{\"u}hren, indem wir die Applikation migrieren. Wir zeigen mit realistischen Beispielen, wie sich z.B. ein traditionelles Genom-Analyse-Programm leicht modifizieren l{\"a}sst, um selbstbestimmte Migrationen in dieser Serviceumgebung durchzuf{\"u}hren.},
  subject      = {Peer-to-Peer-Netz ; GRID computing ; Zuverl{\"a}ssigkeit ; Web Services ; Betriebsmittelverwaltung ; Migration},
  language  = {en}
}
@book{OPUS4-3141,
  title     = {Java language conversion assistant : an analysis},
  editor    = {Richter, Stefan and Henze, Stefan and B{\"u}ttner, Eiko and Bach, Steffen and Polze, Andreas},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-937786-10-0},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-33151},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {166},
  year      = {2004},
  abstract  = {This document is an analysis of the 'Java Language Conversion Assistant'. Itr will also cover a language analysis of the Java Programming Language as well as a survey of related work concerning Java and C\# interoperability on the one hand and language conversion in general on the other. Part I deals with language analysis. Part II covers the JLCA tool and tests used to analyse the tool. Additionally, it gives an overview of the above mentioned related work. Part III presents a complete project that has been translated using the JLCA.},
  language  = {en}
}
@book{OPUS4-3143,
  title     = {Conceptual architecture patterns : FMC-based representations},
  editor    = {Gr{\"o}ne, Bernhard and Keller, Frank},
  isbn      = {978-3-935024-98-3},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-33173},
  publisher      = {Universit{\"a}t Potsdam},
  year      = {2004},
  abstract  = {This document presents the results of the seminar "Coneptual Arachitecture Patterns" of the winter term 2002 in the Hasso-Plattner-Institute. It is a compilation of the student's elaborations dealing with some conceptual architecture patterns which can be found in literature. One important focus laid on the runtime structures and the presentation of the patterns. 1. Introduction 1.1. The Seminar 1.2. Literature 2 Pipes and Filters (Andr{\´e} Langhorst and Martin Steinle) 3 Broker (Konrad H{\"u}bner and Einar L{\"u}ck) 4 Microkernel (Eiko B{\"u}ttner and Stefan Richter) 5 Component Configurator (Stefan R{\"o}ck and Alexander Gierak) 6 Interceptor (Marc F{\"o}rster and Peter Aschenbrenner) 7 Reactor (Nikolai Cieslak and Dennis Eder) 8 Half-Sync/Half-Async (Robert Mitschke and Harald Schubert) 9 Leader/Followers (Dennis Klemann and Steffen Schmidt)},
  language  = {en}
}
@book{GroeneKnoepfelKugeletal.2004,
  author    = {Gr{\"o}ne, Bernhard and Kn{\"o}pfel, Andreas and Kugel, Rudolf and Schmidt, Oliver},
  title     = {The Apache Modeling Project},
  isbn      = {978-3-937786-14-8},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-33147},
  publisher      = {Universit{\"a}t Potsdam},
  year      = {2004},
  abstract  = {This document presents an introduction to the Apache HTTP Server, covering both an overview and implementation details. It presents results of the Apache Modelling Project done by research assistants and students of the Hasso-Plattner-Institute in 2001, 2002 and 2003. The Apache HTTP Server was used to introduce students to the application of the modeling technique FMC, a method that supports transporting knowledge about complex systems in the domain of information processing (software and hardware as well). After an introduction to HTTP servers in general, we will focus on protocols and web technology. Then we will discuss Apache, its operational environment and its extension capabilities— the module API. Finally we will guide the reader through parts of the Apache source code and explain the most important pieces.},
  language  = {en}
}
@phdthesis{Harmeling2004,
  author    = {Harmeling, Stefan},
  title     = {Independent component analysis and beyond},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0001540},
  school      = {Universit{\"a}t Potsdam},
  year      = {2004},
  abstract  = {'Independent component analysis' (ICA) ist ein Werkzeug der statistischen Datenanalyse und Signalverarbeitung, welches multivariate Signale in ihre Quellkomponenten zerlegen kann. Obwohl das klassische ICA Modell sehr n{\"u}tzlich ist, gibt es viele Anwendungen, die Erweiterungen von ICA erfordern. In dieser Dissertation pr{\"a}sentieren wir neue Verfahren, die die Funktionalit{\"a}t von ICA erweitern: (1) Zuverl{\"a}ssigkeitsanalyse und Gruppierung von unabh{\"a}ngigen Komponenten durch Hinzuf{\"u}gen von Rauschen, (2) robuste und {\"u}berbestimmte ('over-complete') ICA durch Ausreissererkennung, und (3) nichtlineare ICA mit Kernmethoden.},
  language  = {en}
}
@book{KuropkaMeyer2005,
  author    = {Kuropka, Dominik and Meyer, Harald},
  title     = {Survey on Service Composition},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {3-937786-78-3},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-33787},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {35},
  year      = {2005},
  abstract  = {It is predicted that Service-oriented Architectures (SOA) will have a high impact on future electronic business and markets. Services will provide an self-contained and standardised interface towards business and are considered as the future platform for business-to-business and business-toconsumer trades. Founded by the complexity of real world business scenarios a huge need for an easy, flexible and automated creation and enactment of service compositions is observed. This survey explores the relationship of service composition with workflow management—a technology/ concept already in use in many business environments. The similarities between the both and the key differences between them are elaborated. Furthermore methods for composition of services ranging from manual, semi- to full-automated composition are sketched. This survey concludes that current tools for service composition are in an immature state and that there is still much research to do before service composition can be used easily and conveniently in real world scenarios. However, since automated service composition is a key enabler for the full potential of Service-oriented Architectures, further research on this field is imperative. This survey closes with a formal sample scenario presented in appendix A to give the reader an impression on how full-automated service composition works.},
  language  = {en}
}
@phdthesis{Ziehe2005,
  author    = {Ziehe, Andreas},
