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 - THES A1 - Lincke, Jens T1 - Evolving Tools in a Collaborative Self-supporting Development Environment Y1 - 2014 ER - TY - THES A1 - Müller, Claudia T1 - Graphentheoretische Analyse der Evolution von Wiki-basierten Netzwerken für selbstorganisiertes Wissensmanagement Y1 - 2008 CY - Potsdam ER - TY - THES A1 - Gharib, Mona T1 - Incremental answer set programming Y1 - 2008 CY - Potsdam ER - TY - BOOK ED - Rabe, Bernhard ED - Rasche, Andreas T1 - Proceedings of the 2nd International Workshop on e-learning and Virtual and Remote Laboratories T3 - Technische Berichte des Hasso-Plattner-Instituts für Softwaresystemtechnik an der Universität Potsda Y1 - 2008 SN - 978-3-940793-17-1 SN - 1613-5652 VL - 21 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - BOOK A1 - de Carvalho, Jackson Marques A1 - Jürgensen, Helmut T1 - Document authoring environments and authoring mathematics T3 - Preprint / Universität Potsdam, Institut für Informatik Y1 - 2008 SN - 0946-7580 VL - 2008, 1 PB - Univ. CY - Potsdam ER - TY - BOOK A1 - Goessel, Michael A1 - Ocheretny, Vitaly A1 - Sogomonyan, Egor S. A1 - Marienfeld, Daniel T1 - New methods of concurrent checking T3 - Frontiers in electronic testing Y1 - 2008 SN - 978-1-402-08419-5 U6 - https://doi.org/10.1007/978-1-4020-8420-1 VL - 42 PB - Springer CY - Dordrecht; Heidelberg ER - TY - BOOK A1 - Tepoyan, Liparit T1 - The Mixed problem for a degenerate operator equation T3 - Preprint / Universität Potsdam, Institut für Mathematik, Arbeitsgruppe Partiell Y1 - 2008 SN - 1437-739X PB - Univ. CY - Potsdam ER - TY - BOOK A1 - Knobelsdorf, Maria A1 - Kreitz, Christoph T1 - Ein konstruktivistischer Lehransatz für die Einführungsveranstaltung der Theoretische Informatik Y1 - 2013 SN - 978-3-86956-220-9 ER - TY - THES A1 - Rasche, Andreas T1 - Ausführung und Entwicklung Adaptiver Komponentenbasierter Anwendungen Y1 - 2008 SN - 978-3-86727-698-6 CY - Potsdam ER - TY - THES A1 - Li, Nanjun T1 - Modeling, Simulation and Evaluation of TCP/IP Networks Y1 - 2008 CY - Potsdam ER - TY - THES A1 - Rasche, Andreas T1 - Ausführung und Entwicklung adaptiver komponentenbasierter Anwendungen Y1 - 2008 SN - 978-3-86727-698-6 PB - Cuvillier CY - Göttingen ER - TY - THES A1 - Tröger, Peter T1 - Dynamische Ressourcenverwaltung für dienstbasierte Software-Systeme Y1 - 2008 SN - 978-3-86727-622-1 PB - Cuvillier CY - Göttingen ER - TY - THES A1 - Li, Nanjun T1 - Modeling, simulation and evaluation of TCP/IP Networks Y1 - 2008 ER -