@phdthesis{Ahmad2014,
  author    = {Ahmad, Nadeem},
  title     = {People centered HMI's for deaf and functionally illiterate users},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70391},
  school      = {Universit{\"a}t Potsdam},
  year      = {2014},
  abstract  = {The objective and motivation behind this research is to provide applications with easy-to-use interfaces to communities of deaf and functionally illiterate users, which enables them to work without any human assistance. Although recent years have witnessed technological advancements, the availability of technology does not ensure accessibility to information and communication technologies (ICT). Extensive use of text from menus to document contents means that deaf or functionally illiterate can not access services implemented on most computer software. Consequently, most existing computer applications pose an accessibility barrier to those who are unable to read fluently. Online technologies intended for such groups should be developed in continuous partnership with primary users and include a thorough investigation into their limitations, requirements and usability barriers. In this research, I investigated existing tools in voice, web and other multimedia technologies to identify learning gaps and explored ways to enhance the information literacy for deaf and functionally illiterate users. I worked on the development of user-centered interfaces to increase the capabilities of deaf and low literacy users by enhancing lexical resources and by evaluating several multimedia interfaces for them. The interface of the platform-independent Italian Sign Language (LIS) Dictionary has been developed to enhance the lexical resources for deaf users. The Sign Language Dictionary accepts Italian lemmas as input and provides their representation in the Italian Sign Language as output. The Sign Language dictionary has 3082 signs as set of Avatar animations in which each sign is linked to a corresponding Italian lemma. I integrated the LIS lexical resources with MultiWordNet (MWN) database to form the first LIS MultiWordNet(LMWN). LMWN contains information about lexical relations between words, semantic relations between lexical concepts (synsets), correspondences between Italian and sign language lexical concepts and semantic fields (domains). The approach enhances the deaf users' understanding of written Italian language and shows that a relatively small set of lexicon can cover a significant portion of MWN. Integration of LIS signs with MWN made it useful tool for computational linguistics and natural language processing. The rule-based translation process from written Italian text to LIS has been transformed into service-oriented system. The translation process is composed of various modules including parser, semantic interpreter, generator, and spatial allocation planner. This translation procedure has been implemented in the Java Application Building Center (jABC), which is a framework for extreme model driven design (XMDD). The XMDD approach focuses on bringing software development closer to conceptual design, so that the functionality of a software solution could be understood by someone who is unfamiliar with programming concepts. The transformation addresses the heterogeneity challenge and enhances the re-usability of the system. For enhancing the e-participation of functionally illiterate users, two detailed studies were conducted in the Republic of Rwanda. In the first study, the traditional (textual) interface was compared with the virtual character-based interactive interface. The study helped to identify usability barriers and users evaluated these interfaces according to three fundamental areas of usability, i.e. effectiveness, efficiency and satisfaction. In another study, we developed four different interfaces to analyze the usability and effects of online assistance (consistent help) for functionally illiterate users and compared different help modes including textual, vocal and virtual character on the performance of semi-literate users. In our newly designed interfaces the instructions were automatically translated in Swahili language. All the interfaces were evaluated on the basis of task accomplishment, time consumption, System Usability Scale (SUS) rating and number of times the help was acquired. The results show that the performance of semi-literate users improved significantly when using the online assistance. The dissertation thus introduces a new development approach in which virtual characters are used as additional support for barely literate or naturally challenged users. Such components enhanced the application utility by offering a variety of services like translating contents in local language, providing additional vocal information, and performing automatic translation from text to sign language. Obviously, there is no such thing as one design solution that fits for all in the underlying domain. Context sensitivity, literacy and mental abilities are key factors on which I concentrated and the results emphasize that computer interfaces must be based on a thoughtful definition of target groups, purposes and objectives.},
