@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{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{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{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} } @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{HollmannFrohmeEndrullatetal.2020, author = {Hollmann, Susanne and Frohme, Marcus and Endrullat, Christoph and Kremer, Andreas and D'Elia, Domenica and Regierer, Babette and Nechyporenko, Alina}, title = {Ten simple rules on how to write a standard operating procedure}, series = {PLOS Computational Biology}, volume = {16}, journal = {PLOS Computational Biology}, number = {9}, publisher = {PLOS}, address = {San Francisco}, pages = {10}, year = {2020}, abstract = {Research publications and data nowadays should be publicly available on the internet and, theoretically, usable for everyone to develop further research, products, or services. The long-term accessibility of research data is, therefore, fundamental in the economy of the research production process. However, the availability of data is not sufficient by itself, but also their quality must be verifiable. Measures to ensure reuse and reproducibility need to include the entire research life cycle, from the experimental design to the generation of data, quality control, statistical analysis, interpretation, and validation of the results. Hence, high-quality records, particularly for providing a string of documents for the verifiable origin of data, are essential elements that can act as a certificate for potential users (customers). These records also improve the traceability and transparency of data and processes, therefore, improving the reliability of results. Standards for data acquisition, analysis, and documentation have been fostered in the last decade driven by grassroot initiatives of researchers and organizations such as the Research Data Alliance (RDA). Nevertheless, what is still largely missing in the life science academic research are agreed procedures for complex routine research workflows. Here, well-crafted documentation like standard operating procedures (SOPs) offer clear direction and instructions specifically designed to avoid deviations as an absolute necessity for reproducibility. Therefore, this paper provides a standardized workflow that explains step by step how to write an SOP to be used as a starting point for appropriate research documentation.}, language = {en} } @article{GebserKaminskiKaufmannetal.2018, author = {Gebser, Martin and Kaminski, Roland and Kaufmann, Benjamin and L{\"u}hne, Patrick and Obermeier, Philipp and Ostrowski, Max and Romero Davila, Javier and Schaub, Torsten H. and Schellhorn, Sebastian and Wanko, Philipp}, title = {The Potsdam Answer Set Solving Collection 5.0}, series = {K{\"u}nstliche Intelligenz}, volume = {32}, journal = {K{\"u}nstliche Intelligenz}, number = {2-3}, publisher = {Springer}, address = {Heidelberg}, issn = {0933-1875}, doi = {10.1007/s13218-018-0528-x}, pages = {181 -- 182}, year = {2018}, abstract = {The Potsdam answer set solving collection, or Potassco for short, bundles various tools implementing and/or applying answer set programming. The article at hand succeeds an earlier description of the Potassco project published in Gebser et al. (AI Commun 24(2):107-124, 2011). Hence, we concentrate in what follows on the major features of the most recent, fifth generation of the ASP system clingo and highlight some recent resulting application systems.}, language = {en} } @article{HaubeltNeubauerSchaubetal.2018, author = {Haubelt, Christian and Neubauer, Kai and Schaub, Torsten H. and Wanko, Philipp}, title = {Design space exploration with answer set programming}, series = {K{\"u}nstliche Intelligenz}, volume = {32}, journal = {K{\"u}nstliche Intelligenz}, number = {2-3}, publisher = {Springer}, address = {Heidelberg}, issn = {0933-1875}, doi = {10.1007/s13218-018-0530-3}, pages = {205 -- 206}, year = {2018}, abstract = {The aim of our project design space exploration with answer set programming is to develop a general framework based on Answer Set Programming (ASP) that finds valid solutions to the system design problem and simultaneously performs Design Space Exploration (DSE) to find the most favorable alternatives. We leverage recent developments in ASP solving that allow for tight integration of background theories to create a holistic framework for effective DSE.}, language = {en} } @article{DimopoulosGebserLuehneetal.2019, author = {Dimopoulos, Yannis and Gebser, Martin and L{\"u}hne, Patrick and Romero Davila, Javier and Schaub, Torsten H.