The Research Of Visual Biological Modeling Language Based On Petri-Net And SBML

With the advent of the post gene era, the technology of the biology simulation has played a more and more remarkable role in many domains. It effectively supports the research of the biologists and other scientists in the domains of medicine and Pharmacy and some other corresponding ones. How to directly represent the complicated model, however, is a question, and one of present researching focuses. On the other hand, the unremitting development of the biological technology has resulted into some bigger and more complicated biological models, therefore, how to make the model share, evaluate, and cooperate between the different users and the software platforms has become more and more significant.In the first place, Petri-Net, owing to its direct graph representation and the outstanding capability of the mathematical analysis, has indicated the advantage in the biological simulation domain. This paper defines a set of graph grammars, making use of the characteristics of the Petri-Net and adding some corresponding knowledge of Petri-Net in the simulation domain and presents a visual language. Secondly, for the aim of realize the share, the scientists present the exchanging criterion of the system biology information: SBML( System Biology Mark-up Language), however, for SBML is essentially one of XML, whose grammar is onerous and difficult for novice to operate, so, this paper visualizes it, resulting into simplicity and directness for the users to operate SBML.This paper implements the exchange between Petri-Net and the SBML. The former similar exchange is mainly based on the textual process, while this paper makes it from the aspect of exchange of two graph grammars, which take possess of two advantages: 1) the textual process is unidirectional, while the one based on the graph grammar is convenient for the two objects to exchange.2)it is convenient to analyze the time complexity from the aspect of theory. The most remarkable problem for the application of one graph is that when there is a huge number of edges and nodes, the process will take on the exponential time complexity, so, this paper presents a graph grammar which takes possess of the polynomial time complexity, and gives the analysis. Finally, this paper, on the platform of AGG(Attributed Graph Grammar), implements the definition of the grammars, and demonstrates how to avoid the similar defect and limit of the former Petri-net, and toward the concrete biological model(Lac control factor), justifies the process of transforming between Petri-net and SBML.