  language  = {en}
}
@article{BaierMendlingWeske2014,
  author    = {Baier, Thomas and Mendling, Jan and Weske, Mathias},
  title     = {Bridging abstraction layers in process mining},
  series = {Information systems},
  volume    = {46},
  journal   = {Information systems},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0306-4379},
  doi       = {10.1016/j.is.2014.04.004},
  pages     = {123 -- 139},
  year      = {2014},
  abstract  = {While the maturity of process mining algorithms increases and more process mining tools enter the market, process mining projects still face the problem of different levels of abstraction when comparing events with modeled business activities. Current approaches for event log abstraction try to abstract from the events in an automated way that does not capture the required domain knowledge to fit business activities. This can lead to misinterpretation of discovered process models. We developed an approach that aims to abstract an event log to the same abstraction level that is needed by the business. We use domain knowledge extracted from existing process documentation to semi-automatically match events and activities. Our abstraction approach is able to deal with n:m relations between events and activities and also supports concurrency. We evaluated our approach in two case studies with a German IT outsourcing company. (C) 2014 Elsevier Ltd. All rights reserved.},
  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}
}
@inproceedings{BreitlauchNoskovaRensingetal.2014,
  author    = {Breitlauch, Linda and Noskova, Tatiana N. and Rensing, Christoph and Ifenthaler, Dirk and Owassapian, Dominik and Hensinger, Johannes and Buschmann, Jana and Glasemann, Marie and Dirwelis, Swenja and Mach, Michael and Kallookaran, Michael and Robra-Bissantz, Susanne and Zoerner, Dietmar and K{\"o}hlmann, Wiebke and Brandt, Christopher and Kutzner, Tobias and Steinert, Christian},
  title     = {E-Learning Symposium 2014},
  editor    = {Lucke, Ulrike and Gr{\"u}newald, Franka and Hafer, J{\"o}rg},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  doi       = {10.25932/publishup-6984},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72154},
  pages     = {59},
  year      = {2014},
  abstract  = {Der Tagungsband zum E-Learning Symposium 2014 an der Universit{\"a}t Potsdam beleuchtet die diversen Zielgruppen und Anwendungsbereiche, die aktuell in der E-Learning-Forschung angesprochen werden. W{\"a}hrend im letzten Symposium 2012 der Dozierende mit den unterschiedlichen M{\"o}glichkeiten der Studierendenaktivierung und Lehrgestaltung im Fokus der Diskussionen stand, werden in diesem Jahr in einem großen Teil der Beitr{\"a}ge die Studierenden ins Zentrum der Aufmerksamkeit ger{\"u}ckt. Dass nicht nur der Inhalt des Lernmediums f{\"u}r den Lernerfolg eine Rolle spielt, sondern auch dessen Unterhaltungswert und die Freude, die die Lernenden w{\"a}hrend 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 Adaptivit{\"a}t von mobilen Lernanwendungen besch{\"a}ftigt. Mit Hilfe zur Verf{\"u}gung stehender Kontextinformationen sollen gezielt individuelle Lernprozesse unterst{\"u}tzt werden. Alle Beitr{\"a}ge, die sich auf mobile Applikationen und auf Spiele beziehen, sprechen auch die zwischenmenschliche Komponente am Lernen an. So wird neben der Mobilit{\"a}t 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 Beitr{\"a}gen ohne Spiel- oder App-Fokussierung eine Rolle. Tutoren werden beispielsweise zur Moderation von Lernprozessen eingesetzt und Lerngruppen gegr{\"u}ndet um das problem-orientierte Lernen st{\"a}rker in den Mittelpunkt zu r{\"u}cken (siehe Beitrag von Mach und Dirwelis) bzw. n{\"a}her 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 Mobilit{\"a}t r{\"u}ckt das Thema Transmedialit{\"a}t st{\"a}rker ins Zentrum der Forschung. W{\"a}hrend schon die Keynote mit ihrem Spielefokus darauf