Kirillova O. V., Samsonova M. G., Serov V. N.
Institute of High Performance Computing and Data Bases, 198005, St.Petersburg, Fontanka 120, office 7, Russia; Fax +7-812-251-8314, E-mail samson@fn.csa.ru
Understanding the mechanisms of cell functioning requires the investigation
of complex behaviour of ensembles of interacting genes. Traditional biochemical
methods are highly biased towards the identification of single genes and
their effects. Thus the elucidation of cell function should call for novel
approaches which go beyond the traditional experimental methods. One of
this approaches is to consider the ensembles of interacting genes as a
genetic networks. The simplest and the most computational effective model
system that gives insights into the overall behaviour of large genetic
networks is the Boolean network. In this model genes are represented as
the elements of the Boolean net, and the wiring of the elements to one
another correspond to the functional links between genes. The visualisation
and user interaction are the important tools and techniques which assist
scientists in evaluation and absorbtion of data. As the genetic networks
consist of tens and perhaps hundreds of genes involved in complex regulatory
interactions it is necessary to develop special purpose computational tools
for their visualization. Moreover deciphering of structure, logic and complex
behavior of large genetic networks will require the development of tools
for simulation of their dynamics. We design the Java applet NetWork (
http://www.csa.ru/Inst/gorb_dep/inbios/Dyn_bool/Dyn.htm)
which enables the user to construct interactively the genetic network of
interest, as well as to evaluate its dynamics in framework of Boolean network
model. The user is presented with the display of genetic network in the
form of oriented graph: genes are represented as rectangles, and their
interactions - as arrows. For the presentation of genes and their interactions
we modified the NODES and EDGES classes developed by Sun Microsystems Inc.
A new class DYNAMICS was developed which contains the method for simulation
of network dynamics based on the Boolean algebra technique. There are only
two parameters in the HTML file containing the applet. One of them points
on the location of the help file, while the other defines the name of the
main applet class. All other aspects of data presentation and applet functionality
are controlled by the user, who inputs the genetic network, optimizes its
visualization and simulates the genetic network dynamics. NetWork displays
the mechanism of genes interactions in the network and enables visualization
of large genetic networks. The applet enables the user to identify rapidly
and to explore attractors. Using NetWork it is possible to model the effects
of the mutations in the network, to reveal gene interactions compensating
for these mutations, as well as to adjust the genetic network structure
to fit biological data.