생물학적 반응네트워크 분석을 위한 통합 모델링 및 시뮬레이션 시스템

Abstract

In order to understand the biological response in a cell, a researcher has to create a biological network and design an experiment to prove it. Although the biological knowledge has been accumulated, we still don’t have enough biological models for explaining the complex biological phenomena. For creating a new biological network, an integrated modeling software supporting various biological models is required. In this paper, we design and implement a unified biological modeling and simulation system, called ezBioNet, for analyzing biological reaction networks. ezBioNet designs kinetic and Boolean network models and simulates the biological networks using a server-side simulation system with OPAL framework. The main advantage of ezBioNet is that a user can create a biological network using unified modeling canvas of kinetic and Boolean models and perform the massive simulation including ordinary differential equations (ODE) analysis, sensitivity analysis, parameter estimation and Boolean network analysis. ezBioNet integrates useful biological databases including the BioModels database by connecting EBI servers through Web services APIs. In addition, we employ Eclipse RCP that is a powerful modularity framework to allow various functional expansions. ezBioNet is intended to be an easy-to-use modeling tool as well as a simulation system to understand the control mechanism by monitoring the change of each component in a biological network. The simulation result can be managed and visualized on ezBioNet that is freely available at http://ezbionet.sourceforge.net or http://ezbionet.cbnu.ac.kr