基因调.pptVIP

模型：Nonlinear ODE * Negative feedback Gene encodes a protein inhibiting its own expression important for homeostasis, maintenance of system near a desired state Steady state analysis Transient behavior simulation 模型：Nonlinear ODE * 模型：Nonlinear ODE Positive feedback Gene encodes a protein activating its own expression. important for differentiation, evolution towards one of two alternative states of system Steady states Transient behaviors * 模型：Nonlinear ODE Applications: * 模型：Piecewise-linear ODE * 模型：Qualitative Differential Equation QDE: Abstraction of the form Qualitative value x: Qualitative function fi: QSIM algorithm?Qualitative behaviors Qualitative simulation * 模型：Spatially Distributed Model Configuration： Discrete model: Continuous model:boundary conditions: * 模型：Stochastic Model * 模型：Stochastic Model Time evolution of p(X,t)：master equation: ＝Stochastic simulation: use r.v. τand ρ * 模型：Stochastic Model Simulations: Applications: * 模型：Rule-based formalism Knowledge base 〔Expert system?〕 Facts： Rules： * 总结与展望 * 总结与展望 Computer tools for modeling and simulation will be necessary to understand genetic regulatory processes Variety of approaches available, representing genetic regulatory systems on different levels of abstraction Choice of approach depends on aim of analysis and on available information: knowledge on reaction mechanisms quantitative data on model parameters and gene expression levels Serious applications are beginning to emerge * 参考文献 Hidde De Jong, Modeling and Simulation of Genetic Regulatory Systems: A Literature Review, Journal Of Computational Biology, 9 (1), 2002. Harley H. McAdams, Adam Arkin, Simulation Of Prokaryotic Genetic Circuits, Annu. Rev. Biophys. Biomol. Struct. 1998. 27:199–224. Paul Smolen, Douglas A. Baxter And John H. Byrne, Modeling Transcriptional Control in Gene Networks—Methods, Recent Results, and Future Directions, Bulletin of Mathematical Biology (2000) 62, 247–292. Christophe Roos, Facing Biological Com