WebCell: An integrated environment for modeling and simulation of cellular networks online

Various softwares and computational environments have been developed as listed in the systems biology community (htlp://sbml.org). Nevertheless, only a handful of projects adopt the platform-independent web-based approach which is a desirable direction for simulation research and development. To this end, we developed WebCell which is an integrated simulation environment for managing information on cellular networks, and for interactively exploring their steady-state and dynamic behaviors over the web. A user friendly web interface allows users to efficiently create, visualize, simulate and store their reaction network models, thereby facilitating kinetic modeling and simulation of biological systems of interest. Supported analysis methods for such models include structural pathway analysis, metabolic control analysis, conservation analysis and time-course simulation. In addition, a variety of model collections publicly available have been compiled to provide comprehensive implications for cellular dynamics of the models. Thus, this comprehensive, web-accessible and integrative system not only serves the educational demonstration site of publicly available kinetic models but also provides the customized modeling environment for quantitatively and qualitatively analyzing the cellular system.