anspricht, geht es in weiteren Beitr{\"a}gen darum Abl{\"a}ufe aus der analogen Welt bestm{\"o}glich in der digitalen Welt abzubilden. Lerninhalte, die bisher mittels Bildern und Texten f{\"u}r Lehrende und Lernende zug{\"a}nglich gemacht wurden, werden nunmehr mit weiteren Medien, insbesondere Videos, angereichert um deren Verst{\"a}ndnis zu erh{\"o}hen. Dies ist beispielsweise geeignet, um Bewegungsabl{\"a}ufe im Sport (vergleiche dazu den Beitrag von Owassapian und Hensinger) oder musikpraktische {\"U}bungen wie Bodyperkussion (beschrieben im Beitrag von Buschmann und Glasemann) zu erlernen Lernendenfokussierung, pers{\"o}nlicher Austausch, Mobilit{\"a}t und Transmedialit{\"a}t sind somit einige der Kernthemen, die Sie in diesem Sammelband erwarten. Auch zeigt die h{\"a}ufige Verkn{\"u}pfung verschedener dieser Kernthemen, dass keines davon ein Randthema ist, sondern sich die Summe aus allen im E-Learning b{\"u}ndelt und damit eine neue Qualit{\"a}t f{\"u}r Lehre, Studium und Forschung erreicht werden kann.},
  language  = {mul}
}
@phdthesis{Fudickar2014,
  author    = {Fudickar, Sebastian},
  title     = {Sub Ghz transceiver for indoor localisation of smartphones},
  school      = {Universit{\"a}t Potsdam},
  pages     = {IV, 167},
  year      = {2014},
  language  = {en}
}
@article{GaroufiKoller2014,
  author    = {Garoufi, Konstantina and Koller, Alexander},
  title     = {Generation of effective referring expressions in situated context},
  series = {Language, cognition and neuroscience},
  volume    = {29},
  journal   = {Language, cognition and neuroscience},
  number    = {8},
  publisher = {Routledge, Taylor \& Francis Group},
  address   = {Abingdon},
  issn      = {2327-3798},
  doi       = {10.1080/01690965.2013.847190},
  pages     = {986 -- 1001},
  year      = {2014},
  abstract  = {In task-oriented communication, references often need to be effective in their distinctive function, that is, help the hearer identify the referent correctly and as effortlessly as possible. However, it can be challenging for computational or empirical studies to capture referential effectiveness. Empirical findings indicate that human-produced references are not always optimally effective, and that their effectiveness may depend on different aspects of the situational context that can evolve dynamically over the course of an interaction. On this basis, we propose a computational model of effective reference generation which distinguishes speaker behaviour according to its helpfulness to the hearer in a certain situation, and explicitly aims at modelling highly helpful speaker behaviour rather than speaker behaviour invariably. Our model, which extends the planning-based paradigm of sentence generation with a statistical account of effectiveness, can adapt to the situational context by making this distinction newly for each new reference. We find that the generated references resemble those of effective human speakers more closely than references of baseline models, and that they are resolved correctly more often than those of other models participating in a shared-task evaluation with human hearers. Finally, we argue that the model could serve as a methodological framework for computational and empirical research on referential effectiveness.},
  language  = {en}
}
@phdthesis{Gericke2014,
  author    = {Gericke, Lutz},
  title     = {Tele-Board - Supporting and analyzing creative collaboration in synchronous and asynchronous scenario},
  pages     = {186},
  year      = {2014},
  language  = {en}
}
@article{GieseHildebrandtLambers2014,
  author    = {Giese, Holger and Hildebrandt, Stephan and Lambers, Leen},
  title     = {Bridging the gap between formal semantics and implementation of triple graph grammars},
  series = {Software and systems modeling},
  volume    = {13},
  journal   = {Software and systems modeling},
  number    = {1},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {1619-1366},
  doi       = {10.1007/s10270-012-0247-y},
  pages     = {273 -- 299},
  year      = {2014},
