@misc{ArvidssonKwasniewskiRianoPachonetal.2008, author = {Arvidsson, Samuel Janne and Kwasniewski, Miroslaw and Ria{\~n}o- Pach{\´o}n, Diego Mauricio and Mueller-Roeber, Bernd}, title = {QuantPrime}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {943}, issn = {1866-8372}, doi = {10.25932/publishup-43153}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431531}, pages = {17}, year = {2008}, abstract = {Background Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays. Results Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet http://www.quantprime.de/ or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (currently 295 species in total), while benefiting from exon-intron border and alternative splice variant information in available genome annotations. Experimental results with the model plant Arabidopsis thaliana, the crop Hordeum vulgare and the model green alga Chlamydomonas reinhardtii show success rates of designed primer pairs exceeding 96\%. Conclusion QuantPrime constitutes a flexible, fully automated web application for reliable primer design for use in larger qPCR experiments, as proven by experimental data. The flexible framework is also open for simple use in other quantification applications, such as hydrolyzation probe design for qPCR and oligonucleotide probe design for quantitative in situ hybridization. Future suggestions made by users can be easily implemented, thus allowing QuantPrime to be developed into a broad-range platform for the design of RNA expression assays.}, language = {en} } @misc{MargariaKubczakSteffen2008, author = {Margaria, Tiziana and Kubczak, Christian and Steffen, Bernhard}, title = {Bio-jETI}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {822}, doi = {10.25932/publishup-42886}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-428868}, pages = {19}, year = {2008}, abstract = {Background: With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms for an LC/MS analysis of FAAH gene knockout. Methods: Bio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution. Conclusions: As a service definition and provisioning platform, Bio-jETI has the potential to become a core technology in interdisciplinary service orchestration and technology transfer. Domain experts, like biologists not trained in computer science, directly define complex service orchestrations as process models and use efficient and complex bioinformatics tools in a simple and intuitive way.}, language = {en} } @misc{DworschakGrellNikiforovaetal.2008, author = {Dworschak, Steve and Grell, Susanne and Nikiforova, Victoria J. and Schaub, Torsten H. and Selbig, Joachim}, title = {Modeling biological networks by action languages via answer set programming}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {843}, issn = {1866-8372}, doi = {10.25932/publishup-42984}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429846}, pages = {47}, year = {2008}, abstract = {We describe an approach to modeling biological networks by action languages via answer set programming. To this end, we propose an action language for modeling biological networks, building on previous work by Baral et al. We introduce its syntax and semantics along with a translation into answer set programming, an efficient Boolean Constraint Programming Paradigm. Finally, we describe one of its applications, namely, the sulfur starvation response-pathway of the model plant Arabidopsis thaliana and sketch the functionality of our system and its usage.}, language = {en} } @misc{AndorfGaertnerSteinfathetal.2008, author = {Andorf, Sandra and G{\"a}rtner, Tanja and Steinfath, Matthias and Witucka-Wall, Hanna and Altmann, Thomas and Repsilber, Dirk}, title = {Towards systems biology of heterosis}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {949}, issn = {1866-8372}, doi = {10.25932/publishup-43627}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-436274}, pages = {14}, year = {2008}, abstract = {We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix) is used in our conceptual approach. It allows for directly relating structural network properties with biological function. Interpreting heterosis as increased adaptability, our model predicts that the biological networks involved show increasing connectivity of regulatory interactions. A detailed analysis of metabolite profile data reveals that the increasing-connectivity prediction is true for graphical Gaussian models in our data from early development. This mirrors properties of observed heterotic Arabidopsis phenotypes. Furthermore, the model predicts a limit for increasing hybrid vigor with increasing heterozygosity—a known phenomenon in the literature.}, language = {en} } @misc{LamprechtMargariaSteffenetal.2008, author = {Lamprecht, Anna-Lena and Margaria, Tiziana and Steffen, Bernhard and Sczyrba, Alexander and Hartmeier, Sven and Giegerich, Robert}, title = {GeneFisher-P}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {868}, issn = {1866-8372}, doi = {10.25932/publishup-43424}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-434241}, pages = {17}, year = {2008}, abstract = {Background: PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using workflow techniques. We apply a service-oriented approach to model and implement GeneFisher-P, a process-based version of the GeneFisher web application, as a part of the Bio-jETI platform for service modeling and execution. We show how to introduce a flexible process layer to meet the growing demand for improved user-friendliness and flexibility. Results: Within Bio-jETI, we model the process using the jABC framework, a mature model-driven, service-oriented process definition platform. We encapsulate remote legacy tools and integrate web services using jETI, an extension of the jABC for seamless integration of remote resources as basic services, ready to be used in the process. Some of the basic services used by GeneFisher are in fact already provided as individual web services at BiBiServ and can be directly accessed. Others are legacy programs, and are made available to Bio-jETI via the jETI technology. The full power of service-based process orientation is required when more bioinformatics tools, available as web services or via jETI, lead to easy extensions or variations of the basic process. This concerns for instance variations of data retrieval or alignment tools as provided by the European Bioinformatics Institute (EBI). Conclusions: The resulting service-and process-oriented GeneFisher-P demonstrates how basic services from heterogeneous sources can be easily orchestrated in the Bio-jETI platform and lead to a flexible family of specialized processes tailored to specific tasks.}, language = {en} }