BINESA — A software tool for evolution modelling of biochemical networks' structure

Abstract

Biochemical networks of different types such as transcription regulatory, gene regulation, metabolic, protein interaction and signal transduction networks have been extensively studied. One of research directions is related with topological properties of biochemical networks and their structure evolution. Earlier research clearly shows that biochemical networks differ considerably from random ones in their network structure. The reason could be mutation and selection based evolution combined with different importance of particular paths of the network for the survival of an organism. It would be useful to investigate and estimate the changes of network structure that are caused by different types of mutation during the evolution, such as point mutations, missense, nonsense mutations, nucleotide inversion, gene inversion, duplication, deletion, and translocation mutations. BINESA (BIochemical NEtwork Structure Analyser) is a standalone software tool developed for evolution modelling of a biochemical network structure founded on evolutionary changes of an underlying artificial genome. This software tool is written in Visual Basic programming language and developed for Windows operating system using Microsoft Access. BINESA has a database for storing of network structure and artificial genome data. This tool provides the exploration of the evolution dynamics of biochemical network structure, supports SBML and GML models import and export, allows visualization of the network structure in graph form visually marking out reactions of different importance and perform a topological analysis of the biochemical network structure.