@misc{KurpiersNeher2016,
  author    = {Kurpiers, Jona and Neher, Dieter},
  title     = {Dispersive Non-Geminate Recombination in an Amorphous Polymer:Fullerene Blend},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-91541},
  pages     = {10},
  year      = {2016},
  abstract  = {Recombination of free charge is a key process limiting the performance of solar cells. For low mobility materials, such as organic semiconductors, the kinetics of non-geminate recombination (NGR) is strongly linked to the motion of charges. As these materials possess significant disorder, thermalization of photogenerated carriers in the inhomogeneously broadened density of state distribution is an unavoidable process. Despite its general importance, knowledge about the kinetics of NGR in complete organic solar cells is rather limited. We employ time delayed collection field (TDCF) experiments to study the recombination of photogenerated charge in the high-performance polymer:fullerene blend PCDTBT:PCBM. NGR in the bulk of this amorphous blend is shown to be highly dispersive, with a continuous reduction of the recombination coefficient throughout the entire time scale, until all charge carriers have either been extracted or recombined. Rapid, contact-mediated recombination is identified as an additional loss channel, which, if not properly taken into account, would erroneously suggest a pronounced field dependence of charge generation. These findings are in stark contrast to the results of TDCF experiments on photovoltaic devices made from ordered blends, such as P3HT:PCBM, where non-dispersive recombination was proven to dominate the charge carrier dynamics under application relevant conditions.},
  language  = {en}
}
@misc{NeherKniepertElimelechetal.2016,
  author    = {Neher, Dieter and Kniepert, Juliane and Elimelech, Arik and Koster, L. Jan Anton},
  title     = {A New Figure of Merit for Organic Solar Cells with Transport-limited Photocurrents},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-91414},
  pages     = {9},
  year      = {2016},
  abstract  = {Compared to their inorganic counterparts, organic semiconductors suffer from relatively low charge carrier mobilities. Therefore, expressions derived for inorganic solar cells to correlate characteristic performance parameters to material properties are prone to fail when applied to organic devices. This is especially true for the classical Shockley-equation commonly used to describe current-voltage (JV)-curves, as it assumes a high electrical conductivity of the charge transporting material. Here, an analytical expression for the JV-curves of organic solar cells is derived based on a previously published analytical model. This expression, bearing a similar functional dependence as the Shockley-equation, delivers a new figure of merit α to express the balance between free charge recombination and extraction in low mobility photoactive materials. This figure of merit is shown to determine critical device parameters such as the apparent series resistance and the fill factor.},
  language  = {en}
}
@misc{FichteTruszczynskiWoltran2015,
  author    = {Fichte, Johannes Klaus and Truszczynski, Miroslaw and Woltran, Stefan},
  title     = {Dual-normal logic programs},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {585},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41449},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414490},
  pages     = {16},
  year      = {2015},
  abstract  = {Disjunctive Answer Set Programming is a powerful declarative programming paradigm with complexity beyond NP. Identifying classes of programs for which the consistency problem is in NP is of interest from the theoretical standpoint and can potentially lead to improvements in the design of answer set programming solvers. One of such classes consists of dual-normal programs, where the number of positive body atoms in proper rules is at most one. Unlike other classes of programs, dual-normal programs have received little attention so far. In this paper we study this class. We relate dual-normal programs to propositional theories and to normal programs by presenting several inter-translations. With the translation from dual-normal to normal programs at hand, we introduce the novel class of body-cycle free programs, which are in many respects dual to head-cycle free programs. We establish the expressive power of dual-normal programs in terms of SE- and UE-models, and compare them to normal programs. We also discuss the complexity of deciding whether dual-normal programs are strongly and uniformly equivalent.},
  language  = {en}
}
@misc{PulkkinenMetzler2015,
  author    = {Pulkkinen, Otto and Metzler, Ralf},
  title     = {Variance-corrected Michaelis-Menten equation predicts transient rates of single-enzyme reactions and response times in bacterial gene-regulation},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-86632},
  year      = {2015},
  abstract  = {Many chemical reactions in biological cells occur at very low concentrations of constituent molecules. Thus, transcriptional gene-regulation is often controlled by poorly expressed transcription-factors, such as E.coli lac repressor with few tens of copies. Here we study the effects of inherent concentration fluctuations of substrate-molecules on the seminal Michaelis-Menten scheme of biochemical reactions. We present a universal correction to the Michaelis-Menten equation for the reaction-rates. The relevance and validity of this correction for enzymatic reactions and intracellular gene-regulation is demonstrated. Our analytical theory and simulation results confirm that the proposed variance-corrected Michaelis-Menten equation predicts the rate of reactions with remarkable accuracy even in the presence of large non-equilibrium concentration fluctuations. The major advantage of our approach is that it involves only the mean and variance of the substrate-molecule concentration. Our theory is therefore accessible to experiments and not specific to the exact source of the concentration fluctuations.},
