ezBioNet: A modeling and simulation system for analyzing biological reaction networks

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• 作者：Seok Jong Yu (1)
  Thai Quang Tung (1)
  Junho Park (2)
  Jongtae Lim (2)
  Jaesoo Yoo (2)
  
• 关键词：Systems biology ; Simulation ; Biological network ; Signal transduction analysis
• 刊名：Journal of the Korean Physical Society
• 出版年：2012
• 出版时间：October 2012
• 年：2012
• 卷：61
• 期：8
• 页码：1267-1273
• 全文大小：281KB
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• 作者单位：Seok Jong Yu (1)
  Thai Quang Tung (1)
  Junho Park (2)
  Jongtae Lim (2)
  Jaesoo Yoo (2)
  
  1. Supercomputing Center, Korea Institute of Science and Technology Information, Daejeon, 305-806, Korea
  2. School of Information and Communication Engineering, Chungbuk National University & CBITRC, Cheongju, 361-763, Korea
  
• ISSN：1976-8524

文摘

To achieve robustness against living environments, a living organism is composed of complicated regulatory mechanisms ranging from gene regulations to signal transduction. If such life phenomena are to be understand, an integrated analysis tool that should have modeling and simulation functions for biological reactions, as well as new experimental methods for measuring biological phenomena, is fundamentally required. We have designed and implemented modeling and simulation software (ezBioNet) for analyzing biological reaction networks. The software can simultaneously perform an integrated modeling of various responses occurring in cells, ranging from gene expressions to signaling processes. To support massive analysis of biological networks, we have constructed a server-side simulation system (VCellSim) that can perform ordinary differential equations (ODE) analysis, sensitivity analysis, and parameter estimates. ezBioNet integrates the BioModel database by connecting the european bioinformatics institute (EBI) servers through Web services APIs and supports the handling of systems biology markup language (SBML) files. In addition, we employed eclipse RCP (rich client platform) which is a powerful modularity framework allowing 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. A researcher may perform the kinetic modeling and execute the simulation. The simulation result can be managed and visualized on ezBioNet, which is freely available at http://ezbionet.cbnu.ac.kr.