Automating mathematical modeling of biochemical reaction networks

摘要: In this chapter we introduce a five-step modeling pipeline that ultimately leads to mathematical description of biochemical reaction system. We discuss how automate each individual step and put these steps together. First, create topology interconversion processes mutual influences between reactive species. The Systems Biology Markup Language (SBML) encodes the model in computer-readable form allows us add semantic information component model. Second, from such an annotated network, procedure known as SBMLsqueezer generates kinetic equations context-sensitive manner. resulting can then be combined with already existing models. Third, estimate values all newly introduced parameters created rate law. This requires time series quantitative measurements species within system available, because calibrate aim will fit experimental data. Fourth, validation is advisable. Fifth, report generated automatically document its components. For better understanding, begin introduction current standardization attempts systems biology generalized approaches for common before discussing computer-aided modeling, parameter estimation, automatic generation. complete discussion possible further improvements our pipeline.