TY - THES A1 - Klein, Alexander T1 - Performance Issues of MAC and Routing Protocols in Wireless Sensor Networks T1 - Leistungsbeschränkende Faktoren von MAC und Routingprotokollen in drahtlosen Sensornetzen N2 - The focus of this work lies on the communication issues of Medium Access Control (MAC) and routing protocols in the context of WSNs. The communication challenges in these networks mainly result from high node density, low bandwidth, low energy constraints and the hardware limitations in terms of memory, computational power and sensing capabilities of low-power transceivers. For this reason, the structure of WSNs is always kept as simple as possible to minimize the impact of communication issues. Thus, the majority of WSNs apply a simple one hop star topology since multi-hop communication has high demands on the routing protocol since it increases the bandwidth requirements of the network. Moreover, medium access becomes a challenging problem due to the fact that low-power transceivers are very limited in their sensing capabilities. The first contribution is represented by the Backoff Preamble-based MAC Protocol with Sequential Contention Resolution (BPS-MAC) which is designed to overcome the limitations of low-power transceivers. Two communication issues, namely the Clear Channel Assessment (CCA) delay and the turnaround time, are directly addressed by the protocol. The CCA delay represents the period of time which is required by the transceiver to detect a busy radio channel while the turnaround time specifies the period of time which is required to switch between receive and transmit mode. Standard Carrier Sense Multiple Access (CSMA) protocols do not achieve high performance in terms of packet loss if the traffic is highly correlated due to the fact that the transceiver is not able to sense the medium during the switching phase. Therefore, a node may start to transmit data while another node is already transmitting since it has sensed an idle medium right before it started to switch its transceiver from receive to transmit mode. The BPS-MAC protocol uses a new sequential preamble-based medium access strategy which can be adapted to the hardware capabilities of the transceivers. The protocol achieves a very low packet loss rate even in wireless networks with high node density and event-driven traffic without the need of synchronization. This makes the protocol attractive to applications such as structural health monitoring, where event suppression is not an option. Moreover, acknowledgments or complex retransmission strategies become almost unnecessary since the sequential preamble-based contention resolution mechanism minimizes the collision probability. However, packets can still be lost as a consequence of interference or other issues which affect signal propagation. The second contribution consists of a new routing protocol which is able to quickly detect topology changes without generating a large amount of overhead. The key characteristics of the Statistic-Based Routing (SBR) protocol are high end-to-end reliability (in fixed and mobile networks), load balancing capabilities, a smooth continuous routing metric, quick adaptation to changing network conditions, low processing and memory requirements, low overhead, support of unidirectional links and simplicity. The protocol can establish routes in a hybrid or a proactive mode and uses an adaptive continuous routing metric which makes it very flexible in terms of scalability while maintaining stable routes. The hybrid mode is optimized for low-power WSNs since routes are only established on demand. The difference of the hybrid mode to reactive routing strategies is that routing messages are periodically transmitted to maintain already established routes. However, the protocol stops the transmission of routing messages if no data packets are transmitted for a certain time period in order to minimize the routing overhead and the energy consumption. The proactive mode is designed for high data rate networks which have less energy constraints. In this mode, the protocol periodically transmits routing messages to establish routes in a proactive way even in the absence of data traffic. Thus, nodes in the network can immediately transmit data since the route to the destination is already established in advance. In addition, a new delay-based routing message forwarding strategy is introduced. The forwarding strategy is part of SBR but can also be applied to many routing protocols in order to modify the established topology. The strategy can be used, e.g. in mobile networks, to decrease the packet loss by deferring routing messages with respect to the neighbor change rate. Thus, nodes with a stable neighborhood forward messages faster than nodes within a fast changing neighborhood. As a result, routes are established through nodes with correlated movement which results in fewer topology changes due