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Colouring fuzziness for systems biology
Theoretical Computer Science ( IF 1.1 ) Pub Date : 2021-04-15 , DOI: 10.1016/j.tcs.2021.04.011
George Assaf , Monika Heiner , Fei Liu

Snoopy is a powerful modelling and simulation tool for various types of Petri nets, which have been applied to a wide range of biochemical reaction networks. We present an enhanced version of Snoopy, now supporting coloured and uncoloured stochastic, continuous and hybrid Petri Nets with fuzzy kinetic parameters. Colour helps to cope with modelling challenges imposed by larger and more complex networks. Fuzzy parameters are specifically useful when kinetic parameter values can not be precisely measured or estimated. By running fuzzy simulation we obtain output bands of the variables of interest induced by the effect of the fuzzy kinetic parameters. Simulation is always done on the uncoloured level. For this purpose, coloured fuzzy Petri nets are automatically unfolded to their corresponding uncoloured counterparts. Combining the power of fuzzy kinetic parameters with the modelling convenience of coloured Petri nets provides a new quality in user support with sophisticated modelling and analysis features.



中文翻译:

系统生物学的着色模糊

史努比(Snoopy)是一种强大的建模和仿真工具,适用于各种类型的Petri网,该网已应用于广泛的生化反应网络。我们提供史努比的增强版,现在支持带有模糊动力学参数的有色和无色随机,连续和混合Petri网。颜色有助于应对更大,更复杂的网络带来的建模挑战。当无法精确测量或估计动力学参数值时,模糊参数特别有用。通过运行模糊仿真,我们获得了受模糊动力学参数影响而引起的目标变量的输出带。模拟总是在无色的水平上进行。为此,有色模糊Petri网会自动展开为其对应的无色对应物。将模糊动力学参数的功能与有色Petri网的建模便利性相结合,可提供具有先进的建模和分析功能的用户支持新品质。

更新日期:2021-05-26
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