TY - JOUR A1 - Zoerner, Dietmar A1 - Köhlmann, Wiebke A1 - Brandt, Christopher T1 - Mobiles spielebasiertes Lernen an historischen Lernorten JF - E-Learning Symposium 2014 : Mobil und vernetzt – studieren im digitalen Zeitalter ; Potsdam, 14. November 2014 N2 - Im Rahmen eines interdisziplinären studentischen Projekts wurde ein Framework für mobile pervasive Lernspiele entwickelt. Am Beispiel des historischen Lernortes Park Sanssouci wurde auf dieser Grundlage ein Lernspiel für Schülerinnen und Schüler implementiert. Die geplante Evaluation soll die Lernwirksamkeit von geobasierten mobilen Lernspielen messen. Dazu wird die Intensität des Flow-Erlebens mit einer ortsgebundenen alternativen Umsetzung verglichen. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-442354 SP - 53 EP - 54 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Zender, Raphael A1 - Metzler, Richard A1 - Lucke, Ulrike T1 - FreshUP-A pervasive educational game for freshmen JF - Pervasive and mobile computing N2 - Students beginning their studies at university face manifold problems such as orientation in a new environment and organizing their courses. This article presents the implementation and successful empirical evaluation of the pervasive browser-based educational game "FreshUP", which aims at helping to overcome the initial difficulties of freshmen. In contrast to a conventional scavenger hunt, mobile pervasive games like FreshUP, bridging in-game and real world activities, have the potential to provide help in a motivating manner using new technology which is currently becoming more and more common. (C) 2013 Elsevier B.V. All rights reserved. KW - Pervasive game KW - Campus KW - Freshmen KW - e-learning KW - Mobile devices KW - SOA KW - Evaluation Y1 - 2014 U6 - https://doi.org/10.1016/j.pmcj.2013.09.003 SN - 1574-1192 SN - 1873-1589 VL - 14 SP - 47 EP - 56 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Weiher, Marcel A1 - Hirschfeld, Robert T1 - Polymorphic identifiers: uniform resource access in objective-smalltalk JF - ACM SIGPLAN notices N2 - In object-oriented programming, polymorphic dispatch of operations decouples clients from specific providers of services and allows implementations to be modified or substituted without affecting clients. The Uniform Access Principle (UAP) tries to extend these qualities to resource access by demanding that access to state be indistinguishable from access to operations. Despite language features supporting the UAP, the overall goal of substitutability has not been achieved for either alternative resources such as keyed storage, files or web pages, or for alternate access mechanisms: specific kinds of resources are bound to specific access mechanisms and vice versa. Changing storage or access patterns either requires changes to both clients and service providers and trying to maintain the UAP imposes significant penalties in terms of code-duplication and/or performance overhead. We propose introducing first class identifiers as polymorphic names for storage locations to solve these problems. With these Polymorphic Identifiers, we show that we can provide uniform access to a wide variety of resource types as well as storage and access mechanisms, whether parametrized or direct, without affecting client code, without causing code duplication or significant performance penalties. KW - Identifiers KW - REST KW - Uniform Access Principle KW - Extensibility Y1 - 2014 U6 - https://doi.org/10.1145/2508168.2508169 SN - 0362-1340 SN - 1558-1160 VL - 49 IS - 2 SP - 61 EP - 71 PB - Association for Computing Machinery CY - New York ER - TY - JOUR A1 - Vierheller, Janine ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Exploratory Data Analysis JF - Process Design for Natural Scientists: an agile model-driven approach N2 - In bioinformatics the term exploratory data analysis refers to different methods to get an overview of large biological data sets. Hence, it helps to create a framework for further analysis and hypothesis testing. The workflow facilitates this first important step of the data analysis created by high-throughput technologies. The results are different plots showing the structure of the measurements. The goal of the workflow is the automatization of the exploratory data analysis, but also the flexibility should be guaranteed. The basic tool is the free software R. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 110 EP - 126 PB - Axel Springer Verlag CY - Berlin ER - TY - THES A1 - Videla, Santiago T1 - Reasoning on the response of logical signaling networks with answer set programming T1 - Modellierung Logischer Signalnetzwerke mittels Antwortmengenprogrammierung N2 - 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. N2 - 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. KW - Systembiologie KW - logische Signalnetzwerke KW - Antwortmengenprogrammierung KW - systems biology KW - logical signaling networks KW - answer set programming Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-71890 ER - TY - JOUR A1 - Troeger, Peter A1 - Merzky, Andre T1 - Towards standardized job submission and control in infrastructure clouds JF - Journal of grid computing N2 - The submission and management of computational jobs is a traditional part of utility computing environments. End users and developers of domain-specific software abstractions often have to deal with the heterogeneity of such batch processing systems. This lead to a number of application programming interface and job description standards in the past, which are implemented and established for cluster and Grid systems. With the recent rise of cloud computing as new utility computing paradigm, the standardized access to batch processing facilities operated on cloud resources becomes an important issue. Furthermore, the design of such a standard has to consider a tradeoff between feature completeness and the achievable level of interoperability. The article discusses this general challenge, and presents some existing standards with traditional cluster and Grid computing background that may be applicable to cloud environments. We present OCCI-DRMAA as one approach for standardized access to batch processing facilities hosted in a cloud. KW - Cloud KW - IaaS KW - DRMS KW - DRMAA KW - OCCI KW - Batch processing KW - Job submission KW - Job monitoring Y1 - 2014 U6 - https://doi.org/10.1007/s10723-013-9275-2 SN - 1570-7873 SN - 1572-9184 VL - 12 IS - 1 SP - 111 EP - 125 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Teske, Daniel T1 - Geocoder accuracy ranking JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 161 EP - 174 PB - Springer CY - Berlin ER - TY - JOUR A1 - Sens, Henriette T1 - Web-Based map generalization tools put to the test: a jABC workflow JF - Process Design for Natural Scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 175 EP - 185 PB - Springer CY - Berlin ER - TY - JOUR A1 - Schütt, Christine T1 - Identification of differentially expressed genes JF - Process design for natural scientists: an agile model-driven approach N2 - With the jABC it is possible to realize workflows for numerous questions in different fields. The goal of this project was to create a workflow for the identification of differentially expressed genes. This is of special interest in biology, for it gives the opportunity to get a better insight in cellular changes due to exogenous stress, diseases and so on. With the knowledge that can be derived from the differentially expressed genes in diseased tissues, it becomes possible to find new targets for treatment. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 127 EP - 139 PB - Springer CY - Berlin ER - TY - JOUR A1 - Schulze, Gunnar T1 - Workflow for rapid metagenome analysis JF - Process design for natural scientists: an agile model-driven approach N2 - 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 Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 88 EP - 100 PB - Springer CY - Berlin ER - TY - THES A1 - Schnjakin, Maxim T1 - Cloud-RAID BT - eine Methode zur Bereitstellung zuverlässiger Speicherressourcen in öffentlichen Clouds Y1 - 2014 ER - TY - JOUR A1 - Schick, Daniel A1 - Bojahr, Andre A1 - Herzog, Marc A1 - Shayduk, Roman A1 - von Korff Schmising, Clemens A1 - Bargheer, Matias T1 - Udkm1Dsim-A simulation toolkit for 1D ultrafast dynamics in condensed matter JF - Computer physics communications : an international journal devoted to computational physics and computer programs in physics N2 - The UDKM1DSIM toolbox is a collection of MATLAB (MathWorks Inc.) classes and routines to simulate the structural dynamics and the according X-ray diffraction response in one-dimensional crystalline sample structures upon an arbitrary time-dependent external stimulus, e.g. an ultrashort laser pulse. The toolbox provides the capabilities to define arbitrary layered structures on the atomic level including a rich database of corresponding element-specific physical properties. The excitation of ultrafast dynamics is represented by an N-temperature model which is commonly applied for ultrafast optical excitations. Structural dynamics due to thermal stress are calculated by a linear-chain model of masses and springs. The resulting X-ray diffraction response is computed by dynamical X-ray theory. The UDKM1DSIM toolbox is highly modular and allows for introducing user-defined results at any step in the simulation procedure. Program summary Program title: udkm1Dsim Catalogue identifier: AERH_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERH_v1_0.html Licensing provisions: BSD No. of lines in distributed program, including test data, etc.: 130221 No. of bytes in distributed program, including test data, etc.: 2746036 Distribution format: tar.gz Programming language: Matlab (MathWorks Inc.). Computer: PC/Workstation. Operating system: Running Matlab installation required (tested on MS Win XP -7, Ubuntu Linux 11.04-13.04). Has the code been vectorized or parallelized?: Parallelization for dynamical XRD computations. Number of processors used: 1-12 for Matlab Parallel Computing Toolbox; 1 - infinity for Matlab Distributed Computing Toolbox