}, title = {plasp 3}, series = {Theory and practice of logic programming}, volume = {19}, journal = {Theory and practice of logic programming}, number = {3}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {1471-0684}, doi = {10.1017/S1471068418000583}, pages = {477 -- 504}, year = {2019}, abstract = {We describe the new version of the Planning Domain Definition Language (PDDL)-to-Answer Set Programming (ASP) translator plasp. First, it widens the range of accepted PDDL features. Second, it contains novel planning encodings, some inspired by Satisfiability Testing (SAT) planning and others exploiting ASP features such as well-foundedness. All of them are designed for handling multivalued fluents in order to capture both PDDL as well as SAS planning formats. Third, enabled by multishot ASP solving, it offers advanced planning algorithms also borrowed from SAT planning. As a result, plasp provides us with an ASP-based framework for studying a variety of planning techniques in a uniform setting. Finally, we demonstrate in an empirical analysis that these techniques have a significant impact on the performance of ASP planning.}, language = {en} } @article{PousttchiGleiss2019, author = {Pousttchi, Key and Gleiß, Alexander}, title = {Surrounded by middlemen - how multi-sided platforms change the insurance industry}, series = {Electron Markets}, volume = {29}, journal = {Electron Markets}, number = {4}, publisher = {Springer}, address = {Heidelberg}, issn = {1019-6781}, doi = {10.1007/s12525-019-00363-w}, pages = {609 -- 629}, year = {2019}, abstract = {Multi-sided platforms (MSP) strongly affect markets and play a crucial part within the digital and networked economy. Although empirical evidence indicates their occurrence in many industries, research has not investigated the game-changing impact of MSP on traditional markets to a sufficient extent. More specifically, we have little knowledge of how MSP affect value creation and customer interaction in entire markets, exploiting the potential of digital technologies to offer new value propositions. Our paper addresses this research gap and provides an initial systematic approach to analyze the impact of MSP on the insurance industry. For this purpose, we analyze the state of the art in research and practice in order to develop a reference model of the value network for the insurance industry. On this basis, we conduct a case-study analysis to discover and analyze roles which are occupied or even newly created by MSP. As a final step, we categorize MSP with regard to their relation to traditional insurance companies, resulting in a classification scheme with four MSP standard types: Competition, Coordination, Cooperation, Collaboration.}, language = {en} } @article{GianniniRichterServettoetal.2018, author = {Giannini, Paola and Richter, Tim and Servetto, Marco and Zucca, Elena}, title = {Tracing sharing in an imperative pure calculus}, series = {Science of computer programming}, volume = {172}, journal = {Science of computer programming}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0167-6423}, doi = {10.1016/j.scico.2018.11.007}, pages = {180 -- 202}, year = {2018}, abstract = {We introduce a type and effect system, for an imperative object calculus, which infers sharing possibly introduced by the evaluation of an expression, represented as an equivalence relation among its free variables. This direct representation of sharing effects at the syntactic level allows us to express in a natural way, and to generalize, widely-used notions in literature, notably uniqueness and borrowing. Moreover, the calculus is pure in the sense that reduction is defined on language terms only, since they directly encode store. The advantage of this non-standard execution model with respect to a behaviorally equivalent standard model using a global auxiliary structure is that reachability relations among references are partly encoded by scoping. (C) 2018 Elsevier B.V. All rights reserved.}, language = {en} } @article{BordihnVaszil2020, author = {Bordihn, Henning and Vaszil, Gy{\"o}rgy}, title = {Deterministic Lindenmayer systems with dynamic control of parallelism}, series = {International journal of foundations of computer science}, volume = {31}, journal = {International journal of foundations of computer science}, number = {1}, publisher = {World Scientific}, address = {Singapore}, issn = {0129-0541}, doi = {10.1142/S0129054120400031}, pages = {37 -- 51}, year = {2020}, abstract = {M-rate 0L systems are interactionless Lindenmayer systems together with a function assigning to every string a set of multisets of productions that may be applied simultaneously to the string. Some questions that have been left open in the forerunner papers are examined, and the computational power of deterministic M-rate 0L systems is investigated, where also tabled and extended variants are taken into consideration.}, language = {en} } @article{BordihnVaszil2021, author = {Bordihn, Henning and Vaszil, Gy{\"o}rgy}, title = {Reversible parallel communicating finite automata systems}, series = {Acta informatica}, volume = {58}, journal = {Acta informatica}, number = {4}, publisher = {Springer}, address = {Berlin ; Heidelberg ; New York, NY}, issn = {0001-5903}, doi = {10.1007/s00236-021-00396-9}, pages = {263 -- 279}, year = {2021}, abstract = {We study the concept of reversibility in connection with parallel communicating systems of finite automata (PCFA in short). We define the notion of reversibility in the case of PCFA (also covering the non-deterministic case) and discuss the relationship of the reversibility of the systems and the reversibility of its components. We show that a system can be reversible with non-reversible components, and the other way around, the reversibility of the components does not necessarily imply the reversibility of the system as a whole. We also investigate the computational power of deterministic centralized reversible PCFA. We show that these very simple types of PCFA (returning or non-returning) can recognize regular languages which cannot be accepted by reversible (deterministic) finite automata, and that they can even accept languages that are not context-free. We also separate the deterministic and non-deterministic variants in the case of systems with non-returning communication. We show that there are languages accepted by non-deterministic centralized PCFA, which cannot be recognized by any deterministic variant of the same type.