Modeling Logic Gene Networks by Means of Probabilistic Dynamic P Systems
Luis Valencia-Cabrera, Manuel Garcia-Quismondo, Mario J. Perez-Jimenez, Yansen Su, Hui Yu and Linqiang Pan
Gene regulatory networks are useful models for biologists to understand the interactions among genes in living organisms. In this work, we consider a special class of gene regulatory networks, called logical networks, where the “links” among genes are inferred by logic analysis of phylogenetic profiles. We provide a formalization of logic networks, and introduce a membrane computing model for reconstructing logical networks and reproducing their dynamics. An example logical network is simulated by using software P-Lingua and MeCoSim. The simulation result shows that membrane computing is a versatile framework for modeling different biological scenarios.
Keywords: System biology, gene, genetic network, logic network, membrane computing, P system