ASP-G : an ASP-based method for finding attractors in genetic regulatory networks

Show simple item record Mushthofa, Mushthofa Torres, Gustavo Van de Peer, Yves Marchal, Kathleen De Cock, Martine
dc.contributor.editor Valencia, Alfonso 2015-09-22T12:01:05Z 2015-09-22T12:01:05Z 2014-07-15
dc.description.abstract MOTIVATION : Boolean network models are suitable to simulate gene regulatory networks (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, since 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 w.r.t. computational time. en_ZA
dc.description.librarian am2015 en_ZA
dc.description.sponsorship The Ghent University Multidisciplinary Research Partnership “Bioinformatics: from nucleotides to networks” and the Interuniversity Attraction Poles Programme [IUAP P6/25], initiated by the Belgian State, Science Policy Office (BioMaGNet) and by the IWT: SBO-NEMOA; FWO: G.0428.13N fund. en_ZA
dc.description.uri en_ZA
dc.identifier.citation Mushthofa, M, Torres, G, Van de Peer, Y, Kathleen, M & De Cock, M 2015, 'ASP-G : an ASP-based method for finding attractors in genetic regulatory networks', Bioinformatics, vol. 30, pp. 1-7. en_ZA
dc.identifier.issn 1367-4803 (print)
dc.identifier.issn 1460-2059 (online)
dc.language.iso en en_ZA
dc.publisher Oxford University Press en_ZA
dc.rights © The Author (2014). Published by Oxford University Press. All rights reserved. en_ZA
dc.subject Gene regulatory networks (GRNs) en_ZA
dc.subject Boolean network en_ZA
dc.subject Simulation en_ZA
dc.subject Models en_ZA
dc.title ASP-G : an ASP-based method for finding attractors in genetic regulatory networks en_ZA
dc.type Postprint Article en_ZA

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