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GeNESiS: gene network evolution simulation software

Anton Kratz, Masaru Tomita and Arun Krishnan*

Author Affiliations

Institute for Advanced Biosciences, Keio University, 14-1, Baba-Cho, Tsuruoka, Yamagata-ken, 997-0035, Japan

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BMC Bioinformatics 2008, 9:541  doi:10.1186/1471-2105-9-541

Published: 16 December 2008

Abstract

Background

There has been a lot of interest in recent years focusing on the modeling and simulation of Gene Regulatory Networks (GRNs). However, the evolutionary mechanisms that give rise to GRNs in the first place are still largely unknown. In an earlier work, we developed a framework to analyze the effect of objective functions, input types and starting populations on the evolution of GRNs with a specific emphasis on the robustness of evolved GRNs.

Results

In this work, we present a parallel software package, GeNESiS for the modeling and simulation of the evolution of gene regulatory networks (GRNs). The software models the process of gene regulation through a combination of finite-state and stochastic models. The evolution of GRNs is then simulated by means of a genetic algorithm with the network connections represented as binary strings. The software allows users to simulate the evolution under varying selective pressures and starting conditions. We believe that the software provides a way for researchers to understand the evolutionary behavior of populations of GRNs.

Conclusion

We believe that GeNESiS will serve as a useful tool for scientists interested in understanding the evolution of gene regulatory networks under a range of different conditions and selective pressures. Such modeling efforts can lead to a greater understanding of the network characteristics of GRNs.