TY - GEN A1 - Stieglitz, Stefan A1 - Fuchß, Christoph A1 - Hillmann, Oliver A1 - Lattemann, Christoph T1 - Mobile learning by using ad hoc messaging network N2 - The requirements of modern e-learning techniques change. Aspects such as community interaction, flexibility, pervasive learning and increasing mobility in communication habits become more important. To meet these challenges e-learning platforms must provide support on mobile learning. Most approaches try to adopt centralised and static e-learning mechanisms to mobile devices. However, often technically it is not possible for all kinds of devices to be connected to a central server. Therefore we introduce an application of a mobile e-learning network which operates totally decentralised with the help of an underlying ad hoc network architecture. Furthermore the concept of ad hoc messaging network (AMNET) is used as basis system architecture for our approach to implement a platform for pervasive mobile e-learning. T3 - Zweitveröffentlichungen der Universität Potsdam : Wirtschafts- und Sozialwissenschaftliche Reihe - paper 015 KW - Mobile learning KW - ad hoc learning KW - community KW - e-learning platform KW - AMNET KW - ad hoc messaging network KW - pervasive learning Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-19960 SN - 1867-5808 ER - TY - GEN A1 - Arvidsson, Samuel Janne A1 - Kwasniewski, Miroslaw A1 - Riaño- Pachón, Diego Mauricio A1 - Mueller-Roeber, Bernd T1 - QuantPrime BT - a flexible tool for reliable high-throughput primer design for quantitative PCR T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 943 KW - prime pair KW - genome annotation KW - specific prime pair KW - primer pair design KW - quantification protocol Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431531 SN - 1866-8372 IS - 943 ER - TY - GEN A1 - Margaria, Tiziana A1 - Kubczak, Christian A1 - Steffen, Bernhard T1 - Bio-jETI BT - a service integration, design, and provisioning platform for orchestrated bioinformatics processes T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 822 KW - fatty acid amide hydrolase KW - composite service KW - service orchestration KW - rest service KW - electronic tool integration Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-428868 IS - 822 ER - TY - GEN A1 - Dworschak, Steve A1 - Grell, Susanne A1 - Nikiforova, Victoria J. A1 - Schaub, Torsten H. A1 - Selbig, Joachim T1 - Modeling biological networks by action languages via answer set programming T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 843 KW - biological network model KW - action language KW - answer set programming Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429846 SN - 1866-8372 IS - 843 ER - TY - GEN A1 - Andorf, Sandra A1 - Gärtner, Tanja A1 - Steinfath, Matthias A1 - Witucka-Wall, Hanna A1 - Altmann, Thomas A1 - Repsilber, Dirk T1 - Towards systems biology of heterosis BT - a hypothesis about molecular network structure applied for the Arabidopsis metabolome T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 949 KW - partial correlation KW - biological network KW - metabolite profile KW - molecular network KW - significant edge Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-436274 SN - 1866-8372 IS - 949 ER - TY - GEN A1 - Lamprecht, Anna-Lena A1 - Margaria, Tiziana A1 - Steffen, Bernhard A1 - Sczyrba, Alexander A1 - Hartmeier, Sven A1 - Giegerich, Robert T1 - GeneFisher-P BT - variations of GeneFisher as processes in Bio-jETI T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 868 KW - Basic Service KW - European Bioinformatics Institute KW - Computation Tree Logic KW - Polymerase Chain Reaction Experiment KW - Input Validation Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-434241 SN - 1866-8372 IS - 868 ER - TY - GEN A1 - Lamprecht, Anna-Lena A1 - Margaria, Tiziana A1 - Steffen, Bernhard T1 - Bio-jETI : a framework for semantics-based service composition N2 - Background: The development of bioinformatics databases, algorithms, and tools throughout the last years has lead to a highly distributedworld of bioinformatics services. Without adequatemanagement and development support, in silico researchers are hardly able to exploit the potential of building complex, specialized analysis processes from these services. The Semantic Web aims at thoroughly equipping individual data and services with machine-processable meta-information, while workflow systems support the construction of service compositions. However, even in this combination, in silico researchers currently would have to deal manually with the service interfaces, the adequacy of the semantic annotations, type incompatibilities, and the consistency of service compositions. Results: In this paper, we demonstrate by means of two examples how Semantic Web technology together with an adequate domain modelling frees in silico researchers from dealing with interfaces, types, and inconsistencies. In Bio-jETI, bioinformatics services can be graphically combined to complex services without worrying about details of their interfaces or about type mismatches of the composition. These issues are taken care of at the semantic level by Bio-jETI’s model checking and