  abstract  = {The correctness of model transformations is a crucial element for model-driven engineering of high-quality software. A prerequisite to verify model transformations at the level of the model transformation specification is that an unambiguous formal semantics exists and that the implementation of the model transformation language adheres to this semantics. However, for existing relational model transformation approaches, it is usually not really clear under which constraints particular implementations really conform to the formal semantics. In this paper, we will bridge this gap for the formal semantics of triple graph grammars (TGG) and an existing efficient implementation. While the formal semantics assumes backtracking and ignores non-determinism, practical implementations do not support backtracking, require rule sets that ensure determinism, and include further optimizations. Therefore, we capture how the considered TGG implementation realizes the transformation by means of operational rules, define required criteria, and show conformance to the formal semantics if these criteria are fulfilled. We further outline how static and runtime checks can be employed to guarantee these criteria.},
  language  = {en}
}
@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{Holler2014,
  author    = {Holler, Robin},
  title     = {GraffDok - a graffiti documentation application},
  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     = {239 -- 251},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{HoosLindauerSchaub2014,
  author    = {Hoos, Holger and Lindauer, Marius and Schaub, Torsten H.},
  title     = {claspfolio 2},
  series = {Theory and practice of logic programming},
  volume    = {14},
  journal   = {Theory and practice of logic programming},
  publisher = {Cambridge Univ. Press},
  address   = {New York},
  issn      = {1471-0684},
  doi       = {10.1017/S1471068414000210},
  pages     = {569 -- 585},
  year      = {2014},
  abstract  = {Building on the award-winning, portfolio-based ASP solver claspfolio, we present claspfolio 2, a modular and open solver architecture that integrates several different portfolio-based algorithm selection approaches and techniques. The claspfolio 2 solver framework supports various feature generators, solver selection approaches, solver portfolios, as well as solver-schedule-based pre-solving techniques. The default configuration of claspfolio 2 relies on a light-weight version of the ASP solver clasp to generate static and dynamic instance features. The flexible open design of claspfolio 2 is a distinguishing factor even beyond ASP. As such, it provides a unique framework for comparing and combining existing portfolio-based algorithm selection approaches and techniques in a single, unified framework. Taking advantage of this, we conducted an extensive experimental study to assess the impact of different feature sets, selection approaches and base solver portfolios. In addition to gaining substantial insights into the utility of the various approaches and techniques, we identified a default configuration of claspfolio 2 that achieves substantial performance gains not only over clasp's default configuration and the earlier version of claspfolio, but also over manually tuned configurations of clasp.},
  language  = {en}
}
@inproceedings{KiyGruenwaldZoerneretal.2014,
  author    = {Kiy, Alexander and Gr{\"u}nwald, Franka and Zoerner, Dietmar and Lucke, Ulrike},
  title     = {Ein Hochschul-App-Framework: Hybrid und modular},
  series = {DeLFI 2014 - Die 12. e-Learning Fachtagung Informatik Lecture Notes in Informatics},
  booktitle = {DeLFI 2014 - Die 12. e-Learning Fachtagung Informatik Lecture Notes in Informatics},
  number    = {P-233},
  editor    = {Trasch, Stephan and Pl{\"o}tzner, Rolf and Schneider, Gerhard and Sassiat, Daniel and Gayer, Claudia and W{\"o}hrle, Nicole},
  publisher = {Gesellschaft f{\"u}r Informatik e.V.},
  address   = {Bonn},
  isbn      = {978-3-88579-627-5},
  pages     = {205 -- 216},
  year      = {2014},
  abstract  = {Mobile Endger{\"a}te und die dazugeh{\"o}rigen Applikationen sind zu einem unverzichtbaren Bestandteil des t{\"a}glichen Lebens geworden und erm{\"o}glichen den ortsund zeitunabh{\"a}ngigen Zugriff auf wichtige Informationen. Hochschulspezifische An- gebote sind im mobilen Bereich hingegen noch immer nicht fl{\"a}chendeckend anzutreffen und lassen sich i. d. R. nur auf Einzelaktivit{\"a}ten Studierender und Lehrender zur{\"u}ckf{\"u}hren. Dabei k{\"o}nnen mobile Applikationen einen essentiellen Beitrag zur Verbesserung der studentischen Selbstorganisation sowie f{\"u}r die Ausgestaltung und Erg{\"a}nzung von konkreten Lehr-/Lernszenarien leisten. Dieser Artikel stellt ein modulares Hochschul-App-Framework vor, das sowohl zentrale campusbezogene Dienste als auch dezentrale Lernapplikationen unter einer Oberfl{\"a}che vereint anbietet. Anhand einer Analyse von St{\"a}rken und Schw{\"a}chen werden verschiedene Ans{\"a}tze in Hinblick auf Anforderungen, Entwicklung, Wartung und Betrieb der Hochschul-App zusammengefasst und bewertet. Es wird auf die zugrundeliegende serviceorientierte Architektur eingegangen, die eine Portierung der Applikation auf andere Hochschulen mit einem vertretbaren Aufwand erm{\"o}glicht. Der Beitrag schließt mit einer Darstellung der ersten Ergebnisse und weiterf{\"u}hrender {\"U}berlegungen und Arbeiten.},
