@article{Hibbe2014,
author = {Hibbe, Marcel},
title = {Spotlocator - Guess Where the Photo Was Taken!},
series = {Process Design for Natural Scientists: an agile model-driven approach},
journal = {Process Design for Natural Scientists: an agile model-driven approach},
number = {500},
editor = {Lambrecht, Anna-Lena and Margaria, Tiziana},
publisher = {Springer Verlag},
address = {Berlin},
isbn = {978-3-662-45005-5},
issn = {1865-0929},
pages = {149 -- 160},
year = {2014},
abstract = {Spotlocator is a game wherein people have to guess the spots of where photos were taken. The photos of a defined area for each game are from panoramio.com. They are published at http://spotlocator. drupalgardens.com with an ID. Everyone can guess the photo spots by sending a special tweet via Twitter that contains the hashtag \#spotlocator, the guessed coordinates and the ID of the photo. An evaluation is published for all tweets. The players are informed about the distance to the real photo spots and the positions are shown on a map.},
language = {en}
}
@article{Blaese2014,
author = {Blaese, Leif},
title = {Data mining for unidentified protein squences},
series = {Process design for natural scientists: an agile model-driven approach},
journal = {Process design for natural scientists: an agile model-driven approach},
number = {500},
publisher = {Springer},
address = {Berlin},
isbn = {978-3-662-45005-5},
issn = {1865-0929},
pages = {73 -- 87},
year = {2014},
abstract = {Through the use of next generation sequencing (NGS) technology, a lot of newly sequenced organisms are now available. Annotating those genes is one of the most challenging tasks in sequence biology. Here, we present an automated workflow to find homologue proteins, annotate sequences according to function and create a three-dimensional model.},
language = {en}
}
@article{Lis2014,
author = {Lis, Monika},
title = {Constructing a Phylogenetic Tree},
series = {Process Design for Natural Scientists: an agile model-driven approach},
journal = {Process Design for Natural Scientists: an agile model-driven approach},
number = {500},
editor = {Lambrecht, Anna-Lena and Margaria, Tiziana},
publisher = {Springer Verlag},
address = {Berlin},
isbn = {978-3-662-45005-5},
issn = {1865-0929},
pages = {101 -- 109},
year = {2014},
abstract = {In this project I constructed a workflow that takes a DNA sequence as input and provides a phylogenetic tree, consisting of the input sequence and other sequences which were found during a database search. In this phylogenetic tree the sequences are arranged depending on similarities. In bioinformatics, constructing phylogenetic trees is often used to explore the evolutionary relationships of genes or organisms and to understand the mechanisms of evolution itself.},
language = {en}
}
@phdthesis{Kilic2016,
author = {Kilic, Mukayil},
title = {Vernetztes Pr{\"u}fen von elektronischen Komponenten {\"u}ber das Internet},
school = {Universit{\"a}t Potsdam},
pages = {104, XVI},
year = {2016},
language = {de}
}
@phdthesis{Dornhege2006,
author = {Dornhege, Guido},
title = {Increasing information transfer rates for brain-computer interfacing},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7690},
school = {Universit{\"a}t Potsdam},
year = {2006},
abstract = {The goal of a Brain-Computer Interface (BCI) consists of the development of a unidirectional interface between a human and a computer to allow control of a device only via brain signals. While the BCI systems of almost all other groups require the user to be trained over several weeks or even months, the group of Prof. Dr. Klaus-Robert M{\"u}ller in Berlin and Potsdam, which I belong to, was one of the first research groups in this field which used machine learning techniques on a large scale. The adaptivity of the processing system to the individual brain patterns of the subject confers huge advantages for the user. Thus BCI research is considered a hot topic in machine learning and computer science. It requires interdisciplinary cooperation between disparate fields such as neuroscience, since only by combining machine learning and signal processing techniques based on neurophysiological knowledge will the largest progress be made. In this work I particularly deal with my part of this project, which lies mainly in the area of computer science. I have considered the following three main points: Establishing a performance measure based on information theory: I have critically illuminated the assumptions of Shannon's information transfer rate for application in a BCI context. By establishing suitable coding strategies I was able to show that this theoretical measure approximates quite well to what is practically achieveable. Transfer and development of suitable signal processing and machine learning techniques: One substantial component of my work was to develop several machine learning and signal processing algorithms to improve the efficiency of a BCI. Based on the neurophysiological knowledge that several independent EEG features can be observed for some mental states, I have developed a