title: ASP-G: an ASP-based method for finding attractors in genetic regulatory networks.
abstract: BACKGROUND
  Boolean network models are suitable to simulate GRNs in the absence of detailed kinetic information. However, reducing the biological reality implies making assumptions on how genes interact (interaction rules) and how their state is updated during the simulation (update scheme). The exact choice of the assumptions largely determines the outcome of the simulations. In most cases, however, the biologically correct assumptions are unknown. An ideal simulation thus implies testing different rules and schemes to determine those that best capture an observed biological phenomenon. This is not trivial because most current methods to simulate Boolean network models of GRNs and to compute their attractors impose specific assumptions that cannot be easily altered, as they are built into the system.
  
  
  RESULTS
  To allow for a more flexible simulation framework, we developed ASP-G. We show the correctness of ASP-G in simulating Boolean network models and obtaining attractors under different assumptions by successfully recapitulating the detection of attractors of previously published studies. We also provide an example of how performing simulation of network models under different settings help determine the assumptions under which a certain conclusion holds. The main added value of ASP-G is in its modularity and declarativity, making it more flexible and less error-prone than traditional approaches. The declarative nature of ASP-G comes at the expense of being slower than the more dedicated systems but still achieves a good efficiency with respect to computational time.
  
  
  METHODS
  The source code of ASP-G is available at http://bioinformatics.intec.ugent.be/kmarchal/Supplementary_Information_Musthofa_2014/asp-g.zip.
authors.affiliation: Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 (S9), 9000 Ghent, Department of Plant Systems Biology, VIB Technologiepark 927, Department of Plant Biotechnology and Bioinformatics, Ghent University Technologiepark 927, 9052 Ghent, Belgium, Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark, Arenberg 20, 3001 Leuven, Belgium, Department of Information Technology, IMinds, Ghent University, Gaston Crommenlaan 8, B-9050 Ghent, Belgium and Center for Web and Data Science, Institute of Technology, University of Washington Tacoma, 1900 Commerce Street, Tacoma, WA-98402, USA.
authors.forename: Mushthofa
authors.initials: M
authors.lastname: Mushthofa
authors.affiliation: Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 (S9), 9000 Ghent, Department of Plant Systems Biology, VIB Technologiepark 927, Department of Plant Biotechnology and Bioinformatics, Ghent University Technologiepark 927, 9052 Ghent, Belgium, Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark, Arenberg 20, 3001 Leuven, Belgium, Department of Information Technology, IMinds, Ghent University, Gaston Crommenlaan 8, B-9050 Ghent, Belgium and Center for Web and Data Science, Institute of Technology, University of Washington Tacoma, 1900 Commerce Street, Tacoma, WA-98402, USA.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Torres
authors.affiliation: Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 (S9), 9000 Ghent, Department of Plant Systems Biology, VIB Technologiepark 927, Department of Plant Biotechnology and Bioinformatics, Ghent University Technologiepark 927, 9052 Ghent, Belgium, Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark, Arenberg 20, 3001 Leuven, Belgium, Department of Information Technology, IMinds, Ghent University, Gaston Crommenlaan 8, B-9050 Ghent, Belgium and Center for Web and Data Science, Institute of Technology, University of Washington Tacoma, 1900 Commerce Street, Tacoma, WA-98402, USA Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 (S9), 9000 Ghent, Department of Plant Systems Biology, VIB Technologiepark 927, Department of Plant Biotechnology and Bioinformatics, Ghent University Technologiepark 927, 9052 Ghent, Belgium, Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark, Arenberg 20, 3001 Leuven, Belgium, Department of Information Technology, IMinds, Ghent University, Gaston Crommenlaan 8, B-9050 Ghent, Belgium and Center for Web and Data Science, Institute of Technology, University of Washington Tacoma, 1900 Commerce Street, Tacoma, WA-98402, USA Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 (S9), 9000 Ghent, Department of Plant Systems Biology, VIB Technologiepark 927, Department of Plant Biotechnology and Bioinformatics, Ghent University Technologiepark 927, 9052 Ghent, Belgium, Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark, Arenberg 20, 3001 Leuven, 
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 (S9), 9000 Ghent, Department of Plant Systems Biology, VIB Technologiepark 927, Department of Plant Biotechnology and Bioinformatics, Ghent University Technologiepark 927, 9052 Ghent, Belgium, Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark, Arenberg 20, 3001 Leuven, Belgium, Department of Information Technology, IMinds, Ghent University, Gaston Crommenlaan 8, B-9050 Ghent, Belgium and Center for Web and Data Science, Institute of Technology, University of Washington Tacoma, 1900 Commerce Street, Tacoma, WA-98402, USA Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 (S9), 9000 Ghent, Department of Plant Systems Biology, VIB Technologiepark 927, Department of Plant Biotechnology and Bioinformatics, Ghent University Technologiepark 927, 9052 Ghent, Belgium, Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark, Arenberg 20, 3001 Leuven, Belgium, Department of Information Technology, IMinds, Ghent University, Gaston Crommenlaan 8, B-9050 Ghent, Belgium and Center for Web and Data Science, Institute of Technology, University of Washington Tacoma, 1900 Commerce Street, Tacoma, WA-98402, USA Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 (S9), 9000 Ghent, Department of Plant Systems Biology, VIB Technologiepark 927, Department of Plant Biotechnology and Bioinformatics, Ghent University Technologiepark 927, 9052 Ghent, Belgium, Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark, Arenberg 20, 3001 Leuven, 
authors.forename: Kathleen
authors.initials: K
authors.lastname: Marchal
authors.affiliation: Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 (S9), 9000 Ghent, Department of Plant Systems Biology, VIB Technologiepark 927, Department of Plant Biotechnology and Bioinformatics, Ghent University Technologiepark 927, 9052 Ghent, Belgium, Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark, Arenberg 20, 3001 Leuven, Belgium, Department of Information Technology, IMinds, Ghent University, Gaston Crommenlaan 8, B-9050 Ghent, Belgium and Center for Web and Data Science, Institute of Technology, University of Washington Tacoma, 1900 Commerce Street, Tacoma, WA-98402, USA Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 (S9), 9000 Ghent, Department of Plant Systems Biology, VIB Technologiepark 927, Department of Plant Biotechnology and Bioinformatics, Ghent University Technologiepark 927, 9052 Ghent, Belgium, Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark, Arenberg 20, 3001 Leuven, Belgium, Department of Information Technology, IMinds, Ghent University, Gaston Crommenlaan 8, B-9050 Ghent, Belgium and Center for Web and Data Science, Institute of Technology, University of Washington Tacoma, 1900 Commerce Street, Tacoma, WA-98402, USA.
authors.forename: Martine
authors.initials: M
authors.lastname: De Cock
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D053263:Gene Regulatory Networks