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Frequently Asked Questions (FAQ)
The questions about GeneNet modelling:
Gene network is a group of coordinately expressed genes controlling a particular function of an organism. A gene network consists of several types of components:
As a mathematical model, we understand the formalized description of the gene network functioning given in terms of some mathematical language.
Under computer model of a gene network, we understand the complex of algorithms and programs, calculating the dynamic characteristics of gene network on the base of mathematical models, in accordance with the ordered initial data.
In the current release, the mathematical models are given in terms of systems of autonomous common differential equations presenting the laws of alteration of concentration rates of biomolecules and their complexes (genes, mRNAs, proteins, enzymes, low molecular compounds, the products of interaction between them, etc.), which are essential for the gene network functioning. The models are constructed within the frames of the generalized chemical kinetic simulation method (GCKSM) and may be referred to the portrait type.
For gene network modeling, the generalized chemical kinetic simulation method (GCKSM) is applied.
The generalized chemical kinetic simulation method (GCKSM) is oriented to the formalized, mainly portrait, description of regularities in functioning of an arbitrary biosystem. [Bazhan S.I., Likoshvai V.A., Belova O.E. (1995) Theoretical analysis of the regulation of interferon expression during priming and blocking. J. Theor. Biol., 175, 149-160.].
Formalizaton in the GCKSM is performed according to a block principle. Due to this principle, a system simulated is divided into elementary subsystems, each of these subsystems being described individually. Description of elementary subsystems is made in terms of formal blocks. The synthesis of models out from elementary subsystems is provided according to the principle of summing the rates of elementary processes.
Elementary subsystem is a part of biosystem that can be described independently from the other parts.
In GCKSM, a formal block means a construction, isolated into a separate unit. This construction is uniquely characterized by an ordered list of formal dynamic variables , ordered list of formal parameters , and the law of transformation of information . When the formal block is used, its formal dynamic variables and parameters are supplied by the definite values. An elementary process is the formal block used in a model. Within the frames of the GCKSM, the elementary subsystems of biosystems are described by the aggregate of elementary processes. Five types of formal blocks may be used for construction of gene network models, namely: constitutive synthesis, monomolecular reaction, bimolecular reaction, generalized Michaelis-Menten reaction of the type 1, generalized Michaelis-Menten reaction of the type 2.
In elementary processes, described by application of five types of formal blocks, the actual variables have the sense of concentrations of definite biomolecules. The law of transformation of information orders the rates of alterations of these concentrations in a process given. Then, following the principle of summing, the total rate of alteration of concentration of a biomolecule equals to the sum of rates of its alteration throughout all elementary processes.
Mathematical models of gene networks are being developed in the Laboratory of Theoretical Genetics and in the Sector of Molecular Evolution of the Institute of Cytology and Genetics SB RAS.
Mathematical models of gene networks are installed in the GeneNet database.
Currently, the mathematical models of dynamics of the following two gene networks have been developed:
By means of mathematical models, it is possible to produce the following operations:
1) Numerical simulation of dynamical characteristics of biological systems under very different conditions, such as:
2) Comparative analysis of numerical data obtained theoretically to experimental data.