to higher link durations. N2 - Im Rahmen dieser Arbeit werden leistungsbeschränkende Faktoren von Medium Access Control (MAC) und Routingprotokollen im Kontext von drahtlosen Sensornetzen untersucht. Zunächst werden typische Probleme des Funkkanals diskutiert. Anschließend führen eine Einteilung von MAC Protokollen, sowie eine Gegenüberstellung relevanter Protokolle in die Thematik ein. Daraufhin werden hardwarelimitierende Faktoren und deren Auswirkung auf die Effizienz von Kanalzugriffsprotokollen untersucht. Des Weiteren wird das vom Autor entwickelte Backoff Preamble-based MAC Protokoll (BPS-MAC) vorgestellt, welches auf die limitierten Fähigkeiten sensortypischer Hardware eingeht und für dichte Sensornetze mit korreliertem Datenverkehr optimiert ist. Ein weiterer Schwerpunkt dieser Arbeit stellt das Thema Routing dar. Hier wird ebenfalls mit einer Einteilung der Protokolle in die Thematik eingeführt. Darüber hinaus werden die wichtigsten Aufgaben von Routingprotokollen vorgestellt. Ein Überblick über häufig verwendete Routingmetriken und Routingprotokolle schließen die Einführung in diesen Themenkomplex ab. Abschließend wird das im Rahmen der Dissertation entwickelte Statistic-Based-Routing (SBR) Protokoll vorgestellt, welches ebenfalls für drahtlose Sensornetze optimiert ist. Der letzte Schwerpunkt beschreibt die Problematik der Leistungsbewertung von Routingprotokollen hinsichtlich klassischer Leistungsparameter wie Paketverlust und Verzögerung. Ebenfalls werden weitere Leistungsparameter wie zum Beispiel die vom Nutzer wahrgenommene Netzqualität genauer untersucht. T3 - Würzburger Beiträge zur Leistungsbewertung Verteilter Systeme - 03/10 KW - Routing KW - Drahtloses Sensorsystem KW - Leistungsbewertung KW - Diskrete Simulation KW - MAC KW - Kanalzugriff KW - Medium KW - MAC KW - routing KW - sensor KW - networks KW - simulation Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-52870 ER - TY - JOUR A1 - Kirikkayis, Yusuf A1 - Gallik, Florian A1 - Winter, Michael A1 - Reichert, Manfred T1 - BPMNE4IoT: a framework for modeling, executing and monitoring IoT-driven processes JF - Future Internet N2 - The Internet of Things (IoT) enables a variety of smart applications, including smart home, smart manufacturing, and smart city. By enhancing Business Process Management Systems with IoT capabilities, the execution and monitoring of business processes can be significantly improved. Providing a holistic support for modeling, executing and monitoring IoT-driven processes, however, constitutes a challenge. Existing process modeling and process execution languages, such as BPMN 2.0, are unable to fully meet the IoT characteristics (e.g., asynchronicity and parallelism) of IoT-driven processes. In this article, we present BPMNE4IoT—A holistic framework for modeling, executing and monitoring IoT-driven processes. We introduce various artifacts and events based on the BPMN 2.0 metamodel that allow realizing the desired IoT awareness of business processes. The framework is evaluated along two real-world scenarios from two different domains. Moreover, we present a user study for comparing BPMNE4IoT and BPMN 2.0. In particular, this study has confirmed that the BPMNE4IoT framework facilitates the support of IoT-driven processes. KW - IoT KW - BPM KW - BPMN KW - IoT-driven processes Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-304097 SN - 1999-5903 VL - 15 IS - 3 ER - TY - THES A1 - Kindermann, Philipp T1 - Angular Schematization in Graph Drawing N2 - Graphs are a frequently used tool to model relationships among entities. A graph is a binary relation between objects, that is, it consists of a set of objects (vertices) and a set of pairs of objects (edges). Networks are common examples of modeling data as a graph. For example, relationships between persons in a social network, or network links between computers in a telecommunication network can be represented by a graph. The clearest way to illustrate the modeled data is to visualize the graphs. The field of Graph Drawing deals with the problem of finding algorithms to automatically generate graph visualizations. The task is to find a "good" drawing, which can be measured by different criteria such as number of crossings between edges or the used area. In this thesis, we study Angular Schematization in Graph Drawing. By this, we mean drawings with large angles (for example, between the edges at common vertices or at crossing points). The thesis consists of three parts. First, we deal with the placement of boxes. Boxes are axis-parallel rectangles that can, for example, contain text. They can be placed on a map to label important sites, or can be used to describe semantic relationships between words in a word network. In the second part of the thesis, we consider graph drawings visually guide the viewer. These drawings generally induce large angles between edges that meet at a vertex. Furthermore, the