TY - JOUR A1 - Schütt, Christine T1 - Identification of differentially expressed genes JF - Process design for natural scientists: an agile model-driven approach N2 - With the jABC it is possible to realize workflows for numerous questions in different fields. The goal of this project was to create a workflow for the identification of differentially expressed genes. This is of special interest in biology, for it gives the opportunity to get a better insight in cellular changes due to exogenous stress, diseases and so on. With the knowledge that can be derived from the differentially expressed genes in diseased tissues, it becomes possible to find new targets for treatment. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 127 EP - 139 PB - Springer CY - Berlin ER - TY - JOUR A1 - Kuntzsch, Christian T1 - Visualization of data transfer paths JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 140 EP - 148 PB - Springer CY - Berlin ER - TY - JOUR A1 - Hibbe, Marcel ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Spotlocator - Guess Where the Photo Was Taken! JF - Process Design for Natural Scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 149 EP - 160 PB - Springer Verlag CY - Berlin ER - TY - JOUR A1 - Blaese, Leif T1 - Data mining for unidentified protein squences JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 73 EP - 87 PB - Springer CY - Berlin ER - TY - JOUR A1 - Lis, Monika ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Constructing a Phylogenetic Tree JF - Process Design for Natural Scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 101 EP - 109 PB - Springer Verlag CY - Berlin ER - TY - JOUR A1 - Hollmann, Susanne A1 - Frohme, Marcus A1 - Endrullat, Christoph A1 - Kremer, Andreas A1 - D’Elia, Domenica A1 - Regierer, Babette A1 - Nechyporenko, Alina T1 - Ten simple rules on how to write a standard operating procedure JF - PLOS Computational Biology N2 - 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. Y1 - 2020 VL - 16 IS - 9 PB - PLOS CY - San Francisco ER - TY - JOUR A1 - Gebser, Martin A1 - Kaminski, Roland A1 - Kaufmann, Benjamin A1 - Lühne, Patrick A1 - Obermeier, Philipp A1 - Ostrowski, Max A1 - Romero Davila, Javier A1 - Schaub, Torsten H. A1 - Schellhorn, Sebastian A1 - Wanko, Philipp T1 - The Potsdam Answer Set Solving Collection 5.0 JF - Künstliche Intelligenz N2 - 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. Y1 - 2018 U6 - https://doi.org/10.1007/s13218-018-0528-x SN - 0933-1875 SN - 1610-1987 VL - 32 IS - 2-3 SP - 181 EP - 182 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Haubelt, Christian A1 - Neubauer, Kai A1 - Schaub, Torsten H. A1 - Wanko, Philipp T1 - Design space exploration with answer set programming JF - Künstliche Intelligenz N2 - 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. Y1 - 2018 U6 - https://doi.org/10.1007/s13218-018-0530-3 SN - 0933-1875 SN - 1610-1987 VL - 32 IS - 2-3 SP - 205 EP - 206 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Dimopoulos, Yannis A1 - Gebser, Martin A1 - Lühne, Patrick A1 - Romero Davila, Javier A1 - Schaub, Torsten H. T1 - plasp 3 BT - Towards Effective ASP Planning JF - Theory and practice of logic programming N2 - 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. KW - knowledge representation and nonmonotonic reasoning KW - technical notes and rapid communications KW - answer set programming KW - automated planning KW - action and change Y1 - 2019 U6 - https://doi.org/10.1017/S1471068418000583 SN - 1471-0684 SN - 1475-3081 VL - 19 IS - 3 SP - 477 EP - 504 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Pousttchi, Key A1 - Gleiß, Alexander T1 - Surrounded by middlemen - how multi-sided platforms change the insurance industry JF - Electron Markets N2 - 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. KW - Multi-sided platforms KW - Insurance industry KW - Value network KW - Digitalization KW - Customer ownership Y1 - 2019 U6 - https://doi.org/10.1007/s12525-019-00363-w SN - 1019-6781 SN - 1422-8890 VL - 29 IS - 4 SP - 609 EP - 629 PB - Springer CY - Heidelberg ER -