}, language = {en} } @article{BordihnHolzer2021, author = {Bordihn, Henning and Holzer, Markus}, title = {On the number of active states in finite automata}, series = {Acta informatica}, volume = {58}, journal = {Acta informatica}, number = {4}, publisher = {Springer}, address = {Berlin ; Heidelberg [u.a.]}, issn = {0001-5903}, doi = {10.1007/s00236-021-00397-8}, pages = {301 -- 318}, year = {2021}, abstract = {We introduce a new measure of descriptional complexity on finite automata, called the number of active states. Roughly speaking, the number of active states of an automaton A on input w counts the number of different states visited during the most economic computation of the automaton A for the word w. This concept generalizes to finite automata and regular languages in a straightforward way. We show that the number of active states of both finite automata and regular languages is computable, even with respect to nondeterministic finite automata. We further compare the number of active states to related measures for regular languages. In particular, we show incomparability to the radius of regular languages and that the difference between the number of active states and the total number of states needed in finite automata for a regular language can be of exponential order.}, language = {en} } @article{KreowskyStabernack2021, author = {Kreowsky, Philipp and Stabernack, Christian Benno}, title = {A full-featured FPGA-based pipelined architecture for SIFT extraction}, series = {IEEE access : practical research, open solutions / Institute of Electrical and Electronics Engineers}, volume = {9}, journal = {IEEE access : practical research, open solutions / Institute of Electrical and Electronics Engineers}, publisher = {Inst. of Electr. and Electronics Engineers}, address = {New York, NY}, issn = {2169-3536}, doi = {10.1109/ACCESS.2021.3104387}, pages = {128564 -- 128573}, year = {2021}, abstract = {Image feature detection is a key task in computer vision. Scale Invariant Feature Transform (SIFT) is a prevalent and well known algorithm for robust feature detection. However, it is computationally demanding and software implementations are not applicable for real-time performance. In this paper, a versatile and pipelined hardware implementation is proposed, that is capable of computing keypoints and rotation invariant descriptors on-chip. All computations are performed in single precision floating-point format which makes it possible to implement the original algorithm with little alteration. Various rotation resolutions and filter kernel sizes are supported for images of any resolution up to ultra-high definition. For full high definition images, 84 fps can be processed. Ultra high definition images can be processed at 21 fps.}, language = {en} } @article{LagriffoulAndres2016, author = {Lagriffoul, Fabien and Andres, Benjamin}, title = {Combining task and motion planning}, series = {The international journal of robotics research}, volume = {35}, journal = {The international journal of robotics research}, number = {8}, publisher = {Sage Science Press}, address = {Thousand Oaks}, issn = {1741-3176}, doi = {10.1177/0278364915619022}, pages = {890 -- 927}, year = {2016}, abstract = {Solving problems combining task and motion planning requires searching across a symbolic search space and a geometric search space. Because of the semantic gap between symbolic and geometric representations, symbolic sequences of actions are not guaranteed to be geometrically feasible. This compels us to search in the combined search space, in which frequent backtracks between symbolic and geometric levels make the search inefficient.We address this problem by guiding symbolic search with rich information extracted from the geometric level through culprit detection mechanisms.