Software Module for Studying the Regulation of Bacterial Metabolic Pathways by Mathematical Modeling Methods

Mathematical modeling is widely used in microbial biotechnology. It is used to describe and understand metabolite fluxes and changes in their concentrations, allows one to consider pathways of protein biosynthesis and make predictions on the costs of culture media for the yield of target products, etc. Standard approaches to modeling bacterial metabolism usually miss the regulatory processes operating at the genetic level. Meanwhile, the development of computational methods of genomic analysis reveals more and more such regulatory relationships. Accounting for regulatory relationships, in the process of model reconstruction, will allow us to investigate finer details of bacterial metabolism control. This paper presents a program module that generates frame-based mathematical models on the structure of the bacterial gene network, extended with tools to take into account regulatory relationships in the bacterial genome. Model generation is performed in terms of ordinary differential equations within the SBML standard. The study of the resulting mathematical model is finally available in a variety of specialized modeling tools.