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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.
Geocoder accuracy ranking
(2014)
Finding an address on a map is sometimes tricky: the chosen map application may be unfamiliar with the enclosed region. There are several geocoders on the market, they have different databases and algorithms to compute the query. Consequently, the geocoding results differ in their quality. Fortunately the geocoders provide a rich set of metadata. The workflow described in this paper compares this metadata with the aim to find out which geocoder is offering the best-fitting coordinate for a given address.
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
This book presents an agile and model-driven approach to manage scientific workflows. The approach is based on the Extreme Model Driven Design (XMDD) paradigm and aims at simplifying and automating the complex data analysis processes carried out by scientists in their day-to-day work. Besides documenting the impact the workflow modeling might have on the work of natural scientists, this book serves three major purposes: 1. It acts as a primer for practitioners who are interested to learn how to think in terms of services and workflows when facing domain-specific scientific processes. 2. It provides interesting material for readers already familiar with this kind of tools, because it introduces systematically both the technologies used in each case study and the basic concepts behind them. 3. As the addressed thematic field becomes increasingly relevant for lectures in both computer science and experimental sciences, it also provides helpful material for teachers that plan similar courses.
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.
In the geoinformatics field, remote sensing data is often used for analyzing the characteristics of the current investigation area. This includes DEMs, which are simple raster grids containing grey scales representing the respective elevation values. The project CREADED that is presented in this paper aims at making these monochrome raster images more significant and more intuitively interpretable. For this purpose, an executable interactive model for creating a colored and relief-shaded Digital Elevation Model (DEM) has been designed using the jABC framework. The process is based on standard jABC-SIBs and SIBs that provide specific GIS functions, which are available as Web services, command line tools and scripts.
This paper describes the implementation of a workflow model for service-oriented computing of potential areas for wind turbines in jABC. By implementing a re-executable model the manual effort of a multi-criteria site analysis can be reduced. The aim is to determine the shift of typical geoprocessing tools of geographic information systems (GIS) from the desktop to the web. The analysis is based on a vector data set and mainly uses web services of the “Center for Spatial Information Science and Systems” (CSISS). This paper discusses effort, benefits and problems associated with the use of the web services.
Location analyses are among the most common tasks while working with spatial data and geographic information systems. Automating the most frequently used procedures is therefore an important aspect of improving their usability. In this context, this project aims to design and implement a workflow, providing some basic tools for a location analysis. For the implementation with jABC, the workflow was applied to the problem of finding a suitable location for placing an artificial reef. For this analysis three parameters (bathymetry, slope and grain size of the ground material) were taken into account, processed, and visualized with the The Generic Mapping Tools (GMT), which were integrated into the workflow as jETI-SIBs. The implemented workflow thereby showed that the approach to combine jABC with GMT resulted in an user-centric yet user-friendly tool with high-quality cartographic outputs.
GraffDok is an application helping to maintain an overview over sprayed images somewhere in a city. At the time of writing it aims at vandalism rather than at beautiful photographic graffiti in an underpass. Looking at hundreds of tags and scribbles on monuments, house walls, etc. it would be interesting to not only record them in writing but even make them accessible electronically, including images.
GraffDok’s workflow is simple and only requires an EXIF-GPS-tagged photograph of a graffito. It automatically determines its location by using reverse geocoding with the given GPS-coordinates and the Gisgraphy WebService. While asking the user for some more meta data, GraffDok analyses the image in parallel with this and tries to detect fore- and background – before extracting the drawing lines and make them stand alone. The command line based tool ImageMagick is used here as well as for accessing EXIF data.
Any meta data is written to csv-files, which will stay easily accessible and can be integrated in TeX-files as well. The latter ones are converted to PDF at the end of the workflow, containing a table about all graffiti and a summary for each – including the generated characteristic graffiti pattern image.
Cloud-RAID
(2014)
Boolean constraint solving technology has made tremendous progress over the last decade, leading to industrial-strength solvers, for example, in the areas of answer set programming (ASP), the constraint satisfaction problem (CSP), propositional satisfiability (SAT) and satisfiability of quantified Boolean formulas (QBF). However, in all these areas, there exist multiple solving strategies that work well on different applications; no strategy dominates all other strategies. Therefore, no individual solver shows robust state-of-the-art performance in all kinds of applications. Additionally, the question arises how to choose a well-performing solving strategy for a given application; this is a challenging question even for solver and domain experts. One way to address this issue is the use of portfolio solvers, that is, a set of different solvers or solver configurations. We present three new automatic portfolio methods: (i) automatic construction of parallel portfolio solvers (ACPP) via algorithm configuration,(ii) solving the $NP$-hard problem of finding effective algorithm schedules with Answer Set Programming (aspeed), and (iii) a flexible algorithm selection framework (claspfolio2) allowing for fair comparison of different selection approaches. All three methods show improved performance and robustness in comparison to individual solvers on heterogeneous instance sets from many different applications. Since parallel solvers are important to effectively solve hard problems on parallel computation systems (e.g., multi-core processors), we extend all three approaches to be effectively applicable in parallel settings. We conducted extensive experimental studies different instance sets from ASP, CSP, MAXSAT, Operation Research (OR), SAT and QBF that indicate an improvement in the state-of-the-art solving heterogeneous instance sets. Last but not least, from our experimental studies, we deduce practical advice regarding the question when to apply which of our methods.