edges are drawn crossing-free and in a way that makes them easy to follow for the human eye. The third and final part is devoted to crossings with large angles. In drawings with crossings, it is important to have large angles between edges at their crossing point, preferably right angles. N2 - Graphen sind häufig verwendete Werkzeuge zur Modellierung von Zusammenhängen zwischen Daten. Ein Graph ist eine binäre Relation zwischen Objekten, das heißt er besteht aus einer Menge von Objekten (Knoten) und einer Menge von Paaren von Objekten (Kanten). Netzwerke sind übliche Beispiele für das Modellieren von Daten als ein Graph. Beispielsweise lassen sich Beziehungen zwischen Personen in einem sozialen Netzwerk oder Netzanbindungen zwischen Computern in einem Telekommunikationsnetz als Graph darstellen. Die modellierten Daten können am anschaulichsten dargestellt werden, indem man die Graphen visualisiert. Der Bereich des Graphenzeichnens behandelt das Problem, Algorithmen zum automatischen Erzeugen von Graphenvisualisierungen zu finden. Das Ziel ist es, eine "gute" Zeichnung zu finden, was durch unterschiedliche Kriterien gemessen werden kann; zum Beispiel durch die Anzahl der Kreuzungen zwischen Kanten oder durch den Platzverbrauch. In dieser Arbeit beschäftigen wir uns mit Winkelschematisierung im Graphenzeichnen. Darunter verstehen wir Zeichnungen, in denen die Winkel (zum Beispiel zwischen Kanten an einem gemeinsamen Knoten oder einem Kreuzungspunkt) möglichst groß gestaltet sind. Die Arbeit besteht aus drei Teilen. Im ersten Teil betrachten wir die Platzierung von Boxen. Boxen sind achsenparallele Rechtecke, die zum Beispiel Text enthalten. Sie können beispielsweise auf einer Karte platziert werden, um wichtige Standorte zu beschriften, oder benutzt werden, um semantische Beziehungen zwischen Wörtern in einem Wortnetzwerk darzustellen. Im zweiten Teil der Arbeit untersuchen wir Graphenzeichnungen, die den Betrachter visuell führen. Im Allgemeinen haben diese Zeichnungen große Winkel zwischen Kanten, die sich in einem Knoten treffen. Außerdem werden die Verbindungen kreuzungsfrei und so gezeichnet, dass es dem menschlichen Auge leicht fällt, ihnen zu folgen. Im dritten und letzten Teil geht es um Kreuzungen mit großen Winkeln. In Zeichnungen mit Kreuzungen ist es wichtig, dass die Winkel zwischen Kanten an Kreuzungspunkten groß sind, vorzugsweise rechtwinklig. KW - graph drawing KW - angular schematization KW - boundary labeling KW - contact representation KW - word clouds KW - monotone drawing KW - smooth orthogonal drawing KW - simultaneous embedding KW - right angle crossing KW - independent crossing KW - Graphenzeichnen KW - Winkel KW - Kreuzung KW - v Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-112549 SN - 978-3-95826-020-7 (print) SN - 978-3-95826-021-4 (online) PB - Würzburg University Press CY - Würzburg ER - TY - JOUR A1 - Kern, Florian A1 - Kullmann, Peter A1 - Ganal, Elisabeth A1 - Korwisi, Kristof A1 - Stingl, René A1 - Niebling, Florian A1 - Latoschik, Marc Erich T1 - Off-The-Shelf Stylus: Using XR Devices for Handwriting and Sketching on Physically Aligned Virtual Surfaces JF - Frontiers in Virtual Reality N2 - This article introduces the Off-The-Shelf Stylus (OTSS), a framework for 2D interaction (in 3D) as well as for handwriting and sketching with digital pen, ink, and paper on physically aligned virtual surfaces in Virtual, Augmented, and Mixed Reality (VR, AR, MR: XR for short). OTSS supports self-made XR styluses based on consumer-grade six-degrees-of-freedom XR controllers and commercially available styluses. The framework provides separate modules for three basic but vital features: 1) The stylus module provides stylus construction and calibration features. 2) The surface module provides surface calibration and visual feedback features for virtual-physical 2D surface alignment using our so-called 3ViSuAl procedure, and surface interaction features. 3) The evaluation suite provides a comprehensive test bed combining technical measurements for precision, accuracy, and latency with extensive usability evaluations including handwriting and sketching tasks based on established visuomotor, graphomotor, and handwriting research. The framework’s development is accompanied by an extensive open source reference implementation targeting the Unity game engine using an Oculus Rift S headset and Oculus Touch controllers. The development compares three low-cost and low-tech options to equip controllers with a tip and includes a web browser-based surface providing support for interacting, handwriting, and sketching. The evaluation of the reference implementation based on the OTSS framework identified an average stylus precision of 0.98 mm (SD = 0.54 mm) and an average surface accuracy of 0.60 mm (SD = 0.32 mm) in a seated VR environment. The time for displaying the stylus movement as digital ink on the web browser surface in VR was 79.40 ms on