CYTOSCAPE PLUGIN FOR RECONSTRUCTION OF STRUCTURAL RANDOM GRAPH MODELS OF BIOLOGICAL NETWORKS
https://doi.org/10.25205/1818-7900-2018-16-3-37-50
Abstract
Modern experimental technologies in molecular biology allow reconstructing different types of biological networks, including gene and metabolic networks, networks of interatomic, gene coexpression networks, a network of diseases, etc. This article presents the program tool for reconstructing structural random graph models of biological networks, the structural regularities of which coincide with the structural regularities of the initial biological network. Such structural models can be used to test various statistical hypotheses on networks, to study the influence of structural regularities in biological networks on their function, and so on. Our tool generate the structural random graph models with the following fixed characteristics: the distribution of vertex degrees, the joint distribution of degrees of vertices, the average degree of neighboring vertices, the clustering coefficient, the clustering spectrum, the frequency of structural motifs of various sizes, etc. The developed system is based on the client-server architecture and consists of the Cytoscape plug-application and remote computing service. The interaction between the client and the server is implemented through the gRPC framework using the Protocol Buffers (structured data serialization protocol). The system allows to construct the structural random graph models of the given biological networks asynchronously through software Random Network Generator and GTrie Scanner. The result structural model can be loaded for visualization and analysis using the Cytoscape package. This article also presents the computational experiment for reconstruct the structural random graph models of a number of biological networks. The algorithm for estimating the time of calculations of structural models of this kind of biological networks was constructed.
About the Authors
N. L. Podkolodnyy
Institute of Cytology and Genetics SB RAS; Institute of Computational Mathematics and Mathematical Geophysics SB RAS
Russian Federation
Russian Federation
D. A. Gavrilov
Novosibirsk State University
Russian Federation
Russian Federation
N. N. Tverdokhleb
Institute of Cytology and Genetics SB RAS; Novosibirsk State University
Russian Federation
Russian Federation
O. A. Podkolodnaya
Institute of Cytology and Genetics SB RAS
Russian Federation
Russian Federation
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For citations:
Podkolodnyy N.L., Gavrilov D.A., Tverdokhleb N.N., Podkolodnaya O.A. CYTOSCAPE PLUGIN FOR RECONSTRUCTION OF STRUCTURAL RANDOM GRAPH MODELS OF BIOLOGICAL NETWORKS. Vestnik NSU. Series: Information Technologies. 2018;16(3):37-50. (In Russ.) https://doi.org/10.25205/1818-7900-2018-16-3-37-50
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