The Research Of Calculation Of Extreme Pathways In The Largescale Metabolic Network And Visualization

In the study of bioinformatics, with more species having been sequenced completely and more deeper understanding of gene function, more research is being done on the biological networks, including the metabolic networks, the gene regulation networks and the signal regulation networks. Although nearly complete information of many microorganisms have been well known, people have not understood the information completely, so people want to research and analyze through reconstructing the cell network with the known biological information.There are two methods in the research of the metabolic pathways: elementary flux modes and the extreme pathways. However, it is very difficult to obtain all the elementary flux modes or extreme pathways of a large-scale metabolic network model, because of the expensive cost of both the space and the time. The general procedure is to partition the metabolic network, in this paper two methods are used to partition the network for the purpose of calculating the extreme pathways. The first method, which is proposed by this paper, is similar to the clustering unsupervised method in the machine learning and the second method, which is proposed in the spectrum graph theory, needs to get eigenvalues and eigenvectors of stoichiometric matrix. Both methods divide the network into two modules, and both aiming least relation between two modules. After partitioning the network and calculating the extreme pathways of the two subnetworks, extreme pathways can be obtained by assembling the pathways of the subnetworks. Time and space complexity have been improved by using this method.After calculating the extreme pathways, the pathways should be visualized to the users as graphs. It is a difficult question how to layout the substance nodes and reactor nodes of the pathways so that the graph looks like clearly. This paper proposes a new algorithm, which is used to layout a metabolic pathway. In the end this paper introduces a system, which is used to calculate the extreme pathways. In this system, if the model file is given, the program can calculate all...