average (SD = 23.26 ms), including the physical controller’s motion-to-photon latency visualized by its virtual representation (M = 42.57 ms, SD = 15.70 ms). The usability evaluation (N = 10) revealed a low task load, high usability, and high user experience. Participants successfully reproduced given shapes and created legible handwriting, indicating that the OTSS and it’s reference implementation is ready for everyday use. We provide source code access to our implementation, including stylus and surface calibration and surface interaction features, making it easy to reuse, extend, adapt and/or replicate previous results (https://go.uniwue.de/hci-otss). KW - virtual reality KW - augmented reality KW - handwriting KW - sketching KW - stylus KW - user interaction KW - usability evaluation KW - passive haptic feedback Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-260219 VL - 2 ER - TY - JOUR A1 - Kempf, Sebastian A1 - Krug, Markus A1 - Puppe, Frank T1 - KIETA: Key-insight extraction from scientific tables JF - Applied Intelligence N2 - An important but very time consuming part of the research process is literature review. An already large and nevertheless growing ground set of publications as well as a steadily increasing publication rate continue to worsen the situation. Consequently, automating this task as far as possible is desirable. Experimental results of systems are key-insights of high importance during literature review and usually represented in form of tables. Our pipeline KIETA exploits these tables to contribute to the endeavor of automation by extracting them and their contained knowledge from scientific publications. The pipeline is split into multiple steps to guarantee modularity as well as analyzability, and agnosticim regarding the specific scientific domain up until the knowledge extraction step, which is based upon an ontology. Additionally, a dataset of corresponding articles has been manually annotated with information regarding table and knowledge extraction. Experiments show promising results that signal the possibility of an automated system, while also indicating limits of extracting knowledge from tables without any context. KW - table extraction KW - table understanding KW - ontology KW - key-insight extraction KW - information extraction Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-324180 SN - 0924-669X VL - 53 IS - 8 ER - TY - JOUR A1 - Karl, Stefan A1 - Dandekar, Thomas T1 - Jimena: Efficient computing and system state identification for genetic regulatory networks JF - BMC Bioinformatics N2 - Background: Boolean networks capture switching behavior of many naturally occurring regulatory networks. For semi-quantitative modeling, interpolation between ON and OFF states is necessary. The high degree polynomial interpolation of Boolean genetic regulatory networks (GRNs) in cellular processes such as apoptosis or proliferation allows for the modeling of a wider range of node interactions than continuous activator-inhibitor models, but suffers from scaling problems for networks which contain nodes with more than ~10 inputs. Many GRNs from literature or new gene expression experiments exceed those limitations and a new approach was developed. Results: (i) As a part of our new GRN simulation framework Jimena we introduce and setup Boolean-tree-based data structures; (ii) corresponding algorithms greatly expedite the calculation of the polynomial interpolation in almost all cases, thereby expanding the range of networks which can be simulated by this model in reasonable time. (iii) Stable states for discrete models are efficiently counted and identified using binary decision diagrams. As application example, we show how system states can now be sampled efficiently in small up to large scale hormone disease networks (Arabidopsis thaliana development and immunity, pathogen Pseudomonas syringae and modulation by cytokinins and plant hormones). Conclusions: Jimena simulates currently available GRNs about 10-100 times faster than the previous implementation of the polynomial interpolation model and even greater gains are achieved for large scale-free networks. This speed-up also facilitates a much more thorough sampling of continuous state spaces which may lead to the identification of new stable states. Mutants of large networks can be constructed and analyzed very quickly enabling new insights into network robustness and behavior. KW - Boolean function KW - genetic regulatory network KW - interpolation KW - stable state KW - binary decision diagram KW - Boolean tree Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-128671 VL - 14 ER - TY - THES A1 - Karch, Oliver T1 - Where am I? - Indoor localization based on range measurements T1 - Wo bin ich? - Lokalisation mit Hilfe von Entfernungsmesswerten N2 - Nowadays, robotics plays an important role in increasing fields of application. There exist many environments or