  language  = {en}
}
@misc{HoosKaminskiLindaueretal.2015,
  author    = {Hoos, Holger and Kaminski, Roland and Lindauer, Marius and Schaub, Torsten H.},
  title     = {aspeed},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {588},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41474},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414743},
  pages     = {26},
  year      = {2015},
  abstract  = {Although Boolean Constraint Technology has made tremendous progress over the last decade, the efficacy of state-of-the-art solvers is known to vary considerably across different types of problem instances, and is known to depend strongly on algorithm parameters. This problem was addressed by means of a simple, yet effective approach using handmade, uniform, and unordered schedules of multiple solvers in ppfolio, which showed very impressive performance in the 2011 Satisfiability Testing (SAT) Competition. Inspired by this, we take advantage of the modeling and solving capacities of Answer Set Programming (ASP) to automatically determine more refined, that is, nonuniform and ordered solver schedules from the existing benchmarking data. We begin by formulating the determination of such schedules as multi-criteria optimization problems and provide corresponding ASP encodings. The resulting encodings are easily customizable for different settings, and the computation of optimum schedules can mostly be done in the blink of an eye, even when dealing with large runtime data sets stemming from many solvers on hundreds to thousands of instances. Also, the fact that our approach can be customized easily enabled us to swiftly adapt it to generate parallel schedules for multi-processor machines.},
  language  = {en}
}
@misc{GebserHarrisonKaminskietal.2015,
  author    = {Gebser, Martin and Harrison, Amelia and Kaminski, Roland and Lifschitz, Vladimir and Schaub, Torsten H.},
  title     = {Abstract gringo},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {592},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41475},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414751},
  pages     = {15},
  year      = {2015},
  abstract  = {This paper defines the syntax and semantics of the input language of the ASP grounder gringo. The definition covers several constructs that were not discussed in earlier work on the semantics of that language, including intervals, pools, division of integers, aggregates with non-numeric values, and lparse-style aggregate expressions. The definition is abstract in the sense that it disregards some details related to representing programs by strings of ASCII characters. It serves as a specification for gringo from Version 4.5 on.},
  language  = {en}
}
@misc{Wallenta2014,
  author    = {Wallenta, Daniel},
  title     = {A Lefschetz fixed point formula for elliptic quasicomplexes},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {885},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43547},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435471},
  pages     = {577 -- 587},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@misc{BoeckmannOsterloh2014,
  author    = {B{\"o}ckmann, Christine and Osterloh, Lukas},
  title     = {Runge-Kutta type regularization method for inversion of spheroidal particle distribution from limited optical data},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {907},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44120},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441200},
  pages     = {150 -- 165},
  year      = {2014},
  abstract  = {The Runge-Kutta type regularization method was recently proposed as a potent tool for the iterative solution of nonlinear ill-posed problems. In this paper we analyze the applicability of this regularization method for solving inverse problems arising in atmospheric remote sensing, particularly for the retrieval of spheroidal particle distribution. Our numerical simulations reveal that the Runge-Kutta type regularization method is able to retrieve two-dimensional particle distributions using optical backscatter and extinction coefficient profiles, as well as depolarization information.},
  language  = {en}
}
@misc{HoosLindauerSchaub2014,
  author    = {Hoos, Holger and Lindauer, Marius and Schaub, Torsten H.},
  title     = {claspfolio 2},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {606},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41612},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-416129},
  pages     = {17},
  year      = {2014},
  abstract  = {Building on the award-winning, portfolio-based ASP solver claspfolio, we present claspfolio 2, a modular and open solver architecture that integrates several different portfolio-based algorithm selection approaches and techniques. The claspfolio 2 solver framework supports various feature generators, solver selection approaches, solver portfolios, as well as solver-schedule-based pre-solving techniques. The default configuration of claspfolio 2 relies on a light-weight version of the ASP solver clasp to generate static and dynamic instance features. The flexible open design of claspfolio 2 is a distinguishing factor even beyond ASP. As such, it provides a unique framework for comparing and combining existing portfolio-based algorithm selection approaches and techniques in a single, unified framework. Taking advantage of this, we conducted an extensive experimental study to assess the impact of different feature sets, selection approaches and base solver portfolios. In addition to gaining substantial insights into the utility of the various approaches and techniques, we identified a default configuration of claspfolio 2 that achieves substantial performance gains not only over clasp's default configuration and the earlier version of claspfolio, but also over manually tuned configurations of clasp.},
