@book{OPUS4-6982,
  title     = {HPI Future SOC Lab},
  number    = {88},
  editor    = {Meinel, Christoph and Polze, Andreas and Oswald, Gerhard and Strotmann, Rolf and Seibold, Ulrich and Schulzki, Bernard},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-282-7},
  issn      = {1613-5652},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-68195},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {iii, 174},
  year      = {2014},
  abstract  = {The "HPI Future SOC Lab" is a cooperation of the Hasso-Plattner-Institut (HPI) and industrial partners. Its mission is to enable and promote exchange and interaction between the research community and the industrial partners. The HPI Future SOC Lab provides researchers with free of charge access to a complete infrastructure of state of the art hard- and software. This infrastructure includes components, which might be too expensive for an ordinary research environment, such as servers with up to 64 cores. The offerings address researchers particularly from but not limited to the areas of computer science and business information systems. Main areas of research include cloud computing, parallelization, and In-Memory technologies. This technical report presents results of research projects executed in 2013. Selected projects have presented their results on April 10th and September 24th 2013 at the Future SOC Lab Day events.},
  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}
}
@phdthesis{Abedjan2014,
  author    = {Abedjan, Ziawasch},
  title     = {Improving RDF data with data mining},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-71334},
  school      = {Universit{\"a}t Potsdam},
  year      = {2014},
  abstract  = {Linked Open Data (LOD) comprises very many and often large public data sets and knowledge bases. Those datasets are mostly presented in the RDF triple structure of subject, predicate, and object, where each triple represents a statement or fact. Unfortunately, the heterogeneity of available open data requires significant integration steps before it can be used in applications. Meta information, such as ontological definitions and exact range definitions of predicates, are desirable and ideally provided by an ontology. However in the context of LOD, ontologies are often incomplete or simply not available. Thus, it is useful to automatically generate meta information, such as ontological dependencies, range definitions, and topical classifications. Association rule mining, which was originally applied for sales analysis on transactional databases, is a promising and novel technique to explore such data. We designed an adaptation of this technique for min-ing Rdf data and introduce the concept of "mining configurations", which allows us to mine RDF data sets in various ways. Different configurations enable us to identify schema and value dependencies that in combination result in interesting use cases. To this end, we present rule-based approaches for auto-completion, data enrichment, ontology improvement, and query relaxation. Auto-completion remedies the problem of inconsistent ontology usage, providing an editing user with a sorted list of commonly used predicates. A combination of different configurations step extends this approach to create completely new facts for a knowledge base. We present two approaches for fact generation, a user-based approach where a user selects the entity to be amended with new facts and a data-driven approach where an algorithm discovers entities that have to be amended with missing facts. As knowledge bases constantly grow and evolve, another approach to improve the usage of RDF data is to improve existing ontologies. Here, we present an association rule based approach to reconcile ontology and data. Interlacing different mining configurations, we infer an algorithm to discover synonymously used predicates. Those predicates can be used to expand query results and to support users during query formulation. We provide a wide range of experiments on real world datasets for each use case. The experiments and evaluations show the added value of association rule mining for the integration and usability of RDF data and confirm the appropriateness of our mining configuration methodology.},
  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{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}
}
@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}
}
@misc{EhrigGolasHabeletal.2014,
  author    = {Ehrig, Hartmut and Golas, Ulrike and Habel, Annegret and Lambers, Leen and Orejas, Fernando},
  title     = {M-adhesive transformation systems with nested application conditions},
  series = {Postprints der Universit{\"a}t Potsdam : Digital Engineering Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Digital Engineering Reihe},