method for combining different and maybe independent features which improved performance. In some cases the performance of the combination algorithm outperforms the best single performance by more than 50 \%. Furthermore, I have theoretically and practically addressed via the development of suitable algorithms the question of the optimal number of classes which should be used for a BCI. It transpired that with BCI performances reported so far, three or four different mental states are optimal. For another extension I have combined ideas from signal processing with those of machine learning since a high gain can be achieved if the temporal filtering, i.e., the choice of frequency bands, is automatically adapted to each subject individually. Implementation of the Berlin brain computer interface and realization of suitable experiments: Finally a further substantial component of my work was to realize an online BCI system which includes the developed methods, but is also flexible enough to allow the simple realization of new algorithms and ideas. So far, bitrates of up to 40 bits per minute have been achieved with this system by absolutely untrained users which, compared to results of other groups, is highly successful.},
subject = {Kybernetik},
language = {en}
}
@phdthesis{Scholz2006,
author = {Scholz, Matthias},
title = {Approaches to analyse and interpret biological profile data},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7839},
school = {Universit{\"a}t Potsdam},
year = {2006},
abstract = {Advances in biotechnologies rapidly increase the number of molecules of a cell which can be observed simultaneously. This includes expression levels of thousands or ten-thousands of genes as well as concentration levels of metabolites or proteins. Such Profile data, observed at different times or at different experimental conditions (e.g., heat or dry stress), show how the biological experiment is reflected on the molecular level. This information is helpful to understand the molecular behaviour and to identify molecules or combination of molecules that characterise specific biological condition (e.g., disease). This work shows the potentials of component extraction algorithms to identify the major factors which influenced the observed data. This can be the expected experimental factors such as the time or temperature as well as unexpected factors such as technical artefacts or even unknown biological behaviour. Extracting components means to reduce the very high-dimensional data to a small set of new variables termed components. Each component is a combination of all original variables. The classical approach for that purpose is the principal component analysis (PCA). It is shown that, in contrast to PCA which maximises the variance only, modern approaches such as independent component analysis (ICA) are more suitable for analysing molecular data. The condition of independence between components of ICA fits more naturally our assumption of individual (independent) factors which influence the data. This higher potential of ICA is demonstrated by a crossing experiment of the model plant Arabidopsis thaliana (Thale Cress). The experimental factors could be well identified and, in addition, ICA could even detect a technical artefact. However, in continuously observations such as in time experiments, the data show, in general, a nonlinear distribution. To analyse such nonlinear data, a nonlinear extension of PCA is used. This nonlinear PCA (NLPCA) is based on a neural network algorithm. The algorithm is adapted to be applicable to incomplete molecular data sets. Thus, it provides also the ability to estimate the missing data. The potential of nonlinear PCA to identify nonlinear factors is demonstrated by a cold stress experiment of Arabidopsis thaliana. The results of component analysis can be used to build a molecular network model. Since it includes functional dependencies it is termed functional network. Applied to the cold stress data, it is shown that functional networks are appropriate to visualise biological processes and thereby reveals molecular dynamics.},
subject = {Bioinformatik},
language = {en}
}
@phdthesis{Weigend2007,
author = {Weigend, Michael},
title = {Intuitive Modelle der Informatik},
publisher = {Universit{\"a}tsverlag Potsdam},
address = {Potsdam},
isbn = {978-3-940793-08-9},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15787},
school = {Universit{\"a}t Potsdam},
pages = {331},
year = {2007},
abstract = {Intuitive Modelle der Informatik sind gedankliche Vorstellungen {\"u}ber informatische Konzepte, die mit subjektiver Gewissheit verbunden sind. Menschen verwenden sie, wenn sie die Arbeitsweise von Computerprogrammen nachvollziehen oder anderen erkl{\"a}ren, die logische Korrektheit eines Programms pr{\"u}fen oder in einem kreativen Prozess selbst Programme entwickeln. Intuitive Modelle k{\"o}nnen auf verschiedene Weise repr{\"a}sentiert und kommuniziert werden, etwa verbal-abstrakt, durch ablauf- oder strukturorientierte Abbildungen und Filme oder konkrete Beispiele. Diskutiert werden in dieser Arbeit grundlegende intuitive Modelle f{\"u}r folgende inhaltliche Aspekte einer Programmausf{\"u}hrung: Allokation von Aktivit{\"a}t bei einer Programmausf{\"u}hrung, Benennung von Entit{\"a}ten, Daten, Funktionen, Verarbeitung, Kontrollstrukturen zur Steuerung von Programml{\"a}ufen, Rekursion, Klassen und Objekte. Mit Hilfe eines Systems von Online-Spielen, der Python Visual Sandbox, werden die psychische Realit{\"a}t verschiedener intuitiver Modelle bei Programmieranf{\"a}ngern nachgewiesen und fehlerhafte Anwendungen (Fehlvorstellungen) identifiziert.},
