Zevedei-Oancea Ionela, Schuster Stefan
Max Delbrück Center for Molecular Medicine, Department of Bioinformatics, Berlin-Buch, Germany.
Stud Health Technol Inform. 2011;162:17-37.
Petri net concepts provide additional tools for the modelling of metabolic networks. Here, the similarities between the counterparts in traditional biochemical modelling and Petri net theory are discussed. For example the stoichiometry matrix of a metabolic network corresponds to the incidence matrix of the Petri net. The flux modes and conservation relations have the T-invariants, respectively, P-invariants as counterparts. We reveal the biological meaning of some notions specific to the Petri net framework (traps, siphons, deadlocks, liveness). We focus on the topological analysis rather than on the analysis of the dynamic behaviour. The treatment of external metabolites is discussed. Some simple theoretical examples are presented for illustration. Also the Petri nets corresponding to some biochemical networks are built to support our results. For example, the role of triose phosphate isomerase (TPI) in Trypanosoma brucei metabolism is evaluated by detecting siphons and traps. All Petri net properties treated in this contribution are exemplified on a system extracted from nucleotide metabolism.
Petri网概念为代谢网络建模提供了额外的工具。在此，讨论了传统生化建模中的对应物与Petri网理论之间的相似性。例如，代谢网络的化学计量矩阵对应于Petri网的关联矩阵。通量模式和守恒关系分别具有T不变量和P不变量作为对应物。我们揭示了Petri网框架特有的一些概念（陷阱、虹吸、死锁、活性）的生物学意义。我们关注拓扑分析而非动态行为分析。讨论了外部代谢物的处理。给出了一些简单的理论示例用于说明。还构建了与一些生化网络相对应的Petri网以支持我们的结果。例如，通过检测虹吸和陷阱来评估磷酸丙糖异构酶（TPI）在布氏锥虫代谢中的作用。本论文中讨论的所有Petri网属性都在从核苷酸代谢中提取的一个系统上进行了举例说明。