  number    = {001},
  doi       = {10.25932/publishup-41565},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415651},
  pages     = {50},
  year      = {2014},
  abstract  = {Nested application conditions generalise the well-known negative application conditions and are important for several application domains. In this paper, we present Local Church-Rosser, Parallelism, Concurrency and Amalgamation Theorems for rules with nested application conditions in the framework of M-adhesive categories, where M-adhesive categories are slightly more general than weak adhesive high-level replacement categories. Most of the proofs are based on the corresponding statements for rules without application conditions and two shift lemmas stating that nested application conditions can be shifted over morphisms and rules.},
  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}
}
@book{MeinelWillems2014,
  author    = {Meinel, Christoph and Willems, Christian},
  title     = {openHPI : 哈索•普拉特纳研究院的 MOOC（大规模公开在线课）计划},
  number    = {89},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-291-9},
  issn      = {1613-5652},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70380},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {22},
  year      = {2014},
  abstract  = {摘要。哈索•普拉特纳研究院 (HPI) 的新型互动在线教育平台 openHPI (https://openHPI.de) 可以为从事信息技术和信息学领域内容的工作和感兴趣的学员提供可自由访问的、免费的在线课程。与斯坦福大学于 2011 年首推，之后也在美国其他精英大学提供的"网络公开群众课"（简称 MOOC）一样，openHPI 同样在互联网中提供学习视频和阅读材料，其中综合了支持学习的自我测试、家庭作业和社交讨论论坛，并刺激对促进学习的虚拟学习团队的培训。与"传统的"讲座平台，比如 tele-TASK 平台 (http://www.tele-task.de) 不同（在该平台中，可调用以多媒体方式记录的和已准备好的讲座），openHPI 提供的是按教学法准备的在线课程。这些课程的开始时间固定，之后在连续六个课程周稳定的提供以多媒体方式准备的、尽可能可以互动的学习材料。每周讲解课程主题的一章。为此在该周开始前会准备一系列学习视频、文字、自我测试和家庭作业材料，课程学员在该周将精力用于处理这些内容。这些计划与一个社交讨论平台相结合，学员在该平台上可以与课程导师和其他学员交换意见、解答问题和讨论更多主题。当然，学员可以自己决定学习活动的类型和范围。他们可以为课程作出自己的贡献，比如在论坛中引用博文或推文。之后其他学员可以评论、讨论或自己扩展这些博文或推文。这样学员、教师和提供的学习内容就在一个虚拟的团体中与社交学习网络相互结合起来。},
  language  = {de}
}
@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}
}
@phdthesis{RoggeSolti2014,
  author    = {Rogge-Solti, Andreas},
  title     = {Probabilistic Estimation of Unobserved Process Events},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70426},
  school      = {Universit{\"a}t Potsdam},
  year      = {2014},
  abstract  = {Organizations try to gain competitive advantages, and to increase customer satisfaction. To ensure the quality and efficiency of their business processes, they perform business process management. An important part of process management that happens on the daily operational level is process controlling. A prerequisite of controlling is process monitoring, i.e., keeping track of the performed activities in running process instances. Only by process monitoring can business analysts detect delays and react to deviations from the expected or guaranteed performance of a process instance. To enable monitoring, process events need to be collected from the process environment. When a business process is orchestrated by a process execution engine, monitoring is available for all orchestrated process activities. Many business processes, however, do not lend themselves to automatic orchestration, e.g., because of required freedom of action. This situation is often encountered in hospitals, where most business processes are manually enacted. Hence, in practice it is often inefficient or infeasible to document and monitor every process activity. Additionally, manual process execution and documentation is prone to errors, e.g., documentation of activities can be forgotten. Thus, organizations face the challenge of process events that occur, but are not observed by the monitoring environment. These unobserved process events can serve as basis for operational process decisions, even without exact knowledge of when they happened or when they will happen. An exemplary decision is whether to invest more resources to manage timely completion of a case, anticipating that the process end event will occur too late. This thesis offers means to reason about unobserved process events in a probabilistic way. We address decisive questions of process managers (e.g., "when will the case be finished?", or "when did we perform the activity that we forgot to document?") in this thesis. As main contribution, we introduce an advanced probabilistic model to business process management that is based on a stochastic variant of Petri nets. We present a holistic approach to use the model effectively along the business process lifecycle. Therefore, we provide techniques to discover such models from historical observations, to predict the termination time of processes, and to ensure quality by missing data management. We propose mechanisms to optimize configuration for monitoring and prediction, i.e., to offer guidance in selecting important activities to monitor. An implementation is provided as a proof of concept. For evaluation, we compare the accuracy of the approach with that of state-of-the-art approaches using real process data of a hospital. Additionally, we show its more general applicability in other domains by applying the approach on process data from logistics and finance.},
