@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{Vierheller2014, author = {Vierheller, Janine}, title = {Exploratory Data 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}, editor = {Lambrecht, Anna-Lena and Margaria, Tiziana}, publisher = {Axel Springer Verlag}, address = {Berlin}, isbn = {978-3-662-45005-5}, issn = {1865-0929}, pages = {110 -- 126}, year = {2014}, abstract = {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.}, language = {en} } @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} } @phdthesis{Lincke2014, author = {Lincke, Jens}, title = {Evolving Tools in a Collaborative Self-supporting Development Environment}, school = {Universit{\"a}t Potsdam}, pages = {164}, year = {2014}, language = {en} } @phdthesis{Mueller2008, author = {M{\"u}ller, Claudia}, title = {Graphentheoretische Analyse der Evolution von Wiki-basierten Netzwerken f{\"u}r selbstorganisiertes Wissensmanagement}, address = {Potsdam}, pages = {x, 287 S. : graph. Darst.}, year = {2008}, language = {de} } @phdthesis{Gharib2008, author = {Gharib, Mona}, title = {Incremental answer set programming}, address = {Potsdam}, pages = {184 S. : graph. Darst.}, year = {2008}, language = {en} } @book{OPUS4-10652, title = {Proceedings of the 2nd International Workshop on e-learning and Virtual and Remote Laboratories}, series = {Technische Berichte des Hasso-Plattner-Instituts f{\"u}r Softwaresystemtechnik an der Universit{\"a}t Potsda}, volume = {21}, journal = {Technische Berichte des Hasso-Plattner-Instituts f{\"u}r Softwaresystemtechnik an der Universit{\"a}t Potsda}, editor = {Rabe, Bernhard and Rasche, Andreas}, publisher = {Universit{\"a}tsverlag Potsdam}, address = {Potsdam}, isbn = {978-3-940793-17-1}, issn = {1613-5652}, pages = {98 S.}, year = {2008}, language = {en} } @book{deCarvalhoJuergensen2008, author = {de Carvalho, Jackson Marques and J{\"u}rgensen, Helmut}, title = {Document authoring environments and authoring mathematics}, series = {Preprint / Universit{\"a}t Potsdam, Institut f{\"u}r Informatik}, volume = {2008, 1}, journal = {Preprint / Universit{\"a}t Potsdam, Institut f{\"u}r Informatik}, publisher = {Univ.}, address = {Potsdam}, issn = {0946-7580}, pages = {8 S.}, year = {2008}, language = {en} } @book{GoesselOcheretnySogomonyanetal.2008, author = {Goessel, Michael and Ocheretny, Vitaly and Sogomonyan, Egor S. and Marienfeld, Daniel}, title = {New methods of concurrent checking}, series = {Frontiers in electronic testing}, volume = {42}, journal = {Frontiers in electronic testing}, publisher = {Springer}, address = {Dordrecht; Heidelberg}, isbn = {978-1-402-08419-5}, doi = {10.1007/978-1-4020-8420-1}, pages = {250 S.}, year = {2008}, language = {en} } @book{Tepoyan2008, author = {Tepoyan, Liparit}, title = {The Mixed problem for a degenerate operator equation}, series = {Preprint / Universit{\"a}t Potsdam, Institut f{\"u}r Mathematik, Arbeitsgruppe Partiell}, journal = {Preprint / Universit{\"a}t Potsdam, Institut f{\"u}r Mathematik, Arbeitsgruppe Partiell}, publisher = {Univ.}, address = {Potsdam}, issn = {1437-739X}, pages = {13 S.}, year = {2008}, language = {en} } @book{KnobelsdorfKreitz2013, author = {Knobelsdorf, Maria and Kreitz, Christoph}, title = {Ein konstruktivistischer Lehransatz f{\"u}r die Einf{\"u}hrungsveranstaltung der Theoretische Informatik}, isbn = {978-3-86956-220-9}, year = {2013}, language = {de} } @phdthesis{Rasche2008, author = {Rasche, Andreas}, title = {Ausf{\"u}hrung und Entwicklung Adaptiver Komponentenbasierter Anwendungen}, address = {Potsdam}, isbn = {978-3-86727-698-6}, pages = {195 S., graph. Darst.}, year = {2008}, language = {de} } @phdthesis{Li2008, author = {Li, Nanjun}, title = {Modeling, Simulation and Evaluation of TCP/IP Networks}, address = {Potsdam}, pages = {124 S., ii-xi, : graph. Darst.}, year = {2008}, language = {en} } @phdthesis{Rasche2008, author = {Rasche, Andreas}, title = {Ausf{\"u}hrung und Entwicklung adaptiver komponentenbasierter Anwendungen}, publisher = {Cuvillier}, address = {G{\"o}ttingen}, isbn = {978-3-86727-698-6}, pages = {195 S.: graph. Darst.}, year = {2008}, language = {de} } @phdthesis{Troeger2008, author = {Tr{\"o}ger, Peter}, title = {Dynamische Ressourcenverwaltung f{\"u}r dienstbasierte Software-Systeme}, publisher = {Cuvillier}, address = {G{\"o}ttingen}, isbn = {978-3-86727-622-1}, pages = {v, 174 S.: Ill., garph. Darst.}, year = {2008}, language = {de} } @phdthesis{Li2008, author = {Li, Nanjun}, title = {Modeling, simulation and evaluation of TCP/IP Networks}, pages = {xi, 124 S.: graph. Drst.}, year = {2008}, language = {en} }