TY - JOUR

T1 - Frame-based mathematical models – a tool for the study of molecular genetic systems

AU - Kazantsev, F. V.

AU - Lashin, S. A.

AU - Matushkin, Yu G.

N1 - Kazantsev, F. V. Frame-based mathematical models - a tool for the study of molecular genetic systems / F. V. Kazantsev, S. A. Lashin, Yu. G. Matushkin // Vavilov Journal of Genetics and Breeding. – 2025. – Vol. 29, No. 8. – P. 1288-1294. – DOI 10.18699/vjgb-25-135. – EDN WJLGNW. This work was supported by the Ministry of Science and Higher Education of the Russian Federation (the Federal Scientific-technical programme for genetic technologies development for 2019-2030, agreement No. 075-15-2025-516).

PY - 2025

Y1 - 2025

N2 - This paper reviews existing approaches for reconstructing frame-based mathematical models of molecular genetic systems from the level of genetic synthesis to models of metabolic networks. A frame-based mathematical model is a model in which the following terms are specified: formal structure, type of mathematical model for a particular biochemical process, reactants and their roles. Typically, such models are generated automatically on the basis of description of biological processes in terms of domain-specific languages. For molecular genetic systems, these languages use constructions familiar to a wide range of biologists in the form of a list of biochemical reactions. They rely on the concepts of elementary subsystems, where complex models are assembled from small block units (“frames”). In this paper, we have shown an example with the generation of a classical repressilator model consisting of three genes that mutually inhibit each other’s synthesis. We have given it in three different versions of the graphic standard, its characteristic mathematical interpretation and variants of its numerical calculation. We have shown that even at the level of frame models it is possible to identify qualitatively new behaviour of the model through the introduction of just one gene into the model structure. This change provides a way to control the modes of behaviour of the model through changing the concentrations of reactants. The frame-based approach opens the way to generate models of cells, tissues, organs, organisms and communities through frame-based model generation tools that specify structure, roles of modelled reactants using domain-specific languages and graphical methods of model specification.

AB - This paper reviews existing approaches for reconstructing frame-based mathematical models of molecular genetic systems from the level of genetic synthesis to models of metabolic networks. A frame-based mathematical model is a model in which the following terms are specified: formal structure, type of mathematical model for a particular biochemical process, reactants and their roles. Typically, such models are generated automatically on the basis of description of biological processes in terms of domain-specific languages. For molecular genetic systems, these languages use constructions familiar to a wide range of biologists in the form of a list of biochemical reactions. They rely on the concepts of elementary subsystems, where complex models are assembled from small block units (“frames”). In this paper, we have shown an example with the generation of a classical repressilator model consisting of three genes that mutually inhibit each other’s synthesis. We have given it in three different versions of the graphic standard, its characteristic mathematical interpretation and variants of its numerical calculation. We have shown that even at the level of frame models it is possible to identify qualitatively new behaviour of the model through the introduction of just one gene into the model structure. This change provides a way to control the modes of behaviour of the model through changing the concentrations of reactants. The frame-based approach opens the way to generate models of cells, tissues, organs, organisms and communities through frame-based model generation tools that specify structure, roles of modelled reactants using domain-specific languages and graphical methods of model specification.

KW - Hill functions

KW - domain-specific languages

KW - frame-based models

KW - gene networks

KW - mathematical modelling

KW - ФУНКЦИИ ХИЛЛА

KW - МАТЕМАТИЧЕСКОЕ МОДЕЛИРОВАНИЕ

KW - ГЕННЫЕ СЕТИ

KW - ФРЕЙМОВЫЕ МОДЕЛИ

KW - ПРЕДМЕТНО-ОРИЕНТИРОВАННЫЕ ЯЗЫКИ СПЕЦИФИКАЦИИ МОДЕЛИ

UR - https://www.scopus.com/pages/publications/105028940310

UR - https://elibrary.ru/item.asp?id=88850563

UR - https://www.mendeley.com/catalogue/b376c311-885a-34dd-98da-14b6f91b5e08/

U2 - 10.18699/vjgb-25-135

DO - 10.18699/vjgb-25-135

M3 - Article

C2 - 41660604

VL - 29

SP - 1288

EP - 1294

JO - Вавиловский журнал генетики и селекции

JF - Вавиловский журнал генетики и селекции

SN - 2500-0462

IS - 8

M1 - 14

ER -