  language  = {en}
}
@book{MeinelPlattnerDoellneretal.2014,
  author    = {Meinel, Christoph and Plattner, Hasso and D{\"o}llner, J{\"u}rgen Roland Friedrich and Weske, Mathias and Polze, Andreas and Hirschfeld, Robert and Naumann, Felix and Giese, Holger and Baudisch, Patrick},
  title     = {Proceedings of the 7th Ph.D. Retreat of the HPI Research School on Service-oriented Systems Engineering},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-273-5},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-63490},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {ii, 218},
  year      = {2014},
  abstract  = {Design and Implementation of service-oriented architectures imposes a huge number of research questions from the fields of software engineering, system analysis and modeling, adaptability, and application integration. Component orientation and web services are two approaches for design and realization of complex web-based system. Both approaches allow for dynamic application adaptation as well as integration of enterprise application. Commonly used technologies, such as J2EE and .NET, form de facto standards for the realization of complex distributed systems. Evolution of component systems has lead to web services and service-based architectures. This has been manifested in a multitude of industry standards and initiatives such as XML, WSDL UDDI, SOAP, etc. All these achievements lead to a new and promising paradigm in IT systems engineering which proposes to design complex software solutions as collaboration of contractually defined software services. Service-Oriented Systems Engineering represents a symbiosis of best practices in object-orientation, component-based development, distributed computing, and business process management. It provides integration of business and IT concerns. The annual Ph.D. Retreat of the Research School provides each member the opportunity to present his/her current state of their research and to give an outline of a prospective Ph.D. thesis. Due to the interdisciplinary structure of the Research Scholl, this technical report covers a wide range of research topics. These include but are not limited to: Self-Adaptive Service-Oriented Systems, Operating System Support for Service-Oriented Systems, Architecture and Modeling of Service-Oriented Systems, Adaptive Process Management, Services Composition and Workflow Planning, Security Engineering of Service-Based IT Systems, Quantitative Analysis and Optimization of Service-Oriented Systems, Service-Oriented Systems in 3D Computer Graphics sowie Service-Oriented Geoinformatics.},
  language  = {en}
}
@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}
}
@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}
}
@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}
}
@misc{BoeckmannOsterloh2014,
  author    = {B{\"o}ckmann, Christine and Osterloh, Lukas},
  title     = {Runge-Kutta type regularization method for inversion of spheroidal particle distribution from limited optical data},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {907},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44120},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441200},
  pages     = {150 -- 165},
  year      = {2014},
  abstract  = {The Runge-Kutta type regularization method was recently proposed as a potent tool for the iterative solution of nonlinear ill-posed problems. In this paper we analyze the applicability of this regularization method for solving inverse problems arising in atmospheric remote sensing, particularly for the retrieval of spheroidal particle distribution. Our numerical simulations reveal that the Runge-Kutta type regularization method is able to retrieve two-dimensional particle distributions using optical backscatter and extinction coefficient profiles, as well as depolarization information.},
  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{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}
}
@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{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{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}
}
@phdthesis{Truemper2014,
  author    = {Tr{\"u}mper, Jonas},
  title     = {Visualization techniques for the analysis of software behavior and related structures},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72145},
  school      = {Universit{\"a}t Potsdam},
  year      = {2014},