synthesis features. Whenever possible, they automatically resolve type mismatches in the considered service setting. Otherwise, they graphically indicate impossible/incorrect service combinations. In the latter case, the workflow developermay either modify his service composition using semantically similar services, or ask for help in developing the missing mediator that correctly bridges the detected type gap. Newly developed mediators should then be adequately annotated semantically, and added to the service library for later reuse in similar situations. Conclusion: We show the power of semantic annotations in an adequately modelled and semantically enabled domain setting. Using model checking and synthesis methods, users may orchestrate complex processes from a wealth of heterogeneous services without worrying about interfaces and (type) consistency. The success of this method strongly depends on a careful semantic annotation of the provided services and on its consequent exploitation for analysis, validation, and synthesis. We are convinced that these annotations will become standard, as they will become preconditions for the success and widespread use of (preferred) services in the Semantic Web T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 136 KW - European Bioinformatics Institute KW - Integration KW - Tool KW - Alignment KW - Workflow Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-45066 ER - TY - GEN A1 - Repsilber, Dirk A1 - Kern, Sabine A1 - Telaar, Anna A1 - Walzl, Gerhard A1 - Black, Gillian F. A1 - Selbig, Joachim A1 - Parida, Shreemanta K. A1 - Kaufmann, Stefan H. E. A1 - Jacobsen, Marc T1 - Biomarker discovery in heterogeneous tissue samples BT - taking the in-silico deconfounding approach T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: For heterogeneous tissues, such as blood, measurements of gene expression are confounded by relative proportions of cell types involved. Conclusions have to rely on estimation of gene expression signals for homogeneous cell populations, e.g. by applying micro-dissection, fluorescence activated cell sorting, or in-silico deconfounding. We studied feasibility and validity of a non-negative matrix decomposition algorithm using experimental gene expression data for blood and sorted cells from the same donor samples. Our objective was to optimize the algorithm regarding detection of differentially expressed genes and to enable its use for classification in the difficult scenario of reversely regulated genes. This would be of importance for the identification of candidate biomarkers in heterogeneous tissues. Results: Experimental data and simulation studies involving noise parameters estimated from these data revealed that for valid detection of differential gene expression, quantile normalization and use of non-log data are optimal. We demonstrate the feasibility of predicting proportions of constituting cell types from gene expression data of single samples, as a prerequisite for a deconfounding-based classification approach. Classification cross-validation errors with and without using deconfounding results are reported as well as sample-size dependencies. Implementation of the algorithm, simulation and analysis scripts are available. Conclusions: The deconfounding algorithm without decorrelation using quantile normalization on non-log data is proposed for biomarkers that are difficult to detect, and for cases where confounding by varying proportions of cell types is the suspected reason. In this case, a deconfounding ranking approach can be used as a powerful alternative to, or complement of, other statistical learning approaches to define candidate biomarkers for molecular diagnosis and prediction in biomedicine, in realistically noisy conditions and with moderate sample sizes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 854 KW - differential gene expression KW - quantile normalization KW - heterogeneous tissue KW - gene expression matrix KW - homogeneous cell population KW - selection KW - microdissection Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429343 SN - 1866-8372 IS - 854 ER - TY - GEN A1 - Margaria, Tiziana A1 - Steffen, Bernhard A1 - Kubczak, Christian T1 - Evolution support in heterogeneous service-oriented landscapes T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We present an approach that provides automatic or semi-automatic support for evolution and change management in heterogeneous legacy landscapes where (1) legacy heterogeneous, possibly distributed platforms are integrated in a service oriented fashion, (2) the coordination of functionality is provided at the service level, through orchestration, (3) compliance and correctness are provided through policies and business rules, (4) evolution and correctness-by-design are supported by the eXtreme Model Driven Development paradigm (XMDD) offered by the jABC (Margaria and Steffen in Annu. Rev. Commun. 