situations where mobile robots instead of human beings are used, since the tasks are too hazardous, uncomfortable, repetitive, or costly for humans to perform. The autonomy and the mobility of the robot are often essential for a good solution of these problems. Thus, such a robot should at least be able to answer the question "Where am I?". This thesis investigates the problem of self-localizing a robot in an indoor environment using range measurements. That is, a robot equipped with a range sensor wakes up inside a building and has to determine its position using only its sensor data and a map of its environment. We examine this problem from an idealizing point of view (reducing it into a pure geometric one) and further investigate a method of Guibas, Motwani, and Raghavan from the field of computational geometry to solving it. Here, so-called visibility skeletons, which can be seen as coarsened representations of visibility polygons, play a decisive role. In the major part of this thesis we analyze the structures and the occurring complexities in the framework of this scheme. It turns out that the main source of complication are so-called overlapping embeddings of skeletons into the map polygon, for which we derive some restrictive visibility constraints. Based on these results we are able to improve one of the occurring complexity bounds in the sense that we can formulate it with respect to the number of reflex vertices instead of the total number of map vertices. This also affects the worst-case bound on the preprocessing complexity of the method. The second part of this thesis compares the previous idealizing assumptions with the properties of real-world environments and discusses the occurring problems. In order to circumvent these problems, we use the concept of distance functions, which model the resemblance between the sensor data and the map, and appropriately adapt the above method to the needs of realistic scenarios. In particular, we introduce a distance function, namely the polar coordinate metric, which seems to be well suited to the localization problem. Finally, we present the RoLoPro software where most of the discussed algorithms are implemented (including the polar coordinate metric). N2 - Heutzutage spielen autonome Roboter bei einer wachsenden Zahl von Anwendungsgebieten eine entscheidende Rolle. Sie werden überall dort anstelle von menschlichen Arbeitskräften eingesetzt, wo die jeweiligen Aufgaben für Menschen zu gefährlich, unangenehm, monoton oder schlicht zu teuer sind. Dabei sind die Autonomie und Mobilität des Roboters sehr oft grundlegend für eine gute Problemlösung. Ein solcher Roboter sollte also zumindest die Frage "Wo bin ich?" zufriedenstellend beantworten können. Diese Arbeit behandelt das Problem der Selbstlokalisation in einer Gebäudeumgebung mit Hilfe von Entfernungsmesswerten. Das heißt, ein Roboter - ausgestattet mit einem Entfernungssensor - wacht innerhalb eines Gebäudes auf und muss mit Hilfe seiner Sensordaten und einer Karte seiner Einsatzumgebung seine Position bestimmen. Wir betrachten eine idealisierte Variante dieser Aufgabe, die ein rein geometrisches Problem zum Inhalt hat, und untersuchen ein Verfahren von Guibas, Motwani und Raghavan aus dem Gebiet der Algorithmischen Geometrie, welches dieses löst. Hierbei spielen sogenannte Sichtbarkeitsskelette (vergröberte Darstellungen von Sichtbarkeitspolygonen) eine entscheidende Rolle. Im Hauptteil der Arbeit analysieren wir die Strukturen und die auftretenden Komplexitäten im Rahmen dieses Verfahrens. Es stellt sich heraus, dass die Hauptschwierigkeiten sogenannte überlappende Einbettungen von Skeletten in das Kartenpolygon zur Ursache haben, für die wir einige einschränkende Sichtbarkeitsbedingungen zeigen. Gestützt auf diese Resultate können wir die auftretenden Komplexitätsschranken dahingehend verbessern, dass wir diese nicht nur in Abhängigkeit der Gesamtzahl aller Kartenecken angeben, sondern in Abhängigkeit der Zahl der konkaven Ecken. Dies hat ebenfalls Auswirkungen auf die Worst-Case-Schranken für die Preprocessing-Komplexität des Verfahrens. Der zweite Teil der Arbeit vergleicht die anfangs gemachten idealisierenden Annahmen mit den Gegebenheiten realer Umgebungen und adressiert die auftretenden Probleme. Um diese zu umgehen verwenden wir das Konzept sogenannter Distanzfunktionen, welche die Ähnlichkeit zwischen den Sensordaten und der Karte modellieren, und passen das Verfahren auf geeignete Weise an die Bedürfnisse realistischer Szenarien an. Insbesondere führen wir eine Distanzfunktion ein - die Polarkoordinatenmetrik - welche sich für das Lokalisationsproblem besonders gut zu eignen scheint. Schlussendlich stellen wir die Software RoLoPro vor, in der die meisten der diskutierten Algorithmen (einschließlich der Polarkoordinatenmetrik) implementiert sind. KW - Autonomer Roboter KW - Mobiler Roboter KW - Lokalisation KW - Lokalisation KW - Autonomer