  abstract  = {Software maintenance encompasses any changes made to a software system after its initial deployment and is thereby one of the key phases in the typical software-engineering lifecycle. In software maintenance, we primarily need to understand structural and behavioral aspects, which are difficult to obtain, e.g., by code reading. Software analysis is therefore a vital tool for maintaining these systems: It provides - the preferably automated - means to extract and evaluate information from their artifacts such as software structure, runtime behavior, and related processes. However, such analysis typically results in massive raw data, so that even experienced engineers face difficulties directly examining, assessing, and understanding these data. Among other things, they require tools with which to explore the data if no clear question can be formulated beforehand. For this, software analysis and visualization provide its users with powerful interactive means. These enable the automation of tasks and, particularly, the acquisition of valuable and actionable insights into the raw data. For instance, one means for exploring runtime behavior is trace visualization. This thesis aims at extending and improving the tool set for visual software analysis by concentrating on several open challenges in the fields of dynamic and static analysis of software systems. This work develops a series of concepts and tools for the exploratory visualization of the respective data to support users in finding and retrieving information on the system artifacts concerned. This is a difficult task, due to the lack of appropriate visualization metaphors; in particular, the visualization of complex runtime behavior poses various questions and challenges of both a technical and conceptual nature. This work focuses on a set of visualization techniques for visually representing control-flow related aspects of software traces from shared-memory software systems: A trace-visualization concept based on icicle plots aids in understanding both single-threaded as well as multi-threaded runtime behavior on the function level. The concept's extensibility further allows the visualization and analysis of specific aspects of multi-threading such as synchronization, the correlation of such traces with data from static software analysis, and a comparison between traces. Moreover, complementary techniques for simultaneously analyzing system structures and the evolution of related attributes are proposed. These aim at facilitating long-term planning of software architecture and supporting management decisions in software projects by extensions to the circular-bundle-view technique: An extension to 3-dimensional space allows for the use of additional variables simultaneously; interaction techniques allow for the modification of structures in a visual manner. The concepts and techniques presented here are generic and, as such, can be applied beyond software analysis for the visualization of similarly structured data. The techniques' practicability is demonstrated by several qualitative studies using subject data from industry-scale software systems. The studies provide initial evidence that the techniques' application yields useful insights into the subject data and its interrelationships in several scenarios.},
  language  = {en}
}
@book{MeyerWeske2014,
  author    = {Meyer, Andreas and Weske, Mathias},
  title     = {Weak conformance between process models and synchronized object life cycles},
  number    = {91},
  publisher = {Universit{\"a}tsverlag Potsdam},
  address   = {Potsdam},
  isbn      = {978-3-86956-303-9},
  issn      = {1613-5652},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-71722},
  publisher      = {Universit{\"a}t Potsdam},
  pages     = {31},
  year      = {2014},
  abstract  = {Process models specify behavioral execution constraints between activities as well as between activities and data objects. A data object is characterized by its states and state transitions represented as object life cycle. For process execution, all behavioral execution constraints must be correct. Correctness can be verified via soundness checking which currently only considers control flow information. For data correctness, conformance between a process model and its object life cycles is checked. Current approaches abstract from dependencies between multiple data objects and require fully specified process models although, in real-world process repositories, often underspecified models are found. Coping with these issues, we introduce the concept of synchronized object life cycles and we define a mapping of data constraints of a process model to Petri nets extending an existing mapping. Further, we apply the notion of weak conformance to process models to tell whether each time an activity needs to access a data object in a particular state, it is guaranteed that the data object is in or can reach the expected state. Then, we introduce an algorithm for an integrated verification of control flow correctness and weak data conformance using soundness checking.},