  language  = {de}
}
@inproceedings{KiyLucke2014,
  author    = {Kiy, Alexander and Lucke, Ulrike},
  title     = {Learning analytic tools in practical comparison},
  series = {DeLFI Workshops of the 12th e-Learning Conference of the German Computer Society, DeLFI 2014; Freiburg; Germany; 15 September 2014 through 15 September 2014 CEUR Workshop Proceedings},
  volume    = {2014},
  booktitle = {DeLFI Workshops of the 12th e-Learning Conference of the German Computer Society, DeLFI 2014; Freiburg; Germany; 15 September 2014 through 15 September 2014 CEUR Workshop Proceedings},
  number    = {1227},
  editor    = {Rensing, C. and Trahasch, S.},
  publisher = {Technical University of Aachen},
  address   = {Aachen},
  issn      = {1613-0073},
  pages     = {104 -- 111},
  year      = {2014},
  language  = {en}
}
@incollection{KiyLuckeZoerner2014,
  author    = {Kiy, Alexander and Lucke, Ulrike and Zoerner, Dietmar},
  title     = {An adaptive personal learning environment architecture},
  series = {Architecture of Computing Systems - ARCS 2014 Lecture Notes in Computer Science},
  volume    = {2014},
  booktitle = {Architecture of Computing Systems - ARCS 2014 Lecture Notes in Computer Science},
  number    = {8350},
  publisher = {Springer},
  isbn      = {978-3-319-04890-1},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {60 -- 71},
  year      = {2014},
  abstract  = {Institutions are facing the challenge to integrate legacy systems with steadily growing new ones, using different technologies and interaction patterns. With the demand of offering the best potential of all systems, several not matching systems including their functions have to be aggregated and offered in a useable way. This paper presents an adaptive, generalizable and self-organized Personal Learning Environment (PLE) framework with the potential to integrate several heterogeneous services using a service-oriented architecture. First, a general overview over the field is given, followed by the description of the core components of the PLE framework. A prototypical implementation is presented. Finally, it's shown how the PLE framework can be dynamically adapted to a changing system environment, reflecting experiences from first user studies.},
  language  = {en}
}
@inproceedings{KnothKiy2014,
  author    = {Knoth, Alexander Henning and Kiy, Alexander},
  title     = {(Self-)confident through the introductory study phase with the Reflect App},
  series = {CEUR Workshop Proceedings},
  booktitle = {CEUR Workshop Proceedings},
  number    = {1227},
  publisher = {CEUR-WS},
  address   = {Freiburg},
  issn      = {1613-0073},
  pages     = {172 -- 179},
  year      = {2014},
  language  = {en}
}
@phdthesis{Krueger2014,
  author    = {Kr{\"u}ger, Jens},
  title     = {Enterprise-specific in-memory data managment : HYRISEc - an in-memory column store engine for OLXP},
  publisher = {Hasso-Plattner-Insitut},
  address   = {Potsdam},
  pages     = {201 S.},
  year      = {2014},
  language  = {en}
}
@article{Kuntzsch2014,
  author    = {Kuntzsch, Christian},
  title     = {Visualization of data transfer paths},
  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     = {140 -- 148},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{LamprechtMargaria2014,
  author    = {Lamprecht, Anna-Lena and Margaria, Tiziana},
  title     = {Scientific Workflows and XMDD},
  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     = {1 -- 13},
  year      = {2014},
  abstract  = {A major part of the scientific experiments that are carried out today requires thorough computational support. While database and algorithm providers face the problem of bundling resources to create and sustain powerful computation nodes, the users have to deal with combining sets of (remote) services into specific data analysis and transformation processes. Today's attention to "big data" amplifies the issues of size, heterogeneity, and process-level diversity/integration. In the last decade, especially workflow-based approaches to deal with these processes have enjoyed great popularity. This book concerns a particularly agile and model-driven approach to manage scientific workflows that is based on the XMDD paradigm. In this chapter we explain the scope and purpose of the book, briefly describe the concepts and technologies of the XMDD paradigm, explain the principal differences to related approaches, and outline the structure of the book.},