57, 2004)—the model-driven service oriented development platform we use here for integration, design, evolution, and governance. The artifacts are here semantically enriched, so that automatic synthesis plugins can field the vision of Enterprise Physics: knowledge driven business process development for the end user. We demonstrate this vision along a concrete case study that became over the past three years a benchmark for Semantic Web Service discovery and mediation. We enhance the Mediation Scenario of the Semantic Web Service Challenge along the 2 central evolution paradigms that occur in practice: (a) Platform migration: platform substitution of a legacy system by an ERP system and (b) Backend extension: extension of the legacy Customer Relationship Management (CRM) and Order Management System (OMS) backends via an additional ERP layer. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 918 KW - evolving systems KW - semantic web services KW - service mediation KW - web services KW - SOA Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-432405 SN - 1866-8372 IS - 918 ER - TY - GEN A1 - Bouma, Gerlof J. A1 - Hendriks, Petra T1 - Partial word order freezing in Dutch T2 - Postprints der Universität Potsdam : Humanwissenschaftliche Reihe N2 - Dutch allows for variation as to whether the first position in the sentence is occupied by the subject or by some other constituent, such as the direct object. In particular situations, however, this commonly observed variation in word order is ‘frozen’ and only the subject appears in first position. We hypothesize that this partial freezing of word order in Dutch can be explained from the dependence of the speaker’s choice of word order on the hearer’s interpretation of this word order. A formal model of this interaction between the speaker’s perspective and the hearer’s perspective is presented in terms of bidirectional Optimality Theory. Empirical predictions of this model regarding the interaction between word order and definiteness are confirmed by a quantitative corpus study. T3 - Zweitveröffentlichungen der Universität Potsdam : Humanwissenschaftliche Reihe - 625 KW - bidirectional optimality theory KW - corpus study KW - definiteness KW - variation KW - word order freezing Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-430496 SN - 1866-8364 IS - 625 ER - TY - GEN A1 - Gebser, Martin A1 - Kaminski, Roland A1 - Schaub, Torsten H. T1 - Complex optimization in answer set programming T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Preference handling and optimization are indispensable means for addressing nontrivial applications in Answer Set Programming (ASP). However, their implementation becomes difficult whenever they bring about a significant increase in computational complexity. As a consequence, existing ASP systems do not offer complex optimization capacities, supporting, for instance, inclusion-based minimization or Pareto efficiency. Rather, such complex criteria are typically addressed by resorting to dedicated modeling techniques, like saturation. Unlike the ease of common ASP modeling, however, these techniques are rather involved and hardly usable by ASP laymen. We address this problem by developing a general implementation technique by means of meta-prpogramming, thus reusing existing ASP systems to capture various forms of qualitative preferences among answer sets. In this way, complex preferences and optimization capacities become readily available for ASP applications. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 554 KW - answer set programming KW - preference handling KW - complex optimization KW - meta-programming Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412436 SN - 1866-8372 IS - 554 ER - TY - GEN A1 - Gebser, Martin A1 - Schaub, Torsten H. A1 - Thiele, Sven A1 - Veber, Philippe T1 - Detecting inconsistencies in large biological networks with answer set programming T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We introduce an approach to detecting inconsistencies in large biological networks by using answer set programming. To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and high-throughput profiles of cell activity. We then present an approach based on answer set programming to check the consistency of large-scale data sets. Moreover, we extend this methodology to provide explanations for inconsistencies by determining minimal representations of conflicts. In practice, this can be used to identify unreliable data or to indicate missing reactions. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 561 KW - answer set programming KW - bioinformatics KW - consistency KW - diagnosis Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412467 SN - 1866-8372 IS - 561 ER - TY - GEN A1 - Durzinsky, Markus A1 - Marwan, Wolfgang A1 - Ostrowski, Max A1 - Schaub, Torsten H. A1 - Wagler, Annegret T1 - Automatic network reconstruction using ASP T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Building biological models by inferring functional dependencies from experimental data is an important issue in Molecular Biology. To relieve the biologist from this traditionally manual process, various approaches have been proposed to increase the degree of automation. However, available approaches often yield a single model only, rely on specific assumptions, and/or use dedicated, heuristic algorithms that are intolerant to changing circumstances or requirements