  language  = {en}
}
@misc{EhrigGolasHabeletal.2014,
  author    = {Ehrig, Hartmut and Golas, Ulrike and Habel, Annegret and Lambers, Leen and Orejas, Fernando},
  title     = {M-adhesive transformation systems with nested application conditions},
  series = {Postprints der Universit{\"a}t Potsdam : Digital Engineering Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Digital Engineering Reihe},
  number    = {001},
  doi       = {10.25932/publishup-41565},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415651},
  pages     = {50},
  year      = {2014},
  abstract  = {Nested application conditions generalise the well-known negative application conditions and are important for several application domains. In this paper, we present Local Church-Rosser, Parallelism, Concurrency and Amalgamation Theorems for rules with nested application conditions in the framework of M-adhesive categories, where M-adhesive categories are slightly more general than weak adhesive high-level replacement categories. Most of the proofs are based on the corresponding statements for rules without application conditions and two shift lemmas stating that nested application conditions can be shifted over morphisms and rules.},
  language  = {en}
}
@misc{HaegeleSchlagenhaufRappetal.2014,
  author    = {H{\"a}gele, Claudia and Schlagenhauf, Florian and Rapp, Michael A. and Sterzer, Philipp and Beck, Anne and Bermpohl, Felix and Stoy, Meline and Str{\"o}hle, Andreas and Wittchen, Hans-Ulrich and Dolan, Raymond J. and Heinz, Andreas},
  title     = {Dimensional psychiatry},
  series = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe},
  number    = {653},
  issn      = {1866-8364},
  doi       = {10.25932/publishup-43106},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431064},
  pages     = {331 -- 341},
  year      = {2014},
  abstract  = {A dimensional approach in psychiatry aims to identify core mechanisms of mental disorders across nosological boundaries. We compared anticipation of reward between major psychiatric disorders, and investigated whether reward anticipation is impaired in several mental disorders and whether there is a common psychopathological correlate (negative mood) of such an impairment. We used functional magnetic resonance imaging (fMRI) and a monetary incentive delay (MID) task to study the functional correlates of reward anticipation across major psychiatric disorders in 184 subjects, with the diagnoses of alcohol dependence (n = 26), schizophrenia (n = 44), major depressive disorder (MDD, n = 24), bipolar disorder (acute manic episode, n = 13), attention deficit/hyperactivity disorder (ADHD, n = 23), and healthy controls (n = 54). Subjects' individual Beck Depression Inventory-and State-Trait Anxiety Inventory-scores were correlated with clusters showing significant activation during reward anticipation. During reward anticipation, we observed significant group differences in ventral striatal (VS) activation: patients with schizophrenia, alcohol dependence, and major depression showed significantly less ventral striatal activation compared to healthy controls. Depressive symptoms correlated with dysfunction in reward anticipation regardless of diagnostic entity. There was no significant correlation between anxiety symptoms and VS functional activation. Our findings demonstrate a neurobiological dysfunction related to reward prediction that transcended disorder categories and was related to measures of depressed mood. The findings underline the potential of a dimensional approach in psychiatry and strengthen the hypothesis that neurobiological research in psychiatric disorders can be targeted at core mechanisms that are likely to be implicated in a range of clinical entities.},
  language  = {en}
}
@misc{BanbaraSohTamuraetal.2013,
  author    = {Banbara, Mutsunori and Soh, Takehide and Tamura, Naoyuki and Inoue, Katsumi and Schaub, Torsten H.},
  title     = {Answer set programming as a modeling language for course timetabling},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {594},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41546},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415469},
  pages     = {783 -- 798},
  year      = {2013},
  abstract  = {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.},
  language  = {en}
}
@misc{KaminskiSchaubSiegeletal.2013,
  author    = {Kaminski, Roland and Schaub, Torsten H. and Siegel, Anne and Videla, Santiago},
  title     = {Minimal intervention strategies in logical signaling networks with ASP},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {4-5},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41570},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415704},
  pages     = {675 -- 690},
  year      = {2013},
  abstract  = {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.},
  language  = {en}
}
@misc{LarhlimiDavidSelbigetal.2012,
  author    = {Larhlimi, Abdelhalim and David, Laszlo and Selbig, Joachim and Bockmayr, Alexander},