  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}
}
@misc{Voland2014,
  type      = {Master Thesis},
  author    = {Voland, Patrick},
  title     = {Webbasierte Visualisierung von Extended Floating Car Data (XFCD)},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-96751},
  school      = {Universit{\"a}t Potsdam},
  pages     = {VIII, 176},
  year      = {2014},
  abstract  = {Moderne Kraftfahrzeuge verf{\"u}gen {\"u}ber eine Vielzahl an Sensoren, welche f{\"u}r einen reibungslosen technischen Betrieb ben{\"o}tigt werden. Hierzu z{\"a}hlen neben fahrzeugspezifischen Sensoren (wie z.B. Motordrehzahl und Fahrzeuggeschwindigkeit) auch umweltspezifische Sensoren (wie z.B. Luftdruck und Umgebungstemperatur). Durch die zunehmende technische Vernetzung wird es m{\"o}glich, diese Daten der Kraftfahrzeugelektronik aus dem Fahrzeug heraus f{\"u}r die verschiedensten Zwecke zu verwenden. Die vorliegende Arbeit soll einen Beitrag dazu leisten, diese neue Art an massenhaften Daten im Sinne des Konzepts der „Extended Floating Car Data" (XFCD) als Geoinformationen nutzbar zu machen und diese f{\"u}r raumzeitliche Visualisierungen (zur visuellen Analyse) anwenden zu k{\"o}nnen. In diesem Zusammenhang wird speziell die Perspektive des Umwelt- und Verkehrsmonitoring betrachtet, wobei die Anforderungen und Potentiale mit Hilfe von Experteninterviews untersucht werden. Es stellt sich die Frage, welche Daten durch die Kraftfahrzeugelektronik geliefert und wie diese m{\"o}glichst automatisiert erfasst, verarbeitet, visualisiert und {\"o}ffentlich bereitgestellt werden k{\"o}nnen. Neben theoretischen und technischen Grundlagen zur Datenerfassung und -nutzung liegt der Fokus auf den Methoden der kartographischen Visualisierung. Dabei soll der Frage nachgegangenen werden, ob eine technische Implementierung ausschließlich unter Verwendung von Open Source Software m{\"o}glich ist. Das Ziel der Arbeit bildet ein zweigliedriger Ansatz, welcher zum einen die Visualisierung f{\"u}r ein exemplarisch gew{\"a}hltes Anwendungsszenario und zum anderen die prototypische Implementierung von der Datenerfassung im Fahrzeug unter Verwendung der gesetzlich vorgeschriebenen „On Board Diagnose"-Schnittstelle und einem Smartphone-gest{\"u}tzten Ablauf bis zur webbasierten Visualisierung umfasst.},
  language  = {de}
}
@phdthesis{Lorey2014,
  author    = {Lorey, Johannes},
  title     = {What's in a query : analyzing, predicting, and managing linked data access},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-72312},
  school      = {Universit{\"a}t Potsdam},
  year      = {2014},
  abstract  = {The term Linked Data refers to connected information sources comprising structured data about a wide range of topics and for a multitude of applications. In recent years, the conceptional and technical foundations of Linked Data have been formalized and refined. To this end, well-known technologies have been established, such as the Resource Description Framework (RDF) as a Linked Data model or the SPARQL Protocol and RDF Query Language (SPARQL) for retrieving this information. Whereas most research has been conducted in the area of generating and publishing Linked Data, this thesis presents novel approaches for improved management. In particular, we illustrate new methods for analyzing and processing SPARQL queries. Here, we present two algorithms suitable for identifying structural relationships between these queries. Both algorithms are applied to a large number of real-world requests to evaluate the performance of the approaches and the quality of their results. Based on this, we introduce different strategies enabling optimized access of Linked Data sources. We demonstrate how the presented approach facilitates effective utilization of SPARQL endpoints by prefetching results relevant for multiple subsequent requests. Furthermore, we contribute a set of metrics for determining technical characteristics of such knowledge bases. To this end, we devise practical heuristics and validate them through thorough analysis of real-world data sources. We discuss the findings and evaluate their impact on utilizing the endpoints. Moreover, we detail the adoption of a scalable infrastructure for improving Linked Data discovery and consumption. As we outline in an exemplary use case, this platform is eligible both for processing and provisioning the corresponding information.},
  language  = {en}
}
@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}
}