TY - JOUR A1 - Teske, Daniel T1 - Geocoder accuracy ranking JF - Process design for natural scientists: an agile model-driven approach N2 - Finding an address on a map is sometimes tricky: the chosen map application may be unfamiliar with the enclosed region. There are several geocoders on the market, they have different databases and algorithms to compute the query. Consequently, the geocoding results differ in their quality. Fortunately the geocoders provide a rich set of metadata. The workflow described in this paper compares this metadata with the aim to find out which geocoder is offering the best-fitting coordinate for a given address. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 161 EP - 174 PB - Springer CY - Berlin ER - TY - JOUR A1 - Sens, Henriette T1 - Web-Based map generalization tools put to the test: a jABC workflow JF - Process Design for Natural Scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 175 EP - 185 PB - Springer CY - Berlin ER - TY - JOUR A1 - Noack, Franziska T1 - CREADED: Colored-Relief application for digital elevation data JF - Process design for natural scientists: an agile model-driven approach N2 - In the geoinformatics field, remote sensing data is often used for analyzing the characteristics of the current investigation area. This includes DEMs, which are simple raster grids containing grey scales representing the respective elevation values. The project CREADED that is presented in this paper aims at making these monochrome raster images more significant and more intuitively interpretable. For this purpose, an executable interactive model for creating a colored and relief-shaded Digital Elevation Model (DEM) has been designed using the jABC framework. The process is based on standard jABC-SIBs and SIBs that provide specific GIS functions, which are available as Web services, command line tools and scripts. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 186 EP - 199 PB - Springer CY - Berlin ER - TY - JOUR A1 - Respondek, Tobias T1 - A workflow for computing potential areas for wind turbines JF - Process design for natural scientists: an agile model-driven approach N2 - This paper describes the implementation of a workflow model for service-oriented computing of potential areas for wind turbines in jABC. By implementing a re-executable model the manual effort of a multi-criteria site analysis can be reduced. The aim is to determine the shift of typical geoprocessing tools of geographic information systems (GIS) from the desktop to the web. The analysis is based on a vector data set and mainly uses web services of the “Center for Spatial Information Science and Systems” (CSISS). This paper discusses effort, benefits and problems associated with the use of the web services. Y1 - 2014 SN - 978-3-662-45005-5 IS - 500 SP - 200 EP - 215 PB - Springer CY - Berlin ER - TY - JOUR A1 - Scheele, Lasse T1 - Location analysis for placing artificial reefs JF - Process design for natural scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 216 EP - 228 PB - Springer CY - Berlin ER - TY - JOUR A1 - Holler, Robin T1 - GraffDok - a graffiti documentation application JF - Process design for natural scientists: an agile model-driven approach N2 - GraffDok is an application helping to maintain an overview over sprayed images somewhere in a city. At the time of writing it aims at vandalism rather than at beautiful photographic graffiti in an underpass. Looking at hundreds of tags and scribbles on monuments, house walls, etc. it would be interesting to not only record them in writing but even make them accessible electronically, including images. GraffDok’s workflow is simple and only requires an EXIF-GPS-tagged photograph of a graffito. It automatically determines its location by using reverse geocoding with the given GPS-coordinates and the Gisgraphy WebService. While asking the user for some more meta data, GraffDok analyses the image in parallel with this and tries to detect fore- and background – before extracting the drawing lines and make them stand alone. The command line based tool ImageMagick is used here as well as for accessing EXIF data. Any meta data is written to csv-files, which will stay easily accessible and can be integrated in TeX-files as well. The latter ones are converted to PDF at the end of the workflow, containing a table about all graffiti and a summary for each – including the generated characteristic graffiti pattern image. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 239 EP - 251 PB - Springer CY - Berlin ER - TY - JOUR A1 - Reso, Judith ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Protein Classification Workflow JF - Process Design for Natural Scientists: an agile model-driven approach N2 - 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. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 65 EP - 72 PB - Springer Verlag CY - Berlin ER - TY - JOUR A1 - Schulze, Gunnar T1 - Workflow for rapid metagenome analysis JF - Process design for natural scientists: an agile model-driven approach N2 - 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 Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 88 EP - 100 PB - Springer CY - Berlin ER - TY - JOUR A1 - Vierheller, Janine ED - Lambrecht, Anna-Lena ED - Margaria, Tiziana T1 - Exploratory Data Analysis JF - Process Design for Natural Scientists: an agile model-driven approach N2 - In bioinformatics the term exploratory data analysis refers to different methods to get an overview of large biological data sets. Hence, it helps to create a framework for further analysis and hypothesis testing. The workflow facilitates this first important step of the data analysis created by high-throughput technologies. The results are different plots showing the structure of the measurements. The goal of the workflow is the automatization of the exploratory data analysis, but also the flexibility should be guaranteed. The basic tool is the free software R. Y1 - 2014 SN - 978-3-662-45005-5 SN - 1865-0929 IS - 500 SP - 110 EP - 126 PB - Axel Springer Verlag CY - Berlin ER - 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 - 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 - TY - JOUR A1 - Giannini, Paola A1 - Richter, Tim A1 - Servetto, Marco A1 - Zucca, Elena T1 - Tracing sharing in an imperative pure calculus JF - Science of computer programming N2 - 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. KW - Imperative calculi KW - Sharing KW - Type and effect systems Y1 - 2018 U6 - https://doi.org/10.1016/j.scico.2018.11.007 SN - 0167-6423 SN - 1872-7964 VL - 172 SP - 180 EP - 202 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Bordihn, Henning A1 - Vaszil, György T1 - Deterministic Lindenmayer systems with dynamic control of parallelism JF - International journal of foundations of computer science N2 - 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. KW - parallel rewriting KW - Lindenmayer systems KW - restricted parallelism KW - determinism KW - developmental systems KW - formal languages Y1 - 2019 U6 - https://doi.org/10.1142/S0129054120400031 SN - 0129-0541 SN - 1793-6373 VL - 31 IS - 1 SP - 37 EP - 51 PB - World Scientific CY - Singapore ER - TY - JOUR A1 - Bordihn, Henning A1 - Vaszil, György T1 - Reversible parallel communicating finite automata systems JF - Acta informatica N2 - 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. KW - Finite automata KW - Reversibility KW - Systems of parallel communicating KW - automata Y1 - 2021 U6 - https://doi.org/10.1007/s00236-021-00396-9 SN - 0001-5903 SN - 1432-0525 VL - 58 IS - 4 SP - 263 EP - 279 PB - Springer CY - Berlin ; Heidelberg ; New York, NY ER - TY - JOUR A1 - Bordihn, Henning A1 - Holzer, Markus T1 - On the number of active states in finite automata JF - Acta informatica N2 - 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. Y1 - 2021 U6 - https://doi.org/10.1007/s00236-021-00397-8 SN - 0001-5903 SN - 1432-0525 VL - 58 IS - 4 SP - 301 EP - 318 PB - Springer CY - Berlin ; Heidelberg [u.a.] ER -