  title     = {Blind source separation based on joint diagonalization of matrices with applications in biomedical signal processing},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-5694},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {This thesis is concerned with the solution of the blind source separation problem (BSS). The BSS problem occurs frequently in various scientific and technical applications. In essence, it consists in separating meaningful underlying components out of a mixture of a multitude of superimposed signals. In the recent research literature there are two related approaches to the BSS problem: The first is known as Independent Component Analysis (ICA), where the goal is to transform the data such that the components become as independent as possible. The second is based on the notion of diagonality of certain characteristic matrices derived from the data. Here the goal is to transform the matrices such that they become as diagonal as possible. In this thesis we study the latter method of approximate joint diagonalization (AJD) to achieve a solution of the BSS problem. After an introduction to the general setting, the thesis provides an overview on particular choices for the set of target matrices that can be used for BSS by joint diagonalization. As the main contribution of the thesis, new algorithms for approximate joint diagonalization of several matrices with non-orthogonal transformations are developed. These newly developed algorithms will be tested on synthetic benchmark datasets and compared to other previous diagonalization algorithms. Applications of the BSS methods to biomedical signal processing are discussed and exemplified with real-life data sets of multi-channel biomagnetic recordings.},
  subject      = {Signaltrennung},
  language  = {en}
}
@phdthesis{Floeter2005,
  author    = {Fl{\"o}ter, Andr{\´e}},
  title     = {Analyzing biological expression data based on decision tree induction},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-6416},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {Modern biological analysis techniques supply scientists with various forms of data. One category of such data are the so called "expression data". These data indicate the quantities of biochemical compounds present in tissue samples. Recently, expression data can be generated at a high speed. This leads in turn to amounts of data no longer analysable by classical statistical techniques. Systems biology is the new field that focuses on the modelling of this information. At present, various methods are used for this purpose. One superordinate class of these meth­ods is machine learning. Methods of this kind had, until recently, predominantly been used for classification and prediction tasks. This neglected a powerful secondary benefit: the ability to induce interpretable models. Obtaining such models from data has become a key issue within Systems biology. Numerous approaches have been proposed and intensively discussed. This thesis focuses on the examination and exploitation of one basic technique: decision trees. The concept of comparing sets of decision trees is developed. This method offers the pos­sibility of identifying significant thresholds in continuous or discrete valued attributes through their corresponding set of decision trees. Finding significant thresholds in attributes is a means of identifying states in living organisms. Knowing about states is an invaluable clue to the un­derstanding of dynamic processes in organisms. Applied to metabolite concentration data, the proposed method was able to identify states which were not found with conventional techniques for threshold extraction. A second approach exploits the structure of sets of decision trees for the discovery of com­binatorial dependencies between attributes. Previous work on this issue has focused either on expensive computational methods or the interpretation of single decision trees ­ a very limited exploitation of the data. This has led to incomplete or unstable results. That is why a new method is developed that uses sets of decision trees to overcome these limitations. Both the introduced methods are available as software tools. They can be applied consecu­tively or separately. That way they make up a package of analytical tools that usefully supplement existing methods. By means of these tools, the newly introduced methods were able to confirm existing knowl­edge and to suggest interesting and new relationships between metabolites.},
  subject      = {Molekulare Bioinformatik},
  language  = {en}
}
@book{DoellnerKirschNienhaus2005,
  author    = {D{\"o}llner, J{\"u}rgen Roland Friedrich and Kirsch, Florian and Nienhaus, Marc},
  title     = {Visualizing Design and Spatial Assembly of Interactive CSG},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-937786-56-2},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-33771},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {8},
  year      = {2005},
  abstract  = {For interactive construction of CSG models understanding the layout of a model is essential for its efficient manipulation. To understand position and orientation of aggregated components of a CSG model, we need to realize its visible and occluded parts as a whole. Hence, transparency and enhanced outlines are key techniques to assist comprehension. We present a novel real-time rendering technique for visualizing design and spatial assembly of CSG models. As enabling technology we combine an image-space CSG rendering algorithm with blueprint rendering. Blueprint rendering applies depth peeling for extracting layers of ordered depth from polygonal models and then composes them in sorted order facilitating a clear insight of the models. We develop a solution for implementing depth peeling for CSG models considering their depth complexity. Capturing surface colors of each layer and later combining the results allows for generating order-independent transparency as one major rendering technique for CSG models. We further define visually important edges for CSG models and integrate an image-space edgeenhancement technique for detecting them in each layer. In this way, we extract visually important edges that are directly and not directly visible to outline a model's layout. Combining edges with transparency rendering, finally, generates edge-enhanced depictions of image-based CSG models and allows us to realize their complex, spatial assembly.},
  language  = {en}
}