@article{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 = {Theory and practice of logic programming},
  volume    = {11},
  journal   = {Theory and practice of logic programming},
  publisher = {Cambridge Univ. Press},
  address   = {New York},
  issn      = {1471-0684},
  doi       = {10.1017/S1471068411000287},
  pages     = {749 -- 766},
  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}
}
@article{GebserKaufmannKaminskietal.2011,
  author    = {Gebser, Martin and Kaufmann, Benjamin and Kaminski, Roland and Ostrowski, Max and Schaub, Torsten H. and Schneider, Marius},
  title     = {Potassco the Potsdam answer set solving collection},
  series = {AI communications : AICOM ; the European journal on artificial intelligence},
  volume    = {24},
  journal   = {AI communications : AICOM ; the European journal on artificial intelligence},
  number    = {2},
  publisher = {IOS Press},
  address   = {Amsterdam},
  issn      = {0921-7126},
  doi       = {10.3233/AIC-2011-0491},
  pages     = {107 -- 124},
  year      = {2011},
  abstract  = {This paper gives an overview of the open source project Potassco, the Potsdam Answer Set Solving Collection, bundling tools for Answer Set Programming developed at the University of Potsdam.},
  language  = {en}
}