Rule-Based Modeling Of Cell Signaling Systems

The stage of identification of biological composition in modern biology is about to be completed.How can a comprehensive understanding of the physiological control mode and the overall function of the information transmission network should be understood at a higher level of abstraction than a single gene level when a clear composition of cells can be obtained more and more important.The need for medicine to understand disease and develop treatment measures also increases the practical need for a particular physiological process.This leads to the need for a system of biometrics to create a set of computable models and methods to analyze and understand the mechanisms and principles of cellular signal conditioning from the system,including how the behavior of the cellular regulatory system is generated from the physical interaction of its constituent biomolecules The basic design principles and representations of these functions,and how these interactions interact with information on how to perform information processing and decision-making options.And it is the main direction of the study to simulate the signal transduction process of the reaction network by computer programming the computable model.In order to learn and understand the process of making decisions and interacting systems in cells,it is impractical to rely solely on human-powered metrological experiments to abstract the computational model to simulate the behavior of such complex systems and to combine the various realities The biological data of the observation data can provide some important analog data to produce novel and useful assumption.However,when trying to construct the model of cell signal transmission network,we must face the complexity of system combination.This is mainly caused by a variety of complex combinations and multiple modifications between protein signaling molecules,and this combination of molecules produces a variety of molecular species processes that increase the number of chemical reactions involved in the signal transduction network,leading to The complexity of the system.Rule-based modeling is a modeling method that solves the above-mentioned complexity problems.The rule-based model replaces the manual enumeration of all possible species and reactions that may be present in the system by defining only the reaction motifs within the macromolecule complex and the motivations and modifications of those motifs involved.The rules have substantially the same form as the chemical reaction,and the function of defining different reaction templates is provided by forming a specific reaction category.Nowadays,there are a variety of different research methods and software using rule-based modeling to complete some of the research process of bioremediation network,and set up a rule-based model of different language constructs.BioNetGen is an open source software package for building and modeling rule-based models.It has been used to simulate a variety of biological processes,including cell signaling,gene regulation and metabolism.The model was written in human-readable,text-based modeling language BNGL.Models can also be exported in different formats,such as SBML and MATLAB languages.In this paper,a rule-based method was used to model the gene expression control process of lactose operon in E.coli.Based on the full understanding of its physiological processes,the use of more precise rules to complete the definition of reaction substances and simulation of positive and negative feedback control mechanism carried out,provided in the BioNetGen calculation model representation of the code design,the use of the corresponding parameters and A curve of the change in the concentration of the reaction substance.By designing a separate and mixed simulation process without the control mechanism and the analysis of the results of a large number of comparative experiments,the paper expatiates on how to use the idea of the regulation module to gradually expand the regular representation of the complex reaction network.Compared with other methods,the results show that the rule-based modeling method is effective in reducing the complexity of the reaction network system,and it also shows that the extended Modeling the feasibility of modeling.