Reserach On Simulation System Of Biological Processes Based On PETRI Nets

In the post-genome era, how to efficiently process biological information has become one of the most important research topics in Bioinformatics; among them, the simulation of biological processes, recurring biological processes through computer simulation, is one of the important aspects. From biochemical and biomedical viewpoint, research progress in this topic will be very beneficial to human beings.However, due to the diversity and complexity of biological processes, visual modeling and simulating biological processes are very difficult. Currently, the primary means to model biological processes are differential equations and Hybrid Functional Petri Net. Existing research results have some deficiencies in the visualization expression, the efficiency of modeling or simulation of the model and so on. For example, modeling with the differential equations is lack of visual expression, and it is difficult to model gene regulatory networks; although modeling with Hybrid functional Petri Net has a good visual expression and can also simulate gene regulatory networks, it has some deficiencies in the clarity of expressions and efficiency of modeling.In this paper, in allusion to the characteristics that the biological process itself is very complicated and difficult to be described and the reuse rates of some typical processes are high, the Object-Oriented Hybrid Functional Petri Net is proposed and defined in detail on the basis of Hybrid Functional Petri Net, integrating with object-oriented thinking in software engineering. Object-Oriented Hybrid Functional Petri Net provides visual modeling and simulating biological processes a good support with its abundant element types and perfect simulation algorithms. It has friendly graphic interface expressions, but also for efficient simulation; in addition, with the introduction of Object-oriented thinking and the establishment of the module, the expressions of biological processes are more intuitively and moreover it can enhance the reuse of modules, reduce complexity of modeling and improve the efficiency of modeling. It has been showed by the researches that the visual modeling of biological processes with Object-Oriented Hybrid Functional Petri Net is very efficient. We designed and developed a software platform—CELLMATLAB based on the theory of Object-Oriented Hybrid Functional Petri Net to model and simulate biological processes with visualization. Then we model the gene regulatory networks such as lac operon regulatory mechanism and metabolic network such as glycolysis model in this platform. According to the analysis of simulation, we gained the correct conclusions and gave wet experiments a meaningful guidance. Consequently, it verified the theory and the feasibility and correctness of the software, and moreover it reflected the value of this software.