  title     = {F2C2},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {921},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43243},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432431},
  pages     = {11},
  year      = {2012},
  abstract  = {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/.},
  language  = {en}
}
@misc{OstrowskiSchaub2012,
  author    = {Ostrowski, Max and Schaub, Torsten H.},
  title     = {ASP modulo CSP},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {579},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41390},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-413908},
  pages     = {19},
  year      = {2012},
  abstract  = {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.},
  language  = {en}
}
@misc{GebserKaufmannSchaub2012,
  author    = {Gebser, Martin and Kaufmann, Benjamin and Schaub, Torsten H.},
  title     = {Multi-threaded ASP solving with clasp},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {586},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41397},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-413977},
  pages     = {21},
  year      = {2012},
  abstract  = {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.},
  language  = {en}
}
@misc{BoumaHendriks2011,
  author    = {Bouma, Gerlof J. and Hendriks, Petra},
  title     = {Partial word order freezing in Dutch},
  series = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Humanwissenschaftliche Reihe},
  number    = {625},
  issn      = {1866-8364},
  doi       = {10.25932/publishup-43049},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-430496},
  pages     = {23},
  year      = {2011},
  abstract  = {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.},
  language  = {en}
}
@misc{GebserKaminskiSchaub2011,
  author    = {Gebser, Martin and Kaminski, Roland and Schaub, Torsten H.},
  title     = {Complex optimization in answer set programming},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {554},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41243},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-412436},
  pages     = {19},
  year      = {2011},
  abstract  = {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.},
  language  = {en}
}
@misc{GebserSchaubThieleetal.2011,
  author    = {Gebser, Martin and Schaub, Torsten H. and Thiele, Sven and Veber, Philippe},
  title     = {Detecting inconsistencies in large biological networks with answer set programming},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {561},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41246},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-412467},
  pages     = {38},
  year      = {2011},
  abstract  = {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.},
  language  = {en}
}
@misc{DurzinskyMarwanOstrowskietal.2011,
  author    = {Durzinsky, Markus and Marwan, Wolfgang and Ostrowski, Max and Schaub, Torsten H. and Wagler, Annegret},
  title     = {Automatic network reconstruction using ASP},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {560},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41241},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-412419},
  pages     = {18},
  year      = {2011},
  abstract  = {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.},
  language  = {en}
}
@misc{GebserLeeLierler2011,
  author    = {Gebser, Martin and Lee, Joohyung and Lierler, Yuliya},
  title     = {On elementary loops of logic programs},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {566},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-41309},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-413091},
  pages     = {36},
  year      = {2011},
  abstract  = {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.},
  language  = {en}
}
@misc{RepsilberKernTelaaretal.2010,
  author    = {Repsilber, Dirk and Kern, Sabine and Telaar, Anna and Walzl, Gerhard and Black, Gillian F. and Selbig, Joachim and Parida, Shreemanta K. and Kaufmann, Stefan H. E. and Jacobsen, Marc},
  title     = {Biomarker discovery in heterogeneous tissue samples},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {854},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42934},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429343},
  pages     = {17},
  year      = {2010},
  abstract  = {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.},
  language  = {en}
}
@misc{MargariaSteffenKubczak2010,
  author    = {Margaria, Tiziana and Steffen, Bernhard and Kubczak, Christian},
  title     = {Evolution support in heterogeneous service-oriented landscapes},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {918},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43240},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-432405},
  pages     = {15},
  year      = {2010},
  abstract  = {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.},
  language  = {en}
}
@misc{LamprechtMargariaSteffen2009,
  author    = {Lamprecht, Anna-Lena and Margaria, Tiziana and Steffen, Bernhard},
  title     = {Bio-jETI : a framework for semantics-based service composition},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45066},
  year      = {2009},
  abstract  = {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},
  language  = {en}
}
@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}
}
@misc{StieglitzFuchssHillmannetal.2007,
  author    = {Stieglitz, Stefan and Fuchß, Christoph and Hillmann, Oliver and Lattemann, Christoph},
  title     = {Mobile learning by using ad hoc messaging network},
  issn      = {1867-5808},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-19960},
  year      = {2007},
  abstract  = {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.},
  language  = {en}
}