E-Learning Symposium 2014
(2014)
Der Tagungsband zum E-Learning Symposium 2014 an der Universität Potsdam beleuchtet die diversen Zielgruppen und Anwendungsbereiche, die aktuell in der E-Learning-Forschung angesprochen werden. Während im letzten Symposium 2012 der Dozierende mit den unterschiedlichen Möglichkeiten der Studierendenaktivierung und Lehrgestaltung im Fokus der Diskussionen stand, werden in diesem Jahr in einem großen Teil der Beiträge die Studierenden ins Zentrum der Aufmerksamkeit gerückt. Dass nicht nur der Inhalt des Lernmediums für den Lernerfolg eine Rolle spielt, sondern auch dessen Unterhaltungswert und die Freude, die die Lernenden während des Prozesses der Wissensakquise empfinden, zeigt sehr anschaulich die Keynote von Linda Breitlauch zum Thema „Faites vos Jeux“ (Spielen Sie jetzt). Der Beitrag von Zoerner et al. verbindet den Gedanken des spiele-basierten Lernens mit dem nach wie vor aktuellen Thema des mobilen Lernens. Auch in diesem Forschungsbereich spielt die Fokussierung auf den Lernenden eine immer herausragendere Rolle. Einen Schritt weiter in Richtung Individualisierung geht in diesem Zusammenhang der eingeladene Vortrag von Christoph Rensing, der sich mit der Adaptivität von mobilen Lernanwendungen beschäftigt. Mit Hilfe zur Verfügung stehender Kontextinformationen sollen gezielt individuelle Lernprozesse unterstützt werden. Alle Beiträge, die sich auf mobile Applikationen und auf Spiele beziehen, sprechen auch die zwischenmenschliche Komponente am Lernen an. So wird neben der Mobilität insbesondere auch der Austausch von Lernobjekten zwischen Lernenden (vergleiche den Beitrag von Zoerner et al.) sowie die Kooperation zwischen Lernenden (siehe Beitrag von Kallookaran und Robra-Bissantz) diskutiert. Der interpersonelle Kontakt spielt allerdings ebenfalls in den Beiträgen ohne Spiel- oder App-Fokussierung eine Rolle. Tutoren werden beispielsweise zur Moderation von Lernprozessen eingesetzt und Lerngruppen gegründet um das problem-orientierte Lernen stärker in den Mittelpunkt zu rücken (siehe Beitrag von Mach und Dirwelis) bzw. näher am Bedarf der Studierenden zu arbeiten (wie in eingeladenen Vortrag von Tatiana N. Noskova sowie in dem Beitrag von Mach und Dirwelis beschrieben). In der Evaluation wird ebenfalls der Schritt weg von anonymen, akkumulierten statistischen Auswertungen hin zu individualisierten Nutzerprofilen im Bereich des Learning Analytics untersucht (vergleiche dazu den Beitrag von Ifenthaler). Neben der Schwerpunktsetzung auf die Lernenden und deren Mobilität rückt das Thema Transmedialität stärker ins Zentrum der Forschung. Während schon die Keynote mit ihrem Spielefokus darauf anspricht, geht es in weiteren Beiträgen darum Abläufe aus der analogen Welt bestmöglich in der digitalen Welt abzubilden. Lerninhalte, die bisher mittels Bildern und Texten für Lehrende und Lernende zugänglich gemacht wurden, werden nunmehr mit weiteren Medien, insbesondere Videos, angereichert um deren Verständnis zu erhöhen. Dies ist beispielsweise geeignet, um Bewegungsabläufe im Sport (vergleiche dazu den Beitrag von Owassapian und Hensinger) oder musikpraktische Übungen wie Bodyperkussion (beschrieben im Beitrag von Buschmann und Glasemann) zu erlernen Lernendenfokussierung, persönlicher Austausch, Mobilität und Transmedialität sind somit einige der Kernthemen, die Sie in diesem Sammelband erwarten. Auch zeigt die häufige Verknüpfung verschedener dieser Kernthemen, dass keines davon ein Randthema ist, sondern sich die Summe aus allen im E-Learning bündelt und damit eine neue Qualität für Lehre, Studium und Forschung erreicht werden kann.
Deciphering the functioning of biological networks is one of the central tasks in systems biology. In particular, signal transduction networks are crucial for the understanding of the cellular response to external and internal perturbations. Importantly, in order to cope with the complexity of these networks, mathematical and computational modeling is required. We propose a computational modeling framework in order to achieve more robust discoveries in the context of logical signaling networks. More precisely, we focus on modeling the response of logical signaling networks by means of automated reasoning using Answer Set Programming (ASP). ASP provides a declarative language for modeling various knowledge representation and reasoning problems. Moreover, available ASP solvers provide several reasoning modes for assessing the multitude of answer sets. Therefore, leveraging its rich modeling language and its highly efficient solving capacities, we use ASP to address three challenging problems in the context of logical signaling networks: learning of (Boolean) logical networks, experimental design, and identification of intervention strategies. Overall, the contribution of this thesis is three-fold. Firstly, we introduce a mathematical framework for characterizing and reasoning on the response of logical signaling networks. Secondly, we contribute to a growing list of successful applications of ASP in systems biology. Thirdly, we present a software providing a complete pipeline for automated reasoning on the response of logical signaling networks.