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Web-based dynamic simulation environment for system-level understanding of cellular network systems
윤좌문,이동엽,오영균,박선원,이상엽 한국화학공학회 2007 화학공학의이론과응용 Vol.10 No.1
We develop WebCellTM which is a java-based simulation environment for system-level understanding of biological systems. A web-accessible repository of cellular network models has been established to investigate the dynamics of such models. In addition, its efficient and userfriendly web interface allows users to import their own models described by SBML (Hucka et al., 2003) for representing computational models in systems biology. Consequently, dynamic simulations of the imported models can be carried out from anywhere an internet connection is available. Acknowledgements: This work was supported by the National Research Laboratory Program (2000- N-NL-01-C-237) of the Ministry of Science and Technology (MOST), the Advanced Backbone IT Development Project (IMT2000-C3-1) of the Ministry of Information and Communication (MIC) and MOST, and by the Brain Korea 21 project from the Ministry of Education.
윤좌문,이동엽,조아연,이상엽,박선원,Yun, Choa-Mun,Lee, Dong-Yup,Cho, A-Youn,Lee, Sang-Yup,Park, Sun-Won 제어로봇시스템학회 2005 제어·로봇·시스템학회 논문지 Vol.11 No.10
The computational modeling and simulation of complex biological systems are indispensable for new knowledge extraction from huge experimental data and ever growing vast amount of information in systems biology. Moreover, gathering and sharing of the existing information and newly-generated knowledge can speed up this research process. In this regard, several modeling projects have been undertaken for quantitatively analyzing the biological systems via the internet. They include Virtual Cell, JWS and OBIYagns. We also develop an integrated web-based environment, which facilitate investigation of dynamic behavior of cellular systems.
윤좌문,박선원,이동엽,오영균,이상엽 한국화학공학회 2007 화학공학의이론과응용 Vol.10 No.2
The fundamental goal of systems biology is to gain greater insight into cell functions and dynamic interactions between pathways, which can describe inter- and extra-cellular dynamics. As cellular networks possess numerous components such as genes, proteins, and other molecules, a major problem in this area is the complexity rising from the huge number of kinetic parameters and intricate interactions among them. Moreover, typical kinetic models span a wide range of orders of magnitude, which result in the stiffness and multiple time-scales of kinetic modeling problems. In this study, model simplification methods such as order reduction are considered to relieve the stiffness and to obtain the accurate information on the dominating dynamics.