External routines: Optional: Matlab Parallel Computing Toolbox, Matlab Distributed Computing Toolbox Required (included in the package): mtimesx Fast Matrix Multiply for Matlab by James Tursa, xml io tools by Jaroslaw Tuszynski, textprogressbar by Paul Proteus Nature of problem: Simulate the lattice dynamics of 1D crystalline sample structures due to an ultrafast excitation including thermal transport and compute the corresponding transient X-ray diffraction pattern. Solution method: Restrictions: The program is restricted to 1D sample structures and is further limited to longitudinal acoustic phonon modes and symmetrical X-ray diffraction geometries. Unusual features: The program is highly modular and allows the inclusion of user-defined inputs at any time of the simulation procedure. Running time: The running time is highly dependent on the number of unit cells in the sample structure and other simulation parameters such as time span or angular grid for X-ray diffraction computations. However, the example files are computed in approx. 1-5 min each on a 8 Core Processor with 16 GB RAM available. KW - Ultrafast dynamics KW - Heat diffusion KW - N-temperature model KW - Coherent phonons KW - Incoherent phonons KW - Thermoelasticity KW - Dynamical X-ray theory Y1 - 2014 U6 - https://doi.org/10.1016/j.cpc.2013.10.009 SN - 0010-4655 SN - 1879-2944 VL - 185 IS - 2 SP - 651 EP - 660 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Scheele, Lasse T1 - Location analysis for placing artificial reefs JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 216 EP - 228 PB - Springer CY - Berlin ER - TY - THES A1 - Schacht, Alexander T1 - Konzepte und Strategien mobiler Plattformen zur Erfassung und Anlayse von Vitalparametern in heterogenen Telemonotoring-Systemen Y1 - 2014 ER - TY - JOUR A1 - Respondek, Tobias T1 - A workflow for computing potential areas for wind turbines JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 IS - 500 SP - 200 EP - 215 PB - Springer CY - Berlin ER - TY - JOUR A1 - Reso, Judith ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Protein Classification Workflow JF - Process Design for Natural Scientists: an agile model-driven approach N2 - The protein classification workflow described in this report enables users to get information about a novel protein sequence automatically. The information is derived by different bioinformatic analysis tools which calculate or predict features of a protein sequence. Also, databases are used to compare the novel sequence with known proteins. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 65 EP - 72 PB - Springer Verlag CY - Berlin ER - TY - THES A1 - Rafiee, Hosnieh T1 - Privacy and security issues in IPv6 networks Y1 - 2014 CY - Potsdam ER - TY - JOUR A1 - Noack, Franziska T1 - CREADED: Colored-Relief application for digital elevation data JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 186 EP - 199 PB - Springer CY - Berlin ER - TY - JOUR A1 - Naujokat, Stefan A1 - Neubauer, Johannes A1 - Lamprecht, Anna-Lena A1 - Steffen, Bernhard A1 - Joerges, Sven A1 - Margaria, Tiziana T1 - Simplicity-first model-based plug-in development JF - Software : practice & experience N2 - In this article, we present our experience with over a decade of strict simplicity orientation in the development and evolution of plug-ins. The point of our approach is to enable our graphical modeling framework jABC to capture plug-in development in a domain-specific setting. The typically quite tedious and technical plug-in development is shifted this way from a programming task to the modeling level, where it can be mastered also by application experts without programming expertise. We show how the classical plug-in development profits from a systematic domain-specific API design and how the level of abstraction achieved this way can be further enhanced by defining adequate building blocks for high-level plug-in modeling. As the resulting plug-in models can be compiled and deployed automatically, our approach decomposes plug-in development into three phases where only the realization phase requires plug-in-specific effort. By using our modeling framework jABC, this effort boils down to graphical, tool-supported process modeling. Furthermore, we support the automatic completion of process sketches for executability. All this will be illustrated along the most recent plug-in-based evolution of the jABC framework, which witnessed quite some bootstrapping effects. KW - plug-ins KW - simplicity KW - domain-specific APIs KW - process modeling KW - bootstrapping KW - evolution KW - code generation KW - loose programming KW - dynamic service binding Y1 - 2014 U6 - https://doi.org/10.1002/spe.2243 SN - 0038-0644 SN - 1097-024X VL - 44 IS - 3 SP - 277 EP - 297 PB - Wiley-Blackwell CY - Hoboken ER - TY - INPR A1 - Lucke, Ulrike A1 - Steinmetz, Ralf T1 - Special issue on "Pervasive Education" T2 - Pervasive and mobile computing Y1 - 2014 U6 - https://doi.org/10.1016/j.pmcj.2014.08.001 SN - 1574-1192 SN - 1873-1589 VL - 14 SP - 1 EP - 2 PB - Elsevier CY - Amsterdam ER -