  language  = {en}
}
@article{LamprechtMargariaSteffen2014,
  author    = {Lamprecht, Anna-Lena and Margaria, Tiziana and Steffen, Bernhard},
  title     = {Modeling and Execution of Scientific Workflows with the jABC Framework},
  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     = {14 -- 29},
  year      = {2014},
  abstract  = {We summarize here the main characteristics and features of the jABC framework, used in the case studies as a graphical tool for modeling scientific processes and workflows. As a comprehensive environment for service-oriented modeling and design according to the XMDD (eXtreme Model-Driven Design) paradigm, the jABC offers much more than the pure modeling capability. Associated technologies and plugins provide in fact means for a rich variety of supporting functionality, such as remote service integration, taxonomical service classification, model execution, model verification, model synthesis, and model compilation. We describe here in short both the essential jABC features and the service integration philosophy followed in the environment. In our work over the last years we have seen that this kind of service definition and provisioning platform has the potential to become a core technology in interdisciplinary service orchestration and technology transfer: Domain experts, like scientists not specially trained in computer science, directly define complex service orchestrations as process models and use efficient and complex domain-specific tools in a simple and intuitive way.},
  language  = {en}
}
@article{LamprechtWickert2014,
  author    = {Lamprecht, Anna-Lena and Wickert, Alexander},
  title     = {The Course's SIB Libraries},
  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     = {30 -- 44},
  year      = {2014},
  abstract  = {This chapter gives a detailed description of the service framework underlying all the example projects that form the foundation of this book. It describes the different SIB libraries that we made available for the course "Process modeling in the natural sciences" to provide the functionality that was required for the envisaged applications. The students used these SIB libraries to realize their projects.},
  language  = {en}
}
@article{LamprechtWickertMargaria2014,
  author    = {Lamprecht, Anna-Lena and Wickert, Alexander and Margaria, Tiziana},
  title     = {Lessons Learned},
  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     = {45 -- 64},
  year      = {2014},
  abstract  = {This chapter summarizes the experience and the lessons we learned concerning the application of the jABC as a framework for design and execution of scientific workflows. It reports experiences from the domain modeling (especially service integration) and workflow design phases and evaluates the resulting models statistically with respect to the SIB library and hierarchy levels.},
  language  = {en}
}
@phdthesis{Lincke2014,
  author    = {Lincke, Jens},
  title     = {Evolving Tools in a Collaborative Self-supporting Development Environment},
  school      = {Universit{\"a}t Potsdam},
  pages     = {164},
  year      = {2014},
  language  = {en}
}
@phdthesis{Lindauer2014,
  author    = {Lindauer, T. Marius},
  title     = {Algorithm selection, scheduling and configuration of Boolean constraint solvers},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-71260},
  school      = {Universit{\"a}t Potsdam},
  pages     = {ii, 130},
  year      = {2014},
  abstract  = {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.},
  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}
}
@article{LuckeRensing2014,
  author    = {Lucke, Ulrike and Rensing, Christoph},
  title     = {A survey on pervasive education},
  series = {Pervasive and mobile computing},
  volume    = {14},
  journal   = {Pervasive and mobile computing},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {1574-1192},
  doi       = {10.1016/j.pmcj.2013.12.001},
  pages     = {3 -- 16},
  year      = {2014},
