Hardy S, Robillard P N
Ecole Polytechnique de Montréal, Department of Computer Engineering, Succ. Centre-Ville, Montréal, Qué., Canada H3C 3A7.
Biosystems. 2005 Oct;82(1):26-38. doi: 10.1016/j.biosystems.2005.05.008.
Petri net-based modeling methods have been used in many research projects to represent biological systems. Among these, the hybrid functional Petri net (HFPN) was developed especially for biological modeling in order to provide biologists with a more intuitive Petri net-based method. In the literature, HFPNs are used to represent kinetic models at the molecular level. We present two models of long-term potentiation previously represented by differential equations which we have transformed into HFPN models: a phenomenological synapse model and a molecular-level model of the CaMKII regulation pathway. Through simulation, we obtained results similar to those of previous studies using these models. Our results open the way to a new type of modeling for systems biology where HFPNs are used to combine different levels of abstraction within one model. This approach can be useful in fully modeling a system at the molecular level when kinetic data is missing or when a full study of a system at the molecular level it is not within the scope of the research.
基于Petri网的建模方法已在许多研究项目中用于表示生物系统。其中，混合功能Petri网（HFPN）是专门为生物建模而开发的，以便为生物学家提供一种更直观的基于Petri网的方法。在文献中，HFPN用于表示分子水平的动力学模型。我们展示了两个先前由微分方程表示的长时程增强模型，我们已将其转换为HFPN模型：一个现象学突触模型和一个CaMKII调节途径的分子水平模型。通过模拟，我们获得了与先前使用这些模型的研究相似的结果。我们的结果为系统生物学的一种新型建模开辟了道路，其中HFPN用于在一个模型中组合不同层次的抽象。当动力学数据缺失或对系统进行分子水平的全面研究不在研究范围内时，这种方法对于在分子水平上对系统进行全面建模可能是有用的。
