@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{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{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{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}
}
@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}
}
@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}
}
@phdthesis{Gericke2014,
  author    = {Gericke, Lutz},
  title     = {Tele-Board - Supporting and analyzing creative collaboration in synchronous and asynchronous scenario},
  pages     = {186},
  year      = {2014},
  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{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}
}
@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{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}
}
@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{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}
}
@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}
}
@phdthesis{Rafiee2014,
  author    = {Rafiee, Hosnieh},
  title     = {Privacy and security issues in IPv6 networks},
  address   = {Potsdam},
  pages     = {141 S.},
  year      = {2014},
  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{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{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}
}
@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}
}