  abstract  = {Researchers and developers worldwide have put their efforts into the design, development and use of information and communication technology to support teaching and learning. This research is driven by pedagogical as well as technological disciplines. The most challenging ideas are currently found in the application of mobile, ubiquitous, pervasive, contextualized and seamless technologies for education, which we shall refer to as pervasive education. This article provides a comprehensive overview of the existing work in this field and categorizes it with respect to educational settings. Using this approach, best practice solutions for certain educational settings and open questions for pervasive education are highlighted in order to inspire interested developers and educators. The work is assigned to different fields, identified by the main pervasive technologies used and the educational settings. Based on these assignments we identify areas within pervasive education that are currently disregarded or deemed challenging so that further research and development in these fields are stimulated in a trans-disciplinary approach. (C) 2013 Elsevier B.V. All rights reserved.},
  language  = {en}
}
@unpublished{LuckeSteinmetz2014,
  author    = {Lucke, Ulrike and Steinmetz, Ralf},
  title     = {Special issue on "Pervasive Education"},
  series = {Pervasive and mobile computing},
  volume    = {14},
  journal   = {Pervasive and mobile computing},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {1574-1192},
  doi       = {10.1016/j.pmcj.2014.08.001},
  pages     = {1 -- 2},
  year      = {2014},
  language  = {en}
}
@article{NaujokatNeubauerLamprechtetal.2014,
  author    = {Naujokat, Stefan and Neubauer, Johannes and Lamprecht, Anna-Lena and Steffen, Bernhard and Joerges, Sven and Margaria, Tiziana},
  title     = {Simplicity-first model-based plug-in development},
  series = {Software : practice \& experience},
  volume    = {44},
  journal   = {Software : practice \& experience},
  number    = {3},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0038-0644},
  doi       = {10.1002/spe.2243},
  pages     = {277 -- 297},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Noack2014,
  author    = {Noack, Franziska},
  title     = {CREADED: Colored-Relief application for digital elevation data},
  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     = {186 -- 199},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@phdthesis{Rafiee2014,
  author    = {Rafiee, Hosnieh},
  title     = {Privacy and security issues in IPv6 networks},
  address   = {Potsdam},
  pages     = {141 S.},
  year      = {2014},
  language  = {en}
}
@article{Reso2014,
  author    = {Reso, Judith},
  title     = {Protein Classification Workflow},
  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     = {65 -- 72},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Respondek2014,
  author    = {Respondek, Tobias},
  title     = {A workflow for computing potential areas for wind turbines},
  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},
  pages     = {200 -- 215},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@phdthesis{Schacht2014,
  author    = {Schacht, Alexander},
  title     = {Konzepte und Strategien mobiler Plattformen zur Erfassung und Anlayse von Vitalparametern in heterogenen Telemonotoring-Systemen},
  pages     = {215},
  year      = {2014},
  language  = {de}
}
@article{Scheele2014,
  author    = {Scheele, Lasse},
  title     = {Location analysis for placing artificial reefs},
  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     = {216 -- 228},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{SchickBojahrHerzogetal.2014,
  author    = {Schick, Daniel and Bojahr, Andre and Herzog, Marc and Shayduk, Roman and von Korff Schmising, Clemens and Bargheer, Matias},
  title     = {Udkm1Dsim-A simulation toolkit for 1D ultrafast dynamics in condensed matter},
  series = {Computer physics communications : an international journal devoted to computational physics and computer programs in physics},
  volume    = {185},
  journal   = {Computer physics communications : an international journal devoted to computational physics and computer programs in physics},
  number    = {2},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0010-4655},
  doi       = {10.1016/j.cpc.2013.10.009},
  pages     = {651 -- 660},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@phdthesis{Schnjakin2014,
  author    = {Schnjakin, Maxim},
  title     = {Cloud-RAID},
  pages     = {137},
  year      = {2014},
  language  = {de}
}
@article{Schulze2014,
  author    = {Schulze, Gunnar},
  title     = {Workflow for rapid metagenome analysis},
  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     = {88 -- 100},