Roboter KW - Sichtbarkeit KW - Ähnlichkeitsmaß KW - Algorithmische Geometrie KW - Localization KW - Autonomous Robot KW - Visibility KW - Similarity Measure KW - Computational Geometry Y1 - 2002 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-8442 ER - TY - JOUR A1 - Kammerer, Klaus A1 - Pryss, Rüdiger A1 - Hoppenstedt, Burkhard A1 - Sommer, Kevin A1 - Reichert, Manfred T1 - Process-driven and flow-based processing of industrial sensor data JF - Sensors N2 - For machine manufacturing companies, besides the production of high quality and reliable machines, requirements have emerged to maintain machine-related aspects through digital services. The development of such services in the field of the Industrial Internet of Things (IIoT) is dealing with solutions such as effective condition monitoring and predictive maintenance. However, appropriate data sources are needed on which digital services can be technically based. As many powerful and cheap sensors have been introduced over the last years, their integration into complex machines is promising for developing digital services for various scenarios. It is apparent that for components handling recorded data of these sensors they must usually deal with large amounts of data. In particular, the labeling of raw sensor data must be furthered by a technical solution. To deal with these data handling challenges in a generic way, a sensor processing pipeline (SPP) was developed, which provides effective methods to capture, process, store, and visualize raw sensor data based on a processing chain. Based on the example of a machine manufacturing company, the SPP approach is presented in this work. For the company involved, the approach has revealed promising results. KW - data stream processing KW - cyber-physical systems KW - processing pipeline KW - sensor networks Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-213089 SN - 1424-8220 VL - 20 IS - 18 ER - TY - JOUR A1 - Kammerer, Klaus A1 - Göster, Manuel A1 - Reichert, Manfred A1 - Pryss, Rüdiger T1 - Ambalytics: a scalable and distributed system architecture concept for bibliometric network analyses JF - Future Internet N2 - A deep understanding about a field of research is valuable for academic researchers. In addition to technical knowledge, this includes knowledge about subareas, open research questions, and social communities (networks) of individuals and organizations within a given field. With bibliometric analyses, researchers can acquire quantitatively valuable knowledge about a research area by using bibliographic information on academic publications provided by bibliographic data providers. Bibliometric analyses include the calculation of bibliometric networks to describe affiliations or similarities of bibliometric entities (e.g., authors) and group them into clusters representing subareas or communities. Calculating and visualizing bibliometric networks is a nontrivial and time-consuming data science task that requires highly skilled individuals. In addition to domain knowledge, researchers must often provide statistical knowledge and programming skills or use software tools having limited functionality and usability. In this paper, we present the ambalytics bibliometric platform, which reduces the complexity of bibliometric network analysis and the visualization of results. It accompanies users through the process of bibliometric analysis and eliminates the need for individuals to have programming skills and statistical knowledge, while preserving advanced functionality, such as algorithm parameterization, for experts. As a proof-of-concept, and as an example of bibliometric analyses outcomes, the calculation of research fronts networks based on a hybrid similarity approach is shown. Being designed to scale, ambalytics makes use of distributed systems concepts and technologies. It is based on the microservice architecture concept and uses the Kubernetes framework for orchestration. This paper presents the initial building block of a comprehensive bibliometric analysis platform called ambalytics, which aims at a high usability for users as well as scalability. KW - system architecture design KW - bibliometric analysis KW - community detection Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-244916 SN - 1999-5903 VL - 13 IS - 8 ER - TY - JOUR A1 - Kaltdorf, Kristin Verena A1 - Schulze, Katja A1 - Helmprobst, Frederik A1 - Kollmannsberger, Philip A1 - Dandekar, Thomas A1 - Stigloher, Christian T1 - Fiji macro 3D ART VeSElecT: 3D automated reconstruction tool for vesicle structures of electron tomograms JF - PLoS Computational Biology N2 - Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial. KW - Biology KW - Vesicles KW - Caenorhabditis elegans KW - Zebrafish KW - Septins KW - Synaptic vesicles KW - Neuromuscular junctions KW - Computer software KW - Synapses Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-172112 VL - 13 IS - 1 ER -