in the view of the rapid progress made in Biotechnology. Our aim is to provide a declarative solution to the problem by appeal to Answer Set Programming (ASP) overcoming these difficulties. We build upon an existing approach to Automatic Network Reconstruction proposed by part of the authors. This approach has firm mathematical foundations and is well suited for ASP due to its combinatorial flavor providing a characterization of all models explaining a set of experiments. The usage of ASP has several benefits over the existing heuristic algorithms. First, it is declarative and thus transparent for biological experts. Second, it is elaboration tolerant and thus allows for an easy exploration and incorporation of biological constraints. Third, it allows for exploring the entire space of possible models. Finally, our approach offers an excellent performance, matching existing, special-purpose systems. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 560 KW - regulatory networks KW - biological networks KW - answer Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412419 SN - 1866-8372 IS - 560 ER - TY - GEN A1 - Gebser, Martin A1 - Lee, Joohyung A1 - Lierler, Yuliya T1 - On elementary loops of logic programs T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Using the notion of an elementary loop, Gebser and Schaub (2005. Proceedings of the Eighth International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR’05 ), 53–65) refined the theorem on loop formulas attributable to Lin and Zhao (2004) by considering loop formulas of elementary loops only. In this paper, we reformulate the definition of an elementary loop, extend it to disjunctive programs, and study several properties of elementary loops, including how maximal elementary loops are related to minimal unfounded sets. The results provide useful insights into the stable model semantics in terms of elementary loops. For a nondisjunctive program, using a graph-theoretic characterization of an elementary loop, we show that the problem of recognizing an elementary loop is tractable. On the other hand, we also show that the corresponding problem is coNP-complete for a disjunctive program. Based on the notion of an elementary loop, we present the class of Head-Elementary-loop-Free (HEF) programs, which strictly generalizes the class of Head-Cycle-Free (HCF) programs attributable to Ben-Eliyahu and Dechter (1994. Annals of Mathematics and Artificial Intelligence 12, 53–87). Like an HCF program, an HEF program can be turned into an equivalent nondisjunctive program in polynomial time by shifting head atoms into the body. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 566 KW - stable model semantics KW - loop formulas KW - unfounded sets Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-413091 SN - 1866-8372 IS - 566 ER - TY - GEN A1 - Larhlimi, Abdelhalim A1 - David, Laszlo A1 - Selbig, Joachim A1 - Bockmayr, Alexander T1 - F2C2 BT - a fast tool for the computation of flux coupling in genome-scale metabolic networks T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: Flux coupling analysis (FCA) has become a useful tool in the constraint-based analysis of genome-scale metabolic networks. FCA allows detecting dependencies between reaction fluxes of metabolic networks at steady-state. On the one hand, this can help in the curation of reconstructed metabolic networks by verifying whether the coupling between reactions is in agreement with the experimental findings. On the other hand, FCA can aid in defining intervention strategies to knock out target reactions. Results: We present a new method F2C2 for FCA, which is orders of magnitude faster than previous approaches. As a consequence, FCA of genome-scale metabolic networks can now be performed in a routine manner. Conclusions: We propose F2C2 as a fast tool for the computation of flux coupling in genome-scale metabolic networks. F2C2 is freely available for non-commercial use at https://sourceforge.net/projects/f2c2/files/. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 921 KW - balance analysis KW - reconstruction KW - pathways KW - models KW - metabolic network KW - couple reaction KW - reversible reaction KW - linear programming problem KW - coupling relationship Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-432431 SN - 1866-8372 IS - 921 ER - TY - GEN A1 - Ostrowski, Max A1 - Schaub, Torsten H. T1 - ASP modulo CSP BT - the clingcon system T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We present the hybrid ASP solver clingcon, combining the simple modeling language and the high performance Boolean solving capacities of Answer Set Programming (ASP) with techniques for using non-Boolean constraints from the area of Constraint Programming (CP). The new clingcon system features an extended syntax supporting global constraints and optimize statements for constraint variables. The major technical innovation improves the interaction between ASP and CP solver through elaborated learning techniques based on irreducible inconsistent sets. A broad empirical evaluation shows that these techniques yield a performance improvement of an order of magnitude. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 579 KW - answer set KW - constraints KW - logic KW - SMT Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-413908 SN - 1866-8372 IS - 579 ER - TY - GEN A1 - Gebser, Martin A1 - Kaufmann, Benjamin A1 - Schaub, Torsten H. T1 - Multi-threaded ASP solving with clasp T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We present the new multi-threaded version of the state-of-the-art answer set solver clasp. We detail its component and communication architecture and illustrate how they support the principal functionalities of clasp. Also, we provide some insights into the data representation used for different constraint types handled by clasp. All this is accompanied by an extensive experimental analysis of the major features related to multi-threading in clasp. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 586 KW - propositional satisfiability KW - clause elimination KW - parallel execution KW - SAT KW - algorithm KW - platypus KW - systems KW - search KW - solver Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-413977 SN - 1866-8372 IS - 586 ER - TY - GEN A1 - Banbara, Mutsunori A1 - Soh, Takehide A1 - Tamura, Naoyuki A1 - Inoue, Katsumi A1 - Schaub, Torsten H. T1 - Answer set programming as a modeling language for course timetabling T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - The course timetabling problem can be generally defined as the task of assigning a number of lectures to a limited set of timeslots and rooms, subject to a given set of hard and soft constraints. The modeling language for course timetabling is required to be expressive enough to specify a wide variety of soft constraints and objective functions. Furthermore, the resulting encoding is required to be extensible for capturing new constraints and for switching them between hard and soft, and to be flexible enough to deal with different formulations. In this paper, we propose to make effective use of ASP as a modeling language for course timetabling. We show that our ASP-based approach can naturally satisfy the above requirements, through an ASP encoding of the curriculum-based course timetabling problem proposed in the third track of the second international timetabling competition (ITC-2007). Our encoding is compact and human-readable, since each constraint is individually expressed by either one or two rules. Each hard constraint is expressed by using integrity constraints and aggregates of ASP. Each soft constraint S is expressed by rules in which the head is the form of penalty (S, V, C), and a violation V and its penalty cost C are detected and calculated respectively in the body. We carried out experiments on four different benchmark sets with five different formulations. We succeeded either in improving the bounds or producing the same bounds for many combinations of problem instances and formulations, compared with the previous best known bounds. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 594 KW - answer set programming KW - educational timetabling KW - course timetabling Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-415469 SN - 1866-8372 IS - 594 SP - 783 EP - 798 ER - TY - GEN A1 - Kaminski, Roland A1 - Schaub, Torsten H. A1 - Siegel, Anne A1 - Videla, Santiago T1 - Minimal intervention strategies in logical signaling networks with ASP T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Proposing relevant perturbations to biological signaling networks is central to many problems in biology and medicine because it allows for enabling or disabling certain biological outcomes. In contrast to quantitative methods that permit fine-grained (kinetic) analysis, qualitative approaches allow for addressing large-scale networks. This is accomplished by more abstract representations such as logical networks. We elaborate upon such a qualitative approach aiming at the computation of minimal interventions in logical signaling networks relying on Kleene's three-valued logic and fixpoint semantics. We address this problem within answer set programming and show that it greatly outperforms previous work using dedicated algorithms. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 596 KW - systems biology KW - transduction KW - circuits KW - models KW - sets Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-415704 SN - 1866-8372 IS - 4-5 SP - 675 EP - 690 ER - TY - GEN A1 - Wallenta, Daniel T1 - A Lefschetz fixed point formula for elliptic quasicomplexes T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - In a recent paper, the Lefschetz number for endomorphisms (modulo trace class operators) of sequences of trace class curvature was introduced. We show that this is a well defined, canonical extension of the classical Lefschetz number and establish the homotopy invariance of this number. Moreover, we apply the results to show that the Lefschetz fixed point formula holds for geometric quasiendomorphisms of elliptic quasicomplexes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 885 KW - elliptic complexes KW - Fredholm complexes KW - Lefschetz number Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-435471 SN - 1866-8372 IS - 885 SP - 577 EP - 587 ER -