GeNESiS: Gene network evolution simulation software

Anton Kratz, Masaru Tomita, Arun Krishnan

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

Original languageEnglish
Article number541
JournalBMC Bioinformatics
Volume9
DOIs
Publication statusPublished - 2008 Dec 16

Fingerprint

Network Evolution
Gene Networks
Gene Regulatory Networks
Gene Regulatory Network
Simulation Software
Software
Genes
Modeling and Simulation
Gene Regulation
Stochastic models
Gene expression
Software Package
Software packages
Population
Stochastic Model
Objective function
Strings
Genetic algorithms
Research Personnel
Genetic Algorithm

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Structural Biology
  • Applied Mathematics

Cite this

GeNESiS : Gene network evolution simulation software. / Kratz, Anton; Tomita, Masaru; Krishnan, Arun.

In: BMC Bioinformatics, Vol. 9, 541, 16.12.2008.

Research output: Contribution to journalArticle

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