  year      = {2014},
  abstract  = {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},
  language  = {en}
}
@article{Schuett2014,
  author    = {Sch{\"u}tt, Christine},
  title     = {Identification of differentially expressed genes},
  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     = {127 -- 139},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Sens2014,
  author    = {Sens, Henriette},
  title     = {Web-Based map generalization tools put to the test: a jABC workflow},
  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     = {175 -- 185},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Teske2014,
  author    = {Teske, Daniel},
  title     = {Geocoder accuracy ranking},
  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     = {161 -- 174},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{TroegerMerzky2014,
  author    = {Troeger, Peter and Merzky, Andre},
  title     = {Towards standardized job submission and control in infrastructure clouds},
  series = {Journal of grid computing},
  volume    = {12},
  journal   = {Journal of grid computing},
  number    = {1},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {1570-7873},
  doi       = {10.1007/s10723-013-9275-2},
  pages     = {111 -- 125},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@phdthesis{Videla2014,
  author    = {Videla, Santiago},
  title     = {Reasoning on the response of logical signaling networks with answer set programming},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-71890},
  school      = {Universit{\"a}t Potsdam},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{Vierheller2014,
  author    = {Vierheller, Janine},
  title     = {Exploratory Data Analysis},
  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 = {Axel Springer Verlag},
  address   = {Berlin},
  isbn      = {978-3-662-45005-5},
  issn      = {1865-0929},
  pages     = {110 -- 126},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{WeiherHirschfeld2014,
  author    = {Weiher, Marcel and Hirschfeld, Robert},
  title     = {Polymorphic identifiers: uniform resource access in objective-smalltalk},
  series = {ACM SIGPLAN notices},
  volume    = {49},
  journal   = {ACM SIGPLAN notices},
  number    = {2},
  publisher = {Association for Computing Machinery},
  address   = {New York},
  issn      = {0362-1340},
  doi       = {10.1145/2508168.2508169},
  pages     = {61 -- 71},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{ZenderMetzlerLucke2014,
  author    = {Zender, Raphael and Metzler, Richard and Lucke, Ulrike},
  title     = {FreshUP-A pervasive educational game for freshmen},
  series = {Pervasive and mobile computing},
  volume    = {14},
  journal   = {Pervasive and mobile computing},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {1574-1192},
  doi       = {10.1016/j.pmcj.2013.09.003},
  pages     = {47 -- 56},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{ZoernerKoehlmannBrandt2014,
  author    = {Zoerner, Dietmar and K{\"o}hlmann, Wiebke and Brandt, Christopher},
  title     = {Mobiles spielebasiertes Lernen an historischen Lernorten},
  series = {E-Learning Symposium 2014 : Mobil und vernetzt - studieren im digitalen Zeitalter ; Potsdam, 14. November 2014},
  journal   = {E-Learning Symposium 2014 : Mobil und vernetzt - studieren im digitalen Zeitalter ; Potsdam, 14. November 2014},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  doi       = {10.25932/publishup-44235},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-442354},
  pages     = {53 -- 54},
  year      = {2014},
  abstract  = {Im Rahmen eines interdisziplin{\"a}ren studentischen Projekts wurde ein Framework f{\"u}r mobile pervasive Lernspiele entwickelt. Am Beispiel des historischen Lernortes Park Sanssouci wurde auf dieser Grundlage ein Lernspiel f{\"u}r Sch{\"u}lerinnen und Sch{\"u}ler implementiert. Die geplante Evaluation soll die Lernwirksamkeit von geobasierten mobilen Lernspielen messen. Dazu wird die Intensit{\"a}t des Flow-Erlebens mit einer ortsgebundenen alternativen Umsetzung verglichen.},
  language  = {de}
}
@book{OPUS4-7534,
  title     = {Process design for natural scientists},
  series = {Communications in computer and information science ; 500},
  journal   = {Communications in computer and information science ; 500},
  editor    = {Lambrecht, Anna-Lena and Margaria, Tizian},
  publisher = {Springer},
  address   = {Wiesbaden},
  isbn      = {978-3-662-45005-5},
  pages     = {X, 251},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}