}, language = {en} } @article{SteinertStabernack2022, author = {Steinert, Fritjof and Stabernack, Benno}, title = {Architecture of a low latency H.264/AVC video codec for robust ML based image classification how region of interests can minimize the impact of coding artifacts}, series = {Journal of Signal Processing Systems for Signal, Image, and Video Technology}, volume = {94}, journal = {Journal of Signal Processing Systems for Signal, Image, and Video Technology}, number = {7}, publisher = {Springer}, address = {New York}, issn = {1939-8018}, doi = {10.1007/s11265-021-01727-2}, pages = {693 -- 708}, year = {2022}, abstract = {The use of neural networks is considered as the state of the art in the field of image classification. A large number of different networks are available for this purpose, which, appropriately trained, permit a high level of classification accuracy. Typically, these networks are applied to uncompressed image data, since a corresponding training was also carried out using image data of similar high quality. However, if image data contains image errors, the classification accuracy deteriorates drastically. This applies in particular to coding artifacts which occur due to image and video compression. Typical application scenarios for video compression are narrowband transmission channels for which video coding is required but a subsequent classification is to be carried out on the receiver side. In this paper we present a special H.264/Advanced Video Codec (AVC) based video codec that allows certain regions of a picture to be coded with near constant picture quality in order to allow a reliable classification using neural networks, whereas the remaining image will be coded using constant bit rate. We have combined this feature with the ability to run with lowest latency properties, which is usually also required in remote control applications scenarios. The codec has been implemented as a fully hardwired High Definition video capable hardware architecture which is suitable for Field Programmable Gate Arrays.}, language = {en} } @article{HuangRichterKleickmannetal.2021, author = {Huang, Yizhen and Richter, Eric and Kleickmann, Thilo and Wiepke, Axel and Richter, Dirk}, title = {Classroom complexity affects student teachers' behavior in a VR classroom}, series = {Computers \& education : an international journal}, volume = {163}, journal = {Computers \& education : an international journal}, publisher = {Elsevier}, address = {Oxford}, issn = {0360-1315}, doi = {10.1016/j.compedu.2020.104100}, pages = {15}, year = {2021}, abstract = {Student teachers often struggle to keep track of everything that is happening in the classroom, and particularly to notice and respond when students cause disruptions. The complexity of the classroom environment is a potential contributing factor that has not been empirically tested. In this experimental study, we utilized a virtual reality (VR) classroom to examine whether classroom complexity affects the likelihood of student teachers noticing disruptions and how they react after noticing. Classroom complexity was operationalized as the number of disruptions and the existence of overlapping disruptions (multidimensionality) as well as the existence of parallel teaching tasks (simultaneity). Results showed that student teachers (n = 50) were less likely to notice the scripted disruptions, and also less likely to respond to the disruptions in a comprehensive and effortful manner when facing greater complexity. These results may have implications for both teacher training and the design of VR for training or research purpose. This study contributes to the field from two aspects: 1) it revealed how features of the classroom environment can affect student teachers' noticing of and reaction to disruptions; and 2) it extends the functionality of the VR environment-from a teacher training tool to a testbed of fundamental classroom processes that are difficult to manipulate in real-life.}, language = {en} } @article{BrewkaEllmauthalerKernIsberneretal.2018, author = {Brewka, Gerhard and Ellmauthaler, Stefan and Kern-Isberner, Gabriele and Obermeier, Philipp and Ostrowski, Max and Romero, Javier and Schaub, Torsten H. and Schieweck, Steffen}, title = {Advanced solving technology for dynamic and reactive applications}, series = {K{\"u}nstliche Intelligenz}, volume = {32}, journal = {K{\"u}nstliche Intelligenz}, number = {2-3}, publisher = {Springer}, address = {Heidelberg}, issn = {0933-1875}, doi = {10.1007/s13218-018-0538-8}, pages = {199 -- 200}, year = {2018}, language = {en} } @article{LutherTiberiusBrem2020, author = {Luther, Laura and Tiberius, Victor and Brem, Alexander}, title = {User experience (UX) in business, management, and psychology}, series = {Multimodal technologies and interaction : open access journal}, volume = {4}, journal = {Multimodal technologies and interaction : open access journal}, number = {2}, publisher = {MDPI}, address = {Basel}, issn = {2414-4088}, doi = {10.3390/mti4020018}, pages = {19}, year = {2020}, abstract = {User Experience (UX) describes the holistic experience of a user before, during, and after interaction with a platform, product, or service. UX adds value and attraction to their sole functionality and is therefore highly relevant for firms. The increased interest in UX has produced a vast amount of scholarly research since 1983. The research field is, therefore, complex and scattered. Conducting a bibliometric analysis, we aim at structuring the field quantitatively and rather abstractly. We employed citation analyses, co-citation analyses, and content analyses to evaluate productivity and impact of extant research. We suggest that future research should focus more on business and management related topics.}, language = {en} }