P system Reverse Engineering for Gene Regulatory Networks in S-system Model

Reverse Engineering (RE) can be considered as a process from which is possible inferring structural and dynamics features of a given system from external observations and relevant knowledge. Thanks to this feature, today RE techniques play a central role in systems biology, since it is not only important a knowledge of genes and proteins, but also to understand their structures and dynamics. One of the main applications of reverse engineering methodologies is the identification of genetic networks that is in which way transcription factors are connected to genes. In this work we present a novel algorithmic approach that attempts to inferring the parameters of a genetic network, which influence the interaction among genes. For this optimization task, a membrane algorithm was designed, whose performances are tested on the S-system model. The proposed algorithm was compared with one of the first algorithms tested on S-system model: PEACE1. Albeit in its preliminary version, the obtained results are encouraging and promising, since our "naive algorithm" outperforms GA in order to find the parameters closest to the target ones.