Method for determining multiple optimization targets of microbial metabolism network model and application thereof

A technology of microbial metabolism and network model, which is applied in the application field of multi-objective optimization in the solution of genome-scale metabolic network, can solve the problems that biological systems are difficult to reflect, and achieves the goal of promoting further development, improving the rationality of prediction, and improving reliability. Effect

Pending Publication Date: 2021-10-01
EAST CHINA UNIV OF SCI & TECH
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Problems solved by technology

When using the single-objective linear programming method, a purely mathematical solution method is used to analyze the metabolic network model, and the characteristics of the biological system are difficult to be better reflected in this solution method

Method used

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  • Method for determining multiple optimization targets of microbial metabolism network model and application thereof
  • Method for determining multiple optimization targets of microbial metabolism network model and application thereof
  • Method for determining multiple optimization targets of microbial metabolism network model and application thereof

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Embodiment Construction

[0072] Below by embodiment the present invention will be further described:

[0073] In the multi-optimization target determination and solution method of the microbial metabolic network model, this example uses the genome-scale metabolic network model of Aspergillus niger iJB1325, which is currently one of the most complete models of Aspergillus niger, including 2320 reactions, 1818 metabolites, 1325 genes. In this example, iJB1325 is used to solve and simulate the growth of different strains of Aspergillus niger DS03043 and CBS513.88. figure 1 It is the overall flowchart of the multi-objective differential evolution algorithm in the invention.

[0074] 1. Irreversibility of the model

[0075] The standard iJB1325 model contains 2320 reactions, 1818 metabolites, and 1325 genes, and some of these reactions include reversible reactions. The existence of reversible reactions in the model leads to negative lower bounds for this part of the reversible reactions, and negative va...

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Abstract

The invention discloses a method for determining multiple optimization targets of a microbial metabolism network model and application of the method. According to the method, on the basis of a genome scale metabolic network model of microorganisms, a plurality of optimization targets are defined according to general rules of microorganism growth, constraint conditions are determined through flux equilibrium analysis, an optimization problem is constructed and solved, and a multi-target differential evolution method is adopted for a main body structure of the solving method. Firstly, an objective function is defined, and an initial population meeting constraint conditions is generated by using a general single-objective linear programming method according to a basic rule of biological growth; then, iteration is carried out according to the steps of the adjusted differential evolution algorithm, and a Pareto optimal solution set meeting an optimization target and constraint conditions can be obtained after iteration is completed; and finally, the Pareto optimal solution set is analyzed, and solving of the genome metabolism network model is completed. The method can be applied to prediction of key flux in central metabolism.

Description

technical field [0001] The invention belongs to the interdisciplinary field of biotechnology and information technology, and relates to the determination of the optimization target of the genome-scale metabolic network of microorganisms and the application of multi-objective optimization in solving the genome-scale metabolic network. Background technique [0002] Metabolism refers to a series of chemical reactions that occur in living organisms. General cell metabolism has the following several processes: 1) Obtain nutritional substrates from outside the cell; 2) Decompose substrates into energy units and metabolite molecules; 3) Synthesize macromolecules and energy such as proteins, sugars, and lipids . Therefore, the metabolic system plays a very critical role in the cellular activities in microorganisms. As a bottom-up systems biology tool, the genome-scale metabolic network model connects genes, proteins and reactions in microorganisms, enabling the metabolic network m...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B5/00G16B40/00G06N3/00
CPCG16B5/00G16B40/00G06N3/006
Inventor 颜学峰范星存夏建业周静茹庄英萍
Owner EAST CHINA UNIV OF SCI & TECH
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