language = {de}
}
@misc{Trapp2007,
type = {Master Thesis},
author = {Trapp, Matthias},
title = {Analysis and exploration of virtual 3D city models using 3D information lenses},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-13930},
school = {Universit{\"a}t Potsdam},
year = {2007},
abstract = {This thesis addresses real-time rendering techniques for 3D information lenses based on the focus \& context metaphor. It analyzes, conceives, implements, and reviews its applicability to objects and structures of virtual 3D city models. In contrast to digital terrain models, the application of focus \& context visualization to virtual 3D city models is barely researched. However, the purposeful visualization of contextual data of is extreme importance for the interactive exploration and analysis of this field. Programmable hardware enables the implementation of new lens techniques, that allow the augmentation of the perceptive and cognitive quality of the visualization compared to classical perspective projections. A set of 3D information lenses is integrated into a 3D scene-graph system: • Occlusion lenses modify the appearance of virtual 3D city model objects to resolve their occlusion and consequently facilitate the navigation. • Best-view lenses display city model objects in a priority-based manner and mediate their meta information. Thus, they support exploration and navigation of virtual 3D city models. • Color and deformation lenses modify the appearance and geometry of 3D city models to facilitate their perception. The presented techniques for 3D information lenses and their application to virtual 3D city models clarify their potential for interactive visualization and form a base for further development.},
language = {en}
}
@misc{Piesker2007,
type = {Master Thesis},
author = {Piesker, Bj{\"o}rn},
title = {Constraint-basierte Generierung realit{\"a}tsnaher Eisenbahnnetze},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-15325},
school = {Universit{\"a}t Potsdam},
year = {2007},
abstract = {Diese Arbeit befasst sich mit der Entwicklung einer Applikation, welche Infrastrukturdaten {\"u}ber Eisenbahnnetze generiert. Dabei bildet die Erzeugung der topologischen Informationen den Schwerpunkt dieser Arbeit. Der Anwender charakterisiert hierf{\"u}r vorab das gew{\"u}nschte Eisenbahnnetz, wobei die geforderten Eigenschaften die Randbedingungen darstellen, die bei der Synthese zu beachten sind. Zur Einhaltung dieser Bedingungen wird die Constraint-Programmierung eingesetzt, welche durch ihr spezielles Programmierparadigma konsistente L{\"o}sungen effizient erzeugt. Dies wird u.a. durch die Nachnutzung so genannter globaler Constraints erreicht. Aus diesem Grund wird insbesondere auf den Einsatz der Constraint-Programmierung bei der Modellierung und Implementierung der Applikation eingegangen.},
language = {de}
}
@misc{Kirchner2007,
type = {Master Thesis},
author = {Kirchner, Peter},
title = {Verteilte Autorisierung innerhalb von Single Sign-On-Umgebungen : Analyse, Architektur und Implementation eines Frameworks f{\"u}r verteilte Autorisierung in einer ADFS-Umgebung},
url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-22289},
school = {Universit{\"a}t Potsdam},
year = {2007},
abstract = {Aktuelle Softwaresysteme erlauben die verteilte Authentifizierung von Benutzern {\"u}ber Ver-zeichnisdienste, die sowohl im Intranet als auch im Extranet liegen und die {\"u}ber Dom{\"a}nen-grenzen hinweg die Kooperation mit Partnern erm{\"o}glichen. Der n{\"a}chste Schritt ist es nun, die Autorisierung ebenfalls aus der lokalen Anwendung auszulagern und diese extern durchzu-f{\"u}hren - vorzugsweise unter dem Einfluss der Authentifizierungspartner. Basierend auf der Analyse des State-of-the-Art wird in dieser Arbeit ein Framework vorges-tellt, das die verteilte Autorisierung von ADFS (Active Directory Federation Services) authenti-fizierten Benutzern auf Basis ihrer Gruppen oder ihrer pers{\"o}nlichen Identit{\"a}t erm{\"o}glicht. Es wird eine prototypische Implementation mit Diensten entwickelt, die f{\"u}r authentifizierte Be-nutzer Autorisierungsanfragen extern delegieren, sowie ein Dienst, der diese Autorisierungs-anfragen verarbeitet. Zus{\"a}tzlich zeigt die Arbeit eine Integration dieses Autorisierungs-Frameworks in das .NET Framework, um die praxistaugliche Verwendbarkeit in einer aktuel-len Entwicklungsumgebung zu demonstrieren. Abschließend wird ein Ausblick auf weitere Fragestellungen und Folgearbeiten gegeben.},
language = {de}
}