ASP-G: an ASP-based method for finding attractors in genetic regulatory networks. 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. Availability and implementation: The source code of ASP-G is available at http://bioinformatics.intec.ugent.be/kmarchal/Supplementary_Information_Musthofa_2014/asp-g.zip.
References in zbMATH (referenced in 2 articles )
Showing results 1 to 2 of 2.
- Khaled, Tarek; Benhamou, Belaïd: An ASP-based approach for attractor enumeration in synchronous and asynchronous Boolean networks (2019)
- Mushthofa, Mushthofa; Schockaert, Steven; Hung, Ling-Hong; Marchal, Kathleen; De Cock, Martine: Modeling multi-valued